Judit Zádor

Local and global uncertainty analysis of complex chemical kinetic systems

Computer modelling plays a crucial part in the understanding of complex chemical reactions. Parameters of elementary chemical and physical processes are usually determined in independent experiments and are always associated with uncertainties. Two typical examples of complex chemical kinetic systems are the combustion of gases and the photochemical processes in the atmosphere. In this study, local uncertainty analysis, the Morris method, and Monte Carlo analysis with Latin hypercube sampling were applied to an atmospheric and to a combustion model. These models had 45 and 37 variables along with 141 and 212 uncertain parameters, respectively. The toolkit used here consists of complementary methods and is able to map both the sources and the magnitudes of uncertainties. In the case of the combustion model, the global uncertainties of the local sensitivity coefficients were also investigated, and the order of parameter importance based on local sensitivities were found to be almost independent of the parameter values within their range of uncertainty.

Direct observation and kinetics of a hydroperoxyalkyl radical (QOOH)

Catching a glimpse of the elusive QOOH Its straightforward to write down the net combustion reaction: Oxygen reacts with hydrocarbons to form water and carbon dioxide. The details of how all the bonds break and form in succession are a great deal more complicated. Savee et al. now report direct detection of a long-postulated piece of the puzzle, a so-called QOOH intermediate. This structure results from bound oxygen stripping a hydrogen atom from carbon, leaving a carbon-centered radical behind. The study explores the influence of the hydrocarbons unsaturation on the stability of QOOH, which has implications for both combustion and tropospheric oxidation chemistry. Science, this issue p. 643 A long-sought reactive intermediate in hydrocarbon oxidation is observed via mass spectrometry. Oxidation of organic compounds in combustion and in Earth’s troposphere is mediated by reactive species formed by the addition of molecular oxygen (O2) to organic radicals. Among the most crucial and elusive of these intermediates are hydroperoxyalkyl radicals, often denoted “QOOH.” These species and their reactions with O2 are responsible for the radical chain branching that sustains autoignition and are implicated in tropospheric autoxidation that can form low-volatility, highly oxygenated organic aerosol precursors. We report direct observation and kinetics measurements of a QOOH intermediate in the oxidation of 1,3-cycloheptadiene, a molecule that offers insight into both resonance-stabilized and nonstabilized radical intermediates. The results establish that resonance stabilization dramatically changes QOOH reactivity and, hence, that oxidation of unsaturated organics can produce exceptionally long-lived QOOH intermediates.

First principles study of photo-oxidation degradation mechanisms in P3HT for organic solar cells

We present a theoretical study of degradation mechanisms for photoinduced oxidation in organic polymers in the condensed phase, using poly(3-hexylthiophene) (P3HT) as an example. Applying density functional theory with a hybrid density functional and periodic boundary conditions that account for steric effects and permit the modeling of interchain chemical reactions, we investigate reaction pathways that may lead to the oxidation of the thiophene backbone as a critical step toward disrupting the polymer conjugation. We calculate energy barriers for reactions of the P3HT backbone with oxidizing agents including the hydroxyl radical (OH˙), hydroperoxide (ROOH), and the peroxyl radical (ROO˙), following a UV-driven radical reaction starting at the α-carbon of the alkyl side chain as suggested by infrared (IR) and X-ray photoemission (XPS) spectrosocopy studies. The results strongly suggest that an attack of OH˙ on sulfur in P3HT is unlikely to be thermodynamically favored. On the other hand, an attack of a peroxyl radical on the side chain on the P3HT backbone may provide low barrier reaction pathways to photodegradation of P3HT and other polymers with side chains. The condensed phase setting is found to qualitatively affect predictions of degradation processes.

Directly measuring reaction kinetics of ˙QOOH – a crucial but elusive intermediate in hydrocarbon autoignition

Hydrocarbon autoignition has long been an area of intense fundamental chemical interest, and is a key technological process for emerging clean and efficient combustion strategies. Carbon-centered radicals containing an -OOH group, commonly denoted ˙QOOH radicals, are produced by isomerization of the alkylperoxy radicals that are formed in the first stages of oxidation. These ˙QOOH radicals are among the most critical species for modeling autoignition, as their reactions with O2 are responsible for chain branching below 1000 K. Despite their importance, no ˙QOOH radicals have ever been observed by any means, and only computational and indirect experimental evidence has been available on their reactivity. Here, we directly produce a ˙QOOH radical, 2-hydroperoxy-2-methylprop-1-yl, and experimentally determine rate coefficients for its unimolecular decomposition and its association reaction with O2. The results are supported by high-level theoretical kinetics calculations. Our experimental strategy opens up a new avenue to study the chemistry of ˙QOOH radicals in isolation.

Time scale and dimension analysis of a budding yeast cell cycle model

BackgroundThe progress through the eukaryotic cell division cycle is driven by an underlying molecular regulatory network. Cell cycle progression can be considered as a series of irreversible transitions from one steady state to another in the correct order. Although this view has been put forward some time ago, it has not been quantitatively proven yet. Bifurcation analysis of a model for the budding yeast cell cycle has identified only two different steady states (one for G1 and one for mitosis) using cell mass as a bifurcation parameter. By analyzing the same model, using different methods of dynamical systems theory, we provide evidence for transitions among several different steady states during the budding yeast cell cycle.ResultsBy calculating the eigenvalues of the Jacobian of kinetic differential equations we have determined the stability of the cell cycle trajectories of the Chen model. Based on the sign of the real part of the eigenvalues, the cell cycle can be divided into excitation and relaxation periods. During an excitation period, the cell cycle control system leaves a formerly stable steady state and, accordingly, excitation periods can be associated with irreversible cell cycle transitions like START, entry into mitosis and exit from mitosis. During relaxation periods, the control system asymptotically approaches the new steady state. We also show that the dynamical dimension of the Chens model fluctuates by increasing during excitation periods followed by decrease during relaxation periods. In each relaxation period the dynamical dimension of the model drops to one, indicating a period where kinetic processes are in steady state and all concentration changes are driven by the increase of cytoplasmic growth.ConclusionWe apply two numerical methods, which have not been used to analyze biological control systems. These methods are more sensitive than the bifurcation analysis used before because they identify those transitions between steady states that are not controlled by a bifurcation parameter (e.g. cell mass). Therefore by applying these tools for a cell cycle control model, we provide a deeper understanding of the dynamical transitions in the underlying molecular network.

Unconventional Peroxy Chemistry in Alcohol Oxidation: The Water Elimination Pathway.

Predictive simulation for designing efficient engines requires detailed modeling of combustion chemistry, for which the possibility of unknown pathways is a continual concern. Here, we characterize a low-lying water elimination pathway from key hydroperoxyalkyl (QOOH) radicals derived from alcohols. The corresponding saddle-point structure involves the interaction of radical and zwitterionic electronic states. This interaction presents extreme difficulties for electronic structure characterizations, but we demonstrate that these properties of this saddle point can be well captured by M06-2X and CCSD(T) methods. Experimental evidence for the existence and relevance of this pathway is shown in recently reported data on the low-temperature oxidation of isopentanol and isobutanol. In these systems, water elimination is a major pathway, and is likely ubiquitous in low-temperature alcohol oxidation. These findings will substantially alter current alcohol oxidation mechanisms. Moreover, the methods described will be useful for the more general phenomenon of interacting radical and zwitterionic states.

Pressure-dependent OH yields in alkene + HO2 reactions: a theoretical study.

The major bimolecular product of alkyl + O(2) reactions is alkene + hydroperoxyl radical (HO(2)), but in the reverse direction, the reactants are reformed to a very limited extent only. The most important products of the alkene + HO(2) reactions are alkylperoxy radical (ROO(•)), hydroxyl radical (OH) + cyclic ether, and the corresponding hydroperoxyalkyl ((•)QOOH) species. Moreover, abstraction of allylic hydrogens can compete with the addition, further complicating the possible outcome of this reaction type and its effect on low-temperature combustion chemistry. In this paper, six alkene + HO(2) reactions and the reaction between an unsaturated oxygenate and HO(2) are studied based on previously established potential energy surfaces. The studied unsaturated compounds are ethene, propene, 1-butene, trans-2-butene, isobutene, cyclohexene, and vinyl alcohol. Using multiwell master equations, temperature- (300-1200 K) and pressure-dependent rate coefficients and branching fractions are calculated for these reactions. The importance of this reaction type for the combustion of unsaturated compounds is also assessed, and we show that, to get reliable results, it is important to include the pressure-dependence of the rate coefficients in the calculations.

Low-Temperature Combustion Chemistry of n-Butanol: Principal Oxidation Pathways of Hydroxybutyl Radicals

Reactions of hydroxybutyl radicals with O2 were investigated by a combination of quantum-chemical calculations and experimental measurements of product formation. In pulsed-photolytic Cl-initiated oxidation of n-butanol, the time-resolved and isomer-specific product concentrations were probed using multiplexed tunable synchrotron photoionization mass spectrometry (MPIMS). The interpretation of the experimental data is underpinned by potential energy surfaces for the reactions of O2 with the four hydroxybutyl isomers (1-hydroxybut-1-yl, 1-hydroxybut-2-yl, 4-hydroxybut-2-yl, and 4-hydroxybut-1-yl) calculated at the CBS-QB3 and RQCISD(T)/cc-pV∞Z//B3LYP/6-311++G(d,p) levels of theory. The observed product yields display substantial temperature dependence, arising from a competition among three fundamental pathways: (1) stabilization of hydroxybutylperoxy radicals, (2) bimolecular product formation in the hydroxybutyl + O2 reactions, and (3) decomposition of hydroxybutyl radicals. The 1-hydroxybut-1-yl + O2 reaction is dominated by direct HO2 elimination from the corresponding peroxy radical forming butanal as the stable coproduct. The chemistry of the other three hydroxybutylperoxy radical isomers mainly proceeds via alcohol-specific internal H-atom abstractions involving the H atom from either the -OH group or from the carbon attached to the -OH group. We observe evidence of the recently reported water elimination pathway (Welz et al. J. Phys. Chem. Lett. 2013, 4 (3), 350-354) from the 4-hydroxybut-2-yl + O2 reaction, supporting its importance in γ-hydroxyalkyl + O2 reactions. Experiments using the 1,1-d2 and 4,4,4-d3 isotopologues of n-butanol suggest the presence of yet unexplored pathways to acetaldehyde.

Threshold photoelectron spectrum of the benzyl radical

We measure threshold photoelectron spectra of the benzyl radical, which show transitions to at least three electronic states of the benzylium cation: 1A1, 3B2, and 1B2, with possible contributions from transitions to 3A1. The main features in the vibrationally resolved threshold photoelectron spectrum between 7.1 and 10.5 eV are assigned with the aid of Franck–Condon simulations to these four electronic states of benzylium. We measure the adiabatic ionisation energy of the benzyl radical to be 7.252(5) eV and observe a well-resolved vibrational progression in the lowest triplet state, 3B2, from which we obtain a measured singlet–triplet splitting of 1.928(7) eV in benzylium.

On the similarity of the sensitivity functions of methane combustion models

It is widely known that detailed kinetic mechanisms with identical reaction steps but with very different rate parameters may provide similar simulation results in combustion calculations. This phenomenon is related to the similarity of sensitivity functions, which arises if low-dimensional manifolds in the space of variables, and autocatalytic processes are present. We demonstrated the similarity of sensitivity functions for adiabatic explosions and burner-stabilized laminar flames of stoichiometric methane–air mixtures. The cause of similarities was investigated by calculating the dimension of the corresponding manifolds, and the pseudo-homogeneous property of the sensitivity ordinary differential equation (ODE). The methane explosion model showed global similarity, which means that different parameter sets could provide the same simulation results. This was demonstrated by numerical experiments, in which two significantly different parameter sets resulted in identical concentration profiles for all species. This phenomenon is important from a practical point of view in the fields of ‘validation’ of complex reaction mechanisms and parameter estimation of chemical kinetic systems.