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Binding energies of water to doubly hydrated cationized glutamine and structural analogues in the gas phase.

The modes of metal-ion and water binding in doubly hydrated complexes of lithiated and sodiated glutamine (Gln) are probed using blackbody infrared radiative dissociation experiments and density functional theory calculations. Threshold dissociation energies, E0, for loss of a water molecule from these complexes are obtained from master-equation modeling of these data. The values of E0 are 36 +/- 1 and 38 +/- 2 kJ/mol for the lithiated and sodiated glutamine complexes, respectively, and are consistent with calculated water binding energies for the nonzwitterionic form of these complexes. Calculated water binding energies for the zwitterionic forms of these complexes are significantly higher. In contrast, calculations indicate that the zwitterionic form of Gln in these complexes is more stable than the nonzwitterionic form by 8 and 15 kJ/mol when lithiated and sodiated, respectively. Doubly hydrated lithiated and sodiated complexes of asparagine methyl ester (AsnOMe), asparagine ethyl ester (AsnOEt), and glutamine methyl ester (GlnOMe) were also studied for comparison to Gln. Although these clusters lack the acidic group of Gln and therefore have different water coordination behavior, these results further support the conclusion that Gln is nonzwitterionic in these clusters. Surprisingly, the complexes containing sodium are more stable than those containing lithium, a result that is attributed to subtle differences in how these two metal ions bind to the amino acid esters in these complexes.

Gases↗

Quantum chemical and theoretical kinetics study of the O(3P) + C2H2 reaction: a multistate process.

The potential energy surfaces of the two lowest-lying triplet electronic surfaces 3A'' and 3A' for the O(3P) + C2H2 reaction were theoretically reinvestigated, using various quantum chemical methods including CCSD(T), QCISD, CBS-QCI/APNO, CBS-QB3, G2M(CC,MP2), DFT-B3LYP and CASSCF. An efficient reaction pathway on the electronically excited 3A' surface resulting in H(2S) + HCCO(A2A') was newly identified and is predicted to play an important role at higher temperatures. The primary product distribution for the multistate multiwell reaction was then determined by RRKM statistical rate theory and weak-collision master equation analysis using the exact stochastic simulation method. Allowing for nonstatistical behavior of the internal rotation mode of the initial 3A'' adducts, our computed primary-product distributions agree well with the available experimental results, i.e., ca. 80% H(2S) + HCCO(X2A'' + A2A') and 20% CH2(X3B1) + CO(X1sigma+) independent of temperature and pressure over the wide 300-2000 K and 0-10 atm ranges. The thermal rate coefficient k(O + C2H2) at 200-2000 K was computed using multistate transition state theory: k(T) = 6.14 x 10(-15)T (1.28) exp(-1244 K/T) cm3 molecule(-1) s(-1); this expression, obtained after reducing the CBS-QCI/APNO ab initio entrance barriers by 0.5 kcal/mol, quasi-perfectly matches the experimental k(T) data over the entire 200-2000 K range, spanning 3 orders of magnitude.

Journal Article↗

The addition of hydrogen atoms to diacetylene and the heats of formation of i-C4H3 and n-C4H3.

In this article, we discuss in detail the addition of hydrogen atoms to diacetylene and the reverse dissociation reactions, H + C(4)H(2)<==>i-C(4)H(3) (R1) and H + C(4)H(2)<==>n-C(4)H(3) (R2). The theory utilizes high-level electronic structure methodology to characterize the potential energy surface, Rice-Ramsperger-Kassel-Marcus (RRKM) theory to calculate microcanonical/J-resolved rate coefficients, and a two-dimensional master-equation approach to extract phenomenological (thermal) rate coefficients. Comparison is made with experimental results where they are available. The rate coefficients k1(T, p) and k2(T, p) are cast in forms that can be used in chemical kinetic modeling. In addition, we predict values of the heats of formation of i-C(4)H(3) and n-C(4)H(3) and discuss their importance in flame chemistry. Our basis-set extrapolated, quadratic-configuration-interaction with single and double excitations (and triple excitations added perturbatively), QCISD(T), predictions of these heats of formation at 298 K are 130.8 kcal/mol for n-C(4)H(3) and 119.3 kcal/mol for the i-isomer; multireference CI calculations with a nine-electron, nine-orbital, complete-active-space (CAS) reference wavefunction give just slightly larger values for these parameters. Our results are in good agreement with the recent focal-point analysis of Wheeler et al. (J. Chem. Phys. 2004, 121, 8800-8813), but they differ substantially for DeltaH0(f 298)(n-C(4)H(3)) with the earlier diffusion Monte Carlo predictions of Krokidis et al. (Int. J. Chem. Kinet.2001, 33, 808-820).

Journal Article↗

A two transition state model for radical-molecule reactions: a case study of the addition of OH to C2H4.

A two transition state model is applied to the study of the addition of hydroxyl radical to ethylene. This reaction serves as a prototypical example of a radical-molecule reaction with a negative activation energy in the high-pressure limit. The model incorporates variational treatments of both inner and outer transition states. The outer transition state is treated with a recently derived long-range transition state theory approach focusing on the longest-ranged term in the potential. High-level quantum chemical estimates are incorporated in a variational transition state theory treatment of the inner transition state. Anharmonic effects in the inner transition state region are explored with direct phase space integration. A two-dimensional master equation is employed in treating the pressure dependence of the addition process. An accurate treatment of the two separate transition state regions at the energy and angular momentum resolved level is essential to the prediction of the temperature dependence of the addition rate. The transition from a dominant outer transition state to a dominant inner transition state is predicted to occur at about 130 K, with significant effects from both transition states over the 10 to 400 K temperature range. Modest adjustment in the ab initio predicted inner saddle point energy yields theoretical predictions which are in quantitative agreement with the available experimental observations. The theoretically predicted capture rate is reproduced to within 10% by the expression [4.93 x 10(-12) (T/298)(-2.488) exp(-107.9/RT) + 3.33 x 10(-12) (T/298)(0.451) exp(117.6/RT); with R = 1.987 and T in K] cm3 molecules(-1) s(-1) over the 10-600 K range.

Journal Article↗

Mechanism and rate constants for the decomposition of 1-pentenyl radicals.

This paper is concerned with the mechanisms and rate constants for the decomposition of 1-penten-3-yl, 1-penten-4-yl, and 1-penten-5-yl radicals. They are formed from radical attack on 1-pentene, which is an important decomposition product of normal alkyl radicals with more than 6 carbon atoms in combustion systems. This work is based on related data in the literature. These involve rate constants for the reverse radical addition process under high-pressure conditions, chemical activation experiments, and more recent direct studies. The high-pressure rate constants are based on detailed balance. The energy transfer effects and the pressure dependences of the rate constants are determined through the solution of the master equation and are projected to cover combustion conditions. The low barriers to these reactions make it necessary to treat these thermal reactions as open systems, as in chemical activation studies. The multiple reaction channels make the nature of the pressure effects different from those usually described in standard texts. The order of stability is 1-penten-3-yl approximately 1-penten-4-yl > 1-penten-5-yl and straddles those for the n-alkyl radicals. A key feature in these reactions is the effects traceable to allylic resonance. However, the 50 kJ/mol allylic resonance energy is not fully manifested. The important unsaturated products are 1,3-butadiene, the pentadienes, allyl radicals, and vinyl radicals. The results are compared with the recommendations in the literature, and significant differences are noted. Extensions to larger radicals with similar structures are discussed.

Journal Article↗

On modeling the pressure-dependent photoisomerization of trans-stilbene by including slow intramolecular vibrational energy redistribution.

Experimental data for the photoisomerization of trans-stilbene (S(1)) in thermal bath gases at pressures up to 20 bar obtained previously by Meyer, Schroeder, and Troe (J. Phys. Chem. A 1999, 103, 10528-10539) are modeled by using a full collisional-reaction master equation that includes non-RRKM (Rice-Ramsperger-Kassel-Marcus) effects due to slow intramolecular vibrational energy redistribution (IVR). The slow IVR effects are modeled by incorporating the theoretical results obtained recently by Leitner et al. (J. Phys. Chem. A 2003, 107, 10706-10716), who used the local random matrix theory. The present results show that the experimental rate constants of Meyer et al. are described to within about a factor of 2 over much of the experimental pressure range. However, a number of assumptions and areas of disagreement will require further investigation. These include a discrepancy between the calculated and experimental thermal rate constants near zero pressure, a leveling off of the experimental rate constants that is not predicted by theory and which depends on the identity of the collider gas, the need to use rate constants for collision-induced IVR that are larger than the estimated total collision rate constants, and the choice of barrier-crossing frequency. Despite these unsettled issues, the theory of Leitner et al. shows great promise for accounting for possible non-RRKM effects in an important class of reactions.

Computer Simulation↗

Temperature-dependent relaxation of excitons in tubular molecular aggregates: Fluorescence decay and stokes shift.

We report temperature-dependent steady-state and time-resolved fluorescence studies to probe the exciton dynamics in double-wall tubular J-aggregates formed by self-assembly of the dye 3,3'-bis(3-sulfopropyl)-5,5',6,6'-tetrachloro-1,1'-dioctylbenzimidacarbocyanine. We focus on the lowest energy fluorescence band, originating from the inner cylindrical wall. At low temperatures, the experiments reveal a nonexponential decay of the fluorescence, with a typical time scale that depends on the emission wavelength. At these temperatures we also find a dynamic Stokes shift of the fluorescence spectrum and its nonmonotonic dependence on temperature under steady-state conditions. All these data indicate that below about 20 K the excitons in the lowest fluorescence band do not reach thermal equilibrium before emission occurs, while above about 60 K thermalization on this time scale is complete. By comparing the two lowest fluorescence bands, we also find indications for fast energy transfer from the outer to the inner wall. We show that the Frenkel exciton model with diagonal disorder, which previously has been proposed to explain the absorption and linear dichroism spectra of these aggregates, yields a quantitative explanation to the observed dynamics. To this end, we extend the model to account for weak phonon-induced scattering of the localized exciton states; the spectral dynamics are then described by solving a Pauli master equation for the exciton populations.

Journal Article↗

Quantum chemical and statistical rate study of the reaction of O(3P) with allene: O-addition and H-abstraction channels.

The lowest-lying triplet and singlet potential energy surfaces for the O(3P) + CH2=C=CH2 reaction were theoretically characterized using the complete basis set model chemistry, CBS-QB3. The primary product distributions for the multistate multiwell reactions on the individual surfaces were then determined by RRKM statistical rate theory and weak-collision master equation analysis using the exact stochastic simulation method. The results predict that the electrophilic O-addition pathways on the central and terminal carbon atom are dominant up to combustion temperatures. Major predicted end-products for the addition routes include CO + C2H4, 3CH2 + H2CCO, and CH2=C*-CHO + H*, in agreement with experimental evidence. CO + C2H4 are mainly generated from the lowest-lying singlet surface after an intersystem crossing process from the initial triplet surface. Efficient H-abstraction pathways are newly identified and occur on two different electronic state surfaces, 3A'' and 3A', resulting in OH + propargyl radicals; they are predicted to play an important role at higher temperatures in hydrocarbon combustion chemistry and flames, with estimated contributions of ca. 35% at 2000 K. The overall thermal rate coefficient k(O + C3H4) at 200-1000 K was computed using multistate transition state theory: k(T) = 1.60 x 10(-17) x T (2.05) x exp(-90 K/T) cm3 molecule(-1) s(-1), in good agreement with experimental data available for the 300-600 K range.

Journal Article↗

Deviant effects in molecular reaction pathways.

In biological networks, any manifestations of behaviors substantially 'deviant' from the predictions of continuous-deterministic classical chemical kinetics (CCK) are typically ascribed to systems with complex dynamics and/or a small number of molecules. Here we show that in certain cases such restrictions are not obligatory for CCK to be largely incorrect. By systematically identifying properties that may cause significant divergences between CCK and the more accurate discrete-stochastic chemical master equation (CME) system descriptions, we comprehensively characterize potential CCK failure patterns in biological settings, including consequences of the assertion that CCK is closer to the 'mode' rather than the 'average' of stochastic reaction dynamics, as generally perceived. We demonstrate that mechanisms underlying such nonclassical effects can be very simple, are common in cellular networks and result in often unintuitive system behaviors. This highlights the importance of deviant effects in biotechnologically or biomedically relevant applications, and suggests some approaches to diagnosing them in situ.

Biotechnology↗

Infrared frequency-modulation probing of product formation in alkyl + O2 reactions. Part IV. Reactions of propyl and butyl radicals with O2.

The time-resolved production of HO2 in the Cl-initiated oxidation of iso- and n-butane is measured using continuous-wave (CW) infrared frequency modulation spectroscopy between 298 and 693 K. The yield of HO2 is determined relative to the Cl2/CH3OH/O2 system. As in studies of smaller alkanes, the branching fraction to HO2 + alkene in butyl + O2 displays a dramatic rise with increasing temperature between about 550 and 700 K (the "transition region") which is accompanied by a qualitative change in the time behavior of the HO2 production. At low temperatures the HO2 is formed promptly; a second, slower production of HO2 is responsible for the bulk of the increased yield in the transition temperature region. In contrast to reactions of smaller alkyl radicals with O2, the total HO2 yield in the butyl radical reactions appears to remain significantly below 1 up to 700 K, implying a significant role for OH-producing channels. The slower HO2 production in butane oxidation displays an apparent activation energy similar to that measured for smaller alkyl + O2 reactions, suggesting that the energetics of the HO2 elimination transition state are similar for a broad range of R + O2 systems. A combination of QCISD(T) based characterizations of the propyl and butyl + O2 potential energy surfaces and master equation based characterization of the propyl + O2 kinetics provide the framework for explanation of the experimentally observed HO2 production in Cl-initiated propane and butane oxidation. These calculations suggest that the HO2 elimination channel is similar in all reaction systems, and that hydroperoxyalkyl (QOOH) species produced by internal H-atom abstraction in RO2 can provide a path to OH formation. However, the QOOH formed by the energetically favorable 1,5 isomerization (via a six-membered ring transition state) generally experiences significant barriers (relative to the radical + O2 reactants) to the production of an oxetane + OH. In contrast, the barriers to forming OH + an oxirane or an oxolane, via 1,4 or 1,6 isomerizations, respectively, are generally below reactants.

Journal Article↗

A theoretical analysis of the reaction between propargyl and molecular oxygen.

The temperature- and pressure-dependent kinetics of the reaction between propargyl and molecular oxygen have been studied with a combination of electronic structure theory, transition state theory, and the time-dependent master equation. The stationary points on the potential energy surface were located with B3LYP density functional theory. Approximate QCISD(T,Full)/6-311++G(3df,2pd) energies were obtained at these stationary points. At low temperatures the reaction is dominated by addition to the CH2 side of the propargyl radical followed by stabilization. However, addition to the CH side, which is followed by one of various possible internal rearrangements, becomes the dominant process at higher temperatures. These internal rearrangements involve a splitting of the O2 bond via the formation of 3-, 4- or 5-membered rings, with the apparent products being CH2CO + HCO. Rearrangement via the 3-membered ring is found to dominate the kinetics. Rearrangement from the CH2 addition product, via a 4-membered ring, would yield H2CO + HCCO, but the barrier to this rearrangement is too high to be kinetically significant. Other possible products require H transfers and, as a result, appear to be kinetically irrelevant. Modest variations in the energetics of a few key stationary points (most notably the entrance barrier heights) yield kinetic results that are in good agreement with the experimental results of Slagle and Gutman (I. R. Slagle and D. Gutman, Proc. Combust. Inst., 1986, 21, 875) and of Atkinson and Hudgens (D. B. Atkinson and J. W. Hudgens, J. Phys. Chem. A, 1999, 103, 4242).

Journal Article↗

Cellular growth and division in the Gillespie algorithm.

Recent experimental studies elucidating the importance of noise in gene regulation have ignited widespread interest in Gillespie's stochastic simulation technique for biochemical networks. We formulate modifications to the Gillespie algorithm which are necessary to correctly simulate chemical reactions with time-dependent reaction rates. We concentrate on time dependence of kinetic rates arising from the periodic process of growth and division of the cellular volume, and demonstrate that a careful re-derivation of the Gillespie algorithm is important when all stochastically simulated reactions have rates slower or comparable to the cellular growth rate. For an unregulated single-gene system, we illustrate our findings using recently proposed hybrid simulation techniques, and systematically compare our algorithm with analytic results obtained from the chemical master equation.

Algorithms↗

Modeling quantum measurement probability as a classical stochastic process.

The time-dependent measurement probabilities for the simple two-state quantum oscillator seem to invite description as a classical two-state stochastic process. It has been shown that such a description cannot be achieved using a Markov process. Constructing a more general non-Markov process is a challenging task, requiring as it does the proper generalizations of the Markovian Chapman-Kolmogorov and master equations. Here we describe those non-Markovian generalizations in some detail, and we then apply them to the two-state quantum oscillator. We devise two non-Markovian processes that correctly model the measurement statistics of the oscillator, we clarify a third modeling process that was proposed earlier by others, and we exhibit numerical simulations of all three processes. Our results illuminate some interesting though widely unappreciated points in the theory of non-Markovian stochastic processes. But since quantum theory does not tell us which one of these quite different modeling processes "really" describes the behavior of the oscillator, and also since none of these processes says anything about the dynamics of other (noncommuting) oscillator observables, we can see no justification for regarding any of these processes as being fundamentally descriptive of quantum dynamics. (c) 2001 American Institute of Physics.

Journal Article↗

Self-organized nanostructures in surface chemical reactions: Mechanisms and mesoscopic modeling.

Nanoscale patterns can form in reactive adsorbates on catalytic surfaces as a result of attractive lateral interactions. These structures can be described within a mesoscopic theory that is derived by coarse graining the microscopic master equation thus providing a link between microscopic lattice models and reaction-diffusion equations. Such mesoscopic models allow to systematically investigate mechanisms responsible for the formation of nanoscale nonequilibrium patterns in reactive condensed matter. We have found that stationary and traveling nanostructures may result from the interplay of the attractive lateral interactions and nonequilibrium reactions. Besides reviewing these results, a detailed investigation of a single reactive adsorbate in the presence of attractive lateral interactions and global coupling through the gas phase is presented. Finally, it is outlined how a mesoscopic theory should be constructed for a particular scanning tunneling microscopy experiment [the oxidation of hydrogen on a Pt(111) surface] in order to overcome the failure of a corresponding reaction-diffusion model to quantitatively reproduce the experiments. (c) 2002 American Institute of Physics.

Journal Article↗

State-to-state rotational rate constants for CO + He: infrared double resonance measurements and simulation of the data using the SAPT theoretical potential energy surface.

An extensive data set of 54 time-resolved pump-probe measurements was used to examine CO + He rotational energy transfer within the CO v = 2 rotational manifold. Rotational levels in the range Ji = 2-9 were excited and collisional energy transfer of population to the levels Jf = 1-10 was monitored. The resulting data set was analyzed by fitting to numerical solutions of the master equation. State-to-state rate constant matrices were generated using fitting law functions and ab initio theoretical calculations that employed the SAPT potential energy surface of Heijmen et al. [J. Chem. Phys. 107, 9921 (1997)]. Fitting laws based on the modified exponential gap (MEG), statistical power exponential gap (SPEG), and energy corrected sudden with exponential power (ECS-EP) models all yielded acceptable simulations of the kinetic data, as did the theoretical rate constants. However, the latter were unique in their ability to reproduce both our kinetic data and the pressure broadening coefficients for CO + He. These results provide an impressive demonstration of the quality of the symmetry adapted perturbation theory (SAPT) potential energy surface.

Journal Article↗

Low-temperature dynamics of weakly localized Frenkel excitons in disordered linear chains.

We calculate the temperature dependence of the fluorescence Stokes shift and the fluorescence decay time in linear Frenkel exciton systems resulting from the thermal redistribution of exciton population over the band states. The following factors, relevant to common experimental conditions, are accounted for in our kinetic model: (weak) localization of the exciton states by static disorder, coupling of the localized excitons to vibrations in the host medium, a possible nonequilibrium of the subsystem of localized Frenkel excitons on the time scale of the emission process, and different excitation conditions (resonant or nonresonant). A Pauli master equation, with microscopically calculated transition rates, is used to describe the redistribution of the exciton population over the manifold of localized exciton states. We find a counterintuitive nonmonotonic temperature dependence of the Stokes shift. In addition, we show that depending on experimental conditions, the observed fluorescence decay time may be determined by vibration-induced intraband relaxation, rather than radiative relaxation to the ground state. The model considered has relevance to a wide variety of materials, such as linear molecular aggregates, conjugated polymers, and polysilanes.

Journal Article↗

Hybridization dynamics of surface immobilized DNA.

We model the hybridization kinetics of surface attached DNA oligomers with solubilized targets. Using both master equation and rate equation formalisms, we show that, for surface coverages at which the surface immobilized molecules interact, barriers to penetration create a distribution of target molecule concentrations within the adsorbed layer. By approximately enumerating probe and target conformations, we estimate the probability of overlap between complementary probe and target regions as a function of probe density and chain length. In agreement with experiments, we find that as probe molecules interact more strongly, fewer nucleation sites become accessible and binding rates are diminished relative to those in solution. Nucleation sites near the grafted end of the probes are least accessible; thus targets which preferentially bind to this region show more drastic rate reductions than those that bind near the free end of the probe. The implications of these results for DNA-based biosensors are discussed.

Adsorption↗

Decoupling quantum dissipation interaction via stochastic fields.

Based on the Hubbard-Stratonovich transformation, the dissipative interaction between the system of interest and the heat bath is decoupled and the separated system and bath thus evolve in common classical random fields. This manipulation allows us to establish a novel theoretical methodology by which the reduced density matrix is formulated as an ensemble average of its random realizations in the auxiliary white noise fields. Within the stochastic description, the interaction between the system and the bath is reflected in the mutually induced mean fields. The relationship between the bath-induced field and the influence functional in the path integral framework is revealed. As a demonstration of this approach, we derive the exact master equations for two model systems.

Journal Article↗