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Parametric sensitivity of biochemical networks is an indispensable tool for studying system robustness properties, estimating network parameters, and identifying targets for drug therapy. For discrete stochastic representations of biochemical networks where Monte Carlo methods are commonly used, sensitivity analysis can be particularly challenging, as accurate finite difference computations of sensitivity require a large number of simulations for both nominal and perturbed values of the parameters. In this paper we introduce the common random number (CRN) method in conjunction with Gillespie’s stochastic simulation algorithm, which exploits positive correlations obtained by using CRNs for nominal and perturbed parameters. We also propose a new method called the common reaction path (CRP) method, which uses CRNs together with the random time change representation of discrete state Markov processes due to Kurtz to estimate the sensitivity via a finite difference approximation applied to coupled reaction paths that emerge naturally in this representation. While both methods reduce the variance of the estimator significantly compared to independent random number finite difference implementations, numerical evidence suggests that the CRP method achieves a greater variance reduction. We also provide some theoretical basis for the superior performance of CRP. The improved accuracy of these methods allows for much more efficient sensitivity estimation. In two example systems reported in this work, speedup factors greater than 300 and 10 000 are demonstrated. [ABSTRACT FROM AUTHOR]

In this paper, we investigate the treatment of constraints in rate equations describing the temporal evolution of biological populations or chemical reactions. We present a formulation for arbitrary holonomic and linear nonholonomic constraints which ensures the positivity of the dynamical variables and which is an analog of Gauss’ principle of least constraint in classical mechanics. The approach is illustrated for the replication of molecular species in the Schuster–Eigen hypercycle model, imposing the conservation of the total number of molecules and the entropy production as constraints. The latter is used to model the behavior of an isolated system tending toward equilibrium and, for comparison, a stationary nonequilibrium state of an open system, which is characterized by undamped oscillations. [ABSTRACT FROM AUTHOR]

The self-assembly of the protein shell (“capsid”) of a virus appears to obey the law of mass action (LMA) despite the fact that viral assembly is a nonequilibrium process. In this paper we examine a model for capsid assembly, the “assembly line model,” that can be analyzed analytically. We show that, in this model, efficient viral assembly from a supersaturated solution is characterized by a shock front propagating in the assembly configuration space from small to large aggregate sizes. If this shock front can reach the size of assembled capsids, then capsid assembly follows either the LMA or a “pseudo” LMA that describes partitioning of capsid proteins between assembled capsids and a metastable, supersaturated solution of free proteins that decays logarithmically slowly. We show that the applicability of the LMA and the pseudo-LMA is governed by two dimensionless parameters: the dimensionless nucleation rate and the dimensionless line energy of incomplete capsids. [ABSTRACT FROM AUTHOR]

Sensitivity analysis is an indispensable tool for studying the robustness and fragility properties of biochemical reaction systems as well as for designing optimal approaches for selective perturbation and intervention. Deterministic sensitivity analysis techniques, using derivatives of the system response, have been extensively used in the literature. However, these techniques suffer from several drawbacks, which must be carefully considered before using them in problems of systems biology. We develop here a probabilistic approach to sensitivity analysis of biochemical reaction systems. The proposed technique employs a biophysically derived model for parameter fluctuations and, by using a recently suggested variance-based approach to sensitivity analysis [Saltelli et al., Chem. Rev. (Washington, D.C.) 105, 2811 (2005)], it leads to a powerful sensitivity analysis methodology for biochemical reaction systems. The approach presented in this paper addresses many problems associated with derivative-based sensitivity analysis techniques. Most importantly, it produces thermodynamically consistent sensitivity analysis results, can easily accommodate appreciable parameter variations, and allows for systematic investigation of high-order interaction effects. By employing a computational model of the mitogen-activated protein kinase signaling cascade, we demonstrate that our approach is well suited for sensitivity analysis of biochemical reaction systems and can produce a wealth of information about the sensitivity properties of such systems. The price to be paid, however, is a substantial increase in computational complexity over derivative-based techniques, which must be effectively addressed in order to make the proposed approach to sensitivity analysis more practical. [ABSTRACT FROM AUTHOR]

Gillespie’s direct method (DM) [D. Gillespie, J. Chem. Phys. 81, 2340 (1977)] for exact stochastic simulation of chemical reaction systems has been widely adopted. It is easy to implement but requires large computation for relatively large systems. Recently, two more efficient methods, next reaction method (NRM) [M. A. Gibson and J. Bruck, J. Phys. Chem. A 105, 1876 (2000)] and optimized DM (ODM) [Y. Cao et al., J. Chem. Phys. 121, 4059 (2004)], have been developed to improve simulation speed. It has been demonstrated that the ODM is the state-of-the-art most efficient method for exact stochastic simulation of most practical reaction systems. In this paper, we first develop an exact stochastic simulation algorithm named ODMK that is more efficient than the ODM. We then develop an approximate method named K-skip method to further accelerate simulation. Using two chemical reaction systems, we demonstrate that our ODMK and K-skip method can save 20%–30% and 70%–80% simulation time, respectively, comparing to the ODM. We also show that our ODMK and K-skip method provide almost the same simulation accuracy as the ODM. [ABSTRACT FROM AUTHOR]

The dissociation dynamics of methylsulfonyl radicals generated from the photodissociation of CH3SO2Cl at 193 nm is investigated by measuring product velocities in a crossed laser-molecular beam scattering apparatus. The data evidence three primary photodissociation channels of the precursor: S–Cl fission to produce Cl atoms and ground electronic state CH3SO2 radicals, S–Cl fission to produce Cl atoms and electronically excited CH3SO2 radicals, and S–CH3 fission. Some of the vibrationally excited CH3SO2 radicals undergo subsequent dissociation to CH3+SO2, as do all of the electronically excited radicals. The velocities of the SO2 products show that the vibrationally excited ground state CH3SO2 radicals dissociate via a loose transition state having a small exit barrier beyond the endoergicity. Hence, a statistical recoil kinetic energy distribution should and does fit the distribution of velocities imparted to these SO2 products. The electronically excited CH3SO2 radicals also dissociate to CH3+SO2, but with a larger average release to relative kinetic energy. Interestingly, when using 200 eV electron bombardment detection, the ground electronic state CH3SO2 radicals having too little internal energy to dissociate are not observed at the parent CH3SO2+ ion, but only at the CH3+ daughter ion. They are distinguished by virtue of the velocity imparted in the original photolytic step; the detected velocities of the stable radicals are consistent with the calculated barrier of 14.6 kcal/mol for the dissociation of CH3SO2 to CH3+SO2. We present CCSD(T) calculations of the adiabatic excitation energy to the lowest excited state of CH3SO2 radicals, the 1 2A″ state, as well as the vertical energy from the equilibrium geometry of that excited state to the 2 2A″ state, to aid in the experimental assignment. [ABSTRACT FROM AUTHOR]

These imaging experiments study the formation of the methylsulfonyl radical, CH3SO2, from the photodissociation of CH3SO2Cl at 193 nm and determine the energetic barrier for the radical’s subsequent dissociation to CH3+SO2. We first state-selectively detect the angular and recoil velocity distributions of the Cl(2P3/2) and Cl(2P1/2) atoms to further refine the distribution of internal energy partitioned to the momentum-matched CH3SO2 radicals. The internal energy distribution of the radicals is bimodal, indicating that CH3SO2 is formed in both the ground state and low-lying excited electronic states. All electronically excited CH3SO2 radicals dissociate, while those formed in the ground electronic state have an internal energy distribution which spans the dissociation barrier to CH3+SO2. We detect the recoil velocities of the energetically stable methylsulfonyl radicals with 118 nm photoionization. Comparison of the total recoil translational energy distribution for all radicals to the distribution obtained from the detection of stable radicals yields an onset for dissociation at a translational energy of 70±2 kcal/mol. This onset allows us to derive a CH3SO2→CH3+SO2 barrier height of 14±2 kcal/mol; this determination relies on the S–Cl bond dissociation energy, taken here as the CCSD(T) predicted energy of 65.6 kcal/mol. With 118 nm photoionization, we also detect the velocity distribution of the CH3 radicals produced in this experiment. Using the velocity distributions of the SO2 products from the dissociation of CH3SO2 to CH3+SO2 presented in the following paper, we show that our fastest detected methyl radicals are not from these radical dissociation channels, but rather from a primary S–CH3 bond photofission channel in CH3SO2Cl. We also present critical points on the ground state potential energy surface of CH3SO2 at the //CCSD(T)/aug-cc-pV(Q+d)ZCCSD(T)/6-311++G(2df,p) level. We include harmonic zero-point vibrational corrections as well as core-valence and scalar-relativistic corrections. The CCSD(T) predicted barrier of 14.6 kcal/mol for CH3SO2→CH3+SO2 agrees well with our experimental measurement. These results allow us to predict the unimolecular dissociation kinetics of CH3SO2 radicals and critique the analysis of prior time-resolved photoionization studies on this system. [ABSTRACT FROM AUTHOR]

In this paper we present a new global search strategy named as “compressing liquid” for atomic clusters. In this strategy, a random fragment of liquid structure is adopted as a starting geometry, followed by iterative operations of “compressing” and Monte Carlo adjustment of the atom positions plus structural optimization. It exhibits fair efficiency when it is applied to seeking the global minima of Lennard-Jones clusters. We also employed it to search the low-lying candidates of medium silicon clusters Sin(n=40–60), where the global search is absent. We found the best candidates for most sizes. More importantly, we obtained non-fullerene-based structures for some sized clusters, which were not found from the endohedral-fullerene strategy. These results indicate that the “compressing-liquid” method is highly efficient for global minima search of clusters. [ABSTRACT FROM AUTHOR]

A theoretical analysis of the hydrogen-terminated (100) surface of silicon leads to the identification of a new configuration, formed by a silylene center interacting with vicinal silicon dihydrides. This structure may be viewed as a metastable configuration of 2×1 (100) (SiH)2. Silylene can however be stabilized via interaction with water. The paper proposes that some of the anomalous features observed at the hydrogen-terminated or oxidized (100) Si can be attributed to silylene centers datively stabilized by oxo groups or to structures resulting from their decomposition. [ABSTRACT FROM AUTHOR]

On a new potential energy surface (PES-2008) developed by our group (preceding paper), we performed an extensive kinetics study using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range of 250–2000 K and a dynamics study using quasiclassical trajectory (QCT) and quantum-mechanical (QM) calculations at collision energies between 0.7 and 2.0 eV for the title reaction and isotopically substituted versions. Kinetically, the H+CH4 forward and reverse thermal rate constants reproduce the available experimental data, with a small curvature of the Arrhenius plot indicating the role of tunneling in this hydrogen abstraction reaction. Five sets of kinetic isotope effects are also calculated. In general, they reproduce the experimental information. Dynamically, we focused on the H+CD4 reaction because there are more experimental studies for comparison. Most of the available energy appears as product translational energy (55%–68%), with the HD product being vibrationally cold (v′=0,1) in agreement with experiment, although rotationally hotter than experiment. The reaction cross section is practically negligible at 0.7 eV and still small at 1.5 eV, reproducing the experimental evidence, although our values are smaller. The product angular distribution is analyzed using QCT and QM methods. While at low energies (0.7 eV) both the QCT and the QM calculations yield forward scattered CD3 product, i.e., a rebound mechanism, at high energy (1.2 eV) only the QM calculations reproduce the experiment. The agreement with this wide variety of kinetic and dynamic experimental data (always qualitative and in some cases quantitative) shows the capacity of the PES-2008 surface to describe the reaction system. [ABSTRACT FROM AUTHOR]

The hydrogen [1,3]-sigmatropic shift in propene is predicted by the Woodward–Hoffman rules to occur by an antarafacial pathway, yet the lack of experimental evidence suggests that this pathway is not favorable. Two natural questions arise: (i) can the [1,3]-shift be made more favorable by a symmetry-forbidden multistep pathway, and (ii) can the energetics be influenced by a substituent on propene? As in many chemical reactions, describing the energetics of these reactions requires a balanced treatment of both single-reference and multireference electron correlations, and yet traditional wave function methods often excel in treating only one kind of correlation. An equitable description of correlation effects, however, can be achieved, at a cost similar to efficient single-reference methods, by computing the two-electron reduced density matrix (2-RDM) from the anti-Hermitian part of the contracted Schrödinger equation (ACSE) [D. A. Mazziotti, Phys. Rev. Lett. 97, 143002 (2006)]. As with the contracted Schrödinger equation, the indeterminacy of the ACSE is removed without the many-electron wave function by reconstructing the 3-RDM from the 2-RDM via cumulant theory [D. A. Mazziotti, Chem. Phys. Lett. 289, 419 (1998)]. In this paper we apply the ACSE to study sigmatropic shifts in both propene and acetone enolate while extending its formalism to treat doublet spin states. In the 6-311G** basis set the ACSE predicts the activation energy of the trimethylene-to-propene rearrangement to be 8.8 kcal/mol while multireference perturbation theory yields a smaller barrier of 2.2 kcal/mol and coupled cluster singles-doubles predicts a negative barrier. We further find that the [1,3]-shift in acetone enolate is more favorable by ≈30 kcal/mol than the [1,3]-shift in propene, which is consistent with a prior theoretical investigation as well as experimental observations of these shifts in 2-butanone enolate. [ABSTRACT FROM AUTHOR]

In this paper we present a moment closure method for stochastically modeled chemical or biochemical reaction networks. We derive a system of differential equations which describes the dynamics of means and all central moments from a chemical master equation. Truncating the system for the central moments at a certain moment term and using Taylor approximation, we obtain explicit representations of means and covariances and even higher central moments in recursive forms. This enables us to deal with the moments in successive differential equations and use conventional numerical methods for their approximations. Furthermore, we estimate the errors in the means and central moments generated by the approximation method. We also find the moments at equilibrium by solving truncated algebraic equations. We show in examples that numerical solutions based on the moment closure method are accurate and efficient by comparing the results to those of stochastic simulation algorithms. [ABSTRACT FROM AUTHOR]

We aim to construct higher order tau-leaping methods for numerically simulating stochastic chemical kinetic systems in this paper. By adding a random correction to the primitive tau-leaping scheme in each time step, we greatly improve the accuracy of the tau-leaping approximations. This gain in accuracy actually comes from the reduction in the local truncation error of the scheme in the order of τ, the marching time step size. While the local truncation error of the primitive tau-leaping method is O(τ2) for all moments, our Poisson random correction tau-leaping method, in which the correction term is a Poisson random variable, can reduce the local truncation error for the mean to O(τ3), and both Gaussian random correction tau-leaping methods, in which the correction term is a Gaussian random variable, can reduce the local truncation error for both the mean and covariance to O(τ3). Numerical results demonstrate that these novel methods more accurately capture crucial properties such as the mean and variance than existing methods for simulating chemical reaction systems. This work constitutes a first step to construct high order numerical methods for simulating jump processes. With further refinement and appropriately modified step-size selection procedures, the random correction methods should provide a viable way of simulating chemical reaction systems accurately and efficiently. [ABSTRACT FROM AUTHOR]

The Inhomogeneous Stochastic Simulation Algorithm (ISSA) is a variant of the stochastic simulation algorithm in which the spatially inhomogeneous volume of the system is divided into homogeneous subvolumes, and the chemical reactions in those subvolumes are augmented by diffusive transfers of molecules between adjacent subvolumes. The ISSA can be prohibitively slow when the system is such that diffusive transfers occur much more frequently than chemical reactions. In this paper we present the Multinomial Simulation Algorithm (MSA), which is designed to, on the one hand, outperform the ISSA when diffusive transfer events outnumber reaction events, and on the other, to handle small reactant populations with greater accuracy than deterministic-stochastic hybrid algorithms. The MSA treats reactions in the usual ISSA fashion, but uses appropriately conditioned binomial random variables for representing the net numbers of molecules diffusing from any given subvolume to a neighbor within a prescribed distance. Simulation results illustrate the benefits of the algorithm. [ABSTRACT FROM AUTHOR]

This paper addresses the problem of simplifying chemical reaction networks by adroitly reducing the number of reaction channels and chemical species. The analysis adopts a discrete-stochastic point of view and focuses on the model reaction set S1≤=≥S2→S3, whose simplicity allows all the mathematics to be done exactly. The advantages and disadvantages of replacing this reaction set with a single S3-producing reaction are analyzed quantitatively using novel criteria for measuring simulation accuracy and simulation efficiency. It is shown that in all cases in which such a model reduction can be accomplished accurately and with a significant gain in simulation efficiency, a procedure called the slow-scale stochastic simulation algorithm provides a robust and theoretically transparent way of implementing the reduction [ABSTRACT FROM AUTHOR]

This paper supersedes previous theoretical approaches to conceptual DFT because it provides a unified and systematic approach to all of the commonly considered formulations of conceptual DFT, and even provides the essential mathematical framework for new formulations. Global, local, and nonlocal chemical reactivity indicators associated with the “closed-system representation” ([Nα,Nβ,να(r),νβ(r)]) of spin-polarized density functional theory (SP-DFT) are derived. The links between these indicators and the ones associated with the “open-system representation” ([μα,μβ,να(r),νβ(r)]) are derived, including the spin-resolved Berkowitz–Parr identity. The Legendre transform to the “density representation” ([ρα(r),ρβ(r)]) is performed, and the spin-resolved Harbola–Chattaraj–Cedillo–Parr identities linking the density representation to the closed-system and open-system representations are derived. Taken together, these results provide the framework for understanding chemical reactions from both the electron-following perspective (using either the closed-system or the open-system representation) and electron-preceding perspective (density representation). A powerful matrix-vector notation is developed; with this notation, identities in conceptual DFT become universal. Specifically, this notation allows the fundamental identities in conventional (spin-free) conceptual DFT, the [Nα,Nβ] representation, and the [N=Nα+Nβ,NS=Nα-Nβ] representation to be written in exactly the same forms. In cases where spin transfer and electron transfer are coupled (e.g., radical+molecule reactions), we believe that the [Nα,Nβ] representation may be more useful than the more common [N,NS] representation. [ABSTRACT FROM AUTHOR]

The delay stochastic simulation algorithm (DSSA) by Barrio et al. [Plos Comput. Biol. 2, 117(E) (2006)] was developed to simulate delayed processes in cell biology in the presence of intrinsic noise, that is, when there are small-to-moderate numbers of certain key molecules present in a chemical reaction system. These delayed processes can faithfully represent complex interactions and mechanisms that imply a number of spatiotemporal processes often not explicitly modeled such as transcription and translation, basic in the modeling of cell signaling pathways. However, for systems with widely varying reaction rate constants or large numbers of molecules, the simulation time steps of both the stochastic simulation algorithm (SSA) and the DSSA can become very small causing considerable computational overheads. In order to overcome the limit of small step sizes, various τ-leap strategies have been suggested for improving computational performance of the SSA. In this paper, we present a binomial τ-DSSA method that extends the τ-leap idea to the delay setting and avoids drawing insufficient numbers of reactions, a common shortcoming of existing binomial τ-leap methods that becomes evident when dealing with complex chemical interactions. The resulting inaccuracies are most evident in the delayed case, even when considering reaction products as potential reactants within the same time step in which they are produced. Moreover, we extend the framework to account for multicellular systems with different degrees of intercellular communication. We apply these ideas to two important genetic regulatory models, namely, the hes1 gene, implicated as a molecular clock, and a Her1/Her 7 model for coupled oscillating cells. [ABSTRACT FROM AUTHOR]

In this paper, we describe two types of effective events for describing heat transfer in a kinetic Monte Carlo (KMC) simulation that may involve stochastic chemical reactions. Simulations employing these events are referred to as KMC-TBT and KMC-PHE. In KMC-TBT, heat transfer is modeled as the stochastic transfer of “thermal bits” between adjacent grid points. In KMC-PHE, heat transfer is modeled by integrating the Poisson heat equation for a short time. Either approach is capable of capturing the time dependent system behavior exactly. Both KMC-PHE and KMC-TBT are validated by simulating pure heat transfer in a rod and a square and modeling a heated desorption problem where exact numerical results are available. KMC-PHE is much faster than KMC-TBT and is used to study the endothermic desorption of a lattice gas. Interesting findings from this study are reported. [ABSTRACT FROM AUTHOR]

Chemical reaction systems with a low to moderate number of molecules are typically modeled as discrete jump Markov processes. These systems are oftentimes simulated with methods that produce statistically exact sample paths such as the Gillespie algorithm or the next reaction method. In this paper we make explicit use of the fact that the initiation times of the reactions can be represented as the firing times of independent, unit rate Poisson processes with internal times given by integrated propensity functions. Using this representation we derive a modified next reaction method and, in a way that achieves efficiency over existing approaches for exact simulation, extend it to systems with time dependent propensities as well as to systems with delays. [ABSTRACT FROM AUTHOR]

In this paper, rheological properties evolution of the simple mixed isotactic polypropylene/organoclay composites, impacted by intermediate- or large-amplitude oscillatory shear fields, was followed by dynamic melt rheometry. The physical meanings of such rheological evolution upon oscillatory shearing, which related closely to the dispersion and intercalation of organoclay in polymer, were discussed deeply. Especially, a structural recovery test was adopted to assess microstructure development induced by large-amplitude oscillatory shear and to better understand the intercalation mechanism. Based on the experimental results, a novel intercalation mechanism that was taken to account for the disentanglement of polymer chains was suggested to describe shear-induced dispersion behaviors of organoclay in polymer matrix. [ABSTRACT FROM AUTHOR]

Time-resolved nonlinear optical activity measurement spectroscopy can be a useful tool for studying biomolecular and chemical reaction dynamics of chiral molecules. Only recently, the two-dimensional (2D) circularly polarized photon echo (CP-PE) spectroscopy of polypeptides and a photosynthetic light-harvesting complex were discussed, where the beam configuration was specifically controlled in such a way to eliminate the quadrupole contribution to the CP-PE signal. In this paper, we generalize the CP-PE spectroscopy by including the transition quadrupole contributions from peptide amide I vibrational transition and chlorophyll electronic transition. By using a density functional theory calculation method, the corresponding amide I vibrational and chlorophyll Qy electronic transition quadrupole tensor elements are determined. Amplitude of nonlinear optical transition pathway involving a quadrupole transition is found to be comparable to those of magnetic dipole terms for two different cases considered, i.e., dipeptides and photosynthetic antenna complex. However, due to the rotational averaging factors, the overall quadrupole contribution is an order of magnitude smaller than the magnetic dipole contribution. This suggests that the conventional 2D photon echo method and experimental scheme can be directly used to measure the 2D CP-PE signal from proteins and molecular complexes and that the 2D CP-PE signal is mainly dictated by the magnetic dipole contribution. [ABSTRACT FROM AUTHOR]

We report in this paper a quantum dynamics study for the reaction H+NH3→NH2+H2 on the potential energy surface of Corchado and Espinosa-Garcia [J. Chem. Phys. 106, 4013 (1997)]. The quantum dynamics calculation employs the semirigid vibrating rotor target model [J. Z. H. Zhang, J. Chem. Phys. 111, 3929 (1999)] and time-dependent wave packet method to propagate the wave function. Initial state-specific reaction probabilities are obtained, and an energy correction scheme is employed to account for zero point energy changes for the neglected degrees of freedom in the dynamics treatment. Tunneling effect is observed in the energy dependency of reaction probability, similar to those found in H+CH4 reaction. The influence of rovibrational excitation on reaction probability and stereodynamical effect are investigated. Reaction rate constants from the initial ground state are calculated and are compared to those from the transition state theory and experimental measurement. [ABSTRACT FROM AUTHOR]

In quantum-mechanical/molecular-mechanical (QM/MM) treatment of chemical reactions in condensed phases, one solves the electronic Schrödinger equation for the solute (or an active site) under the electrostatic field from the environment. This Schrödinger equation depends parametrically on the solute nuclear coordinates R and the external electrostatic potential V. This fact suggests that one may use R and V as natural collective coordinates for describing the entire system, where V plays the role of collective solvent variables. In this paper such an (R,V) representation of the QM/MM canonical ensemble is described, with particular focus on how to treat charge transfer processes in this representation. As an example, the above method is applied to the proton-coupled electron transfer of a ubiquinol analog with phenoxyl radical in acetonitrile solvent. Ab initio free-energy surfaces are calculated as functions of R and V using the reference interaction site model self-consistent field method, the equilibrium points and the minimum free-energy crossing point are located in the (R,V) space, and then the kinetic isotope effects (KIEs) are evaluated approximately. The results suggest that a stiffer proton potential at the transition state may be responsible for unusual KIEs observed experimentally for related systems. [ABSTRACT FROM AUTHOR]

The de Broglie-Bohm formulation of the Schrödinger equation implies conservation of the wave function probability density associated with each quantum trajectory in closed systems. This conservation property greatly simplifies numerical implementations of the quantum trajectory dynamics and increases its accuracy. The reconstruction of a wave function, however, becomes expensive or inaccurate as it requires fitting or interpolation procedures. In this paper we present a method of computing wave packet correlation functions and wave function projections, which typically contain all the desired information about dynamics, without the full knowledge of the wave function by making quadratic expansions of the wave function phase and amplitude near each trajectory similar to expansions used in semiclassical methods. Computation of the quantities of interest in this procedure is linear with respect to the number of trajectories. The introduced approximations are consistent with approximate quantum potential dynamics method. The projection technique is applied to model chemical systems and to the H+H2 exchange reaction in three dimensions. [ABSTRACT FROM AUTHOR]

In the exact theory, the ground state energy of an open system varies linearly when the electron number is changed between two adjacent integers. This linear dependence is not reproduced by common approximate density functionals. Deviation from linearity in this dependence has been suggested as a basis for the concept of many-electron self-interaction error (SIE). In this paper, we quantify many-electron SIE of a number of approximations by performing calculations on fractionally charged atoms. We demonstrate the direct relevance of these studies to such problems of common approximate functionals as instabilities of anions, spurious fractional charges on dissociated atoms, and poor description of charge transfer. Semilocal approximations have the largest many-electron SIE, which is only slightly reduced in typical global hybrids. In these approximations the energy versus fractional electron number curves upward, while in Hartree-Fock theory the energy curves downward. Perdew-Zunger self-interaction correction [Phys. Rev. B 23, 5048 (1981)] significantly reduces the many-electron SIE of semilocal functionals but impairs their accuracy for equilibrium properties. In contrast, a long-range corrected hybrid functional can be nearly many-electron SIE-free in many cases (for reasons we discuss) and at the same time performs remarkably well for many molecular properties. [ABSTRACT FROM AUTHOR]

Gillespie’s exact stochastic simulation algorithm (SSA) [J. Phys. Chem. 81, 2350 (1977)] has been widely used to simulate the stochastic dynamics of chemically reacting systems. In this algorithm, it is assumed that all reactions occur instantly. While this is true in many cases, it is also possible that some chemical reactions, such as gene transcription and translation in living cells, take certain time to finish after they are initiated. Thus, the product of such reactions will emerge after certain delays. Apparently, Gillespie’s SSA is not an exact algorithm for chemical reaction systems with delays. In this paper, the author develops an exact SSA for chemical reaction systems with delays, based upon the same fundamental premise of stochastic kinetics used by Gillespie in the development of his SSA. He then shows that an algorithm modified from Gillespie’s SSA by Barrio et al. [PLOS Comput. Biol. 2, 1017 (2006)] is also an exact SSA for chemical reaction systems with delays, but it needs to generate more random variables than the author’s algorithm. [ABSTRACT FROM AUTHOR]

The noisy fluctuation of chemical reactions should profoundly affect the oscillatory dynamics of gene circuit. In this paper a prototypical genetic oscillator, repressilator, is numerically simulated to analyze effects of noise on oscillatory dynamics. The oscillation is coherent when the protein number and the rate of the DNA state alteration are within appropriate ranges, showing the phenomenon of coherence resonance. Stochastic fluctuation not only disturbs the coherent oscillation in a chaotic way but also destabilizes the stationary state to make the oscillation relatively stable. Bursting in translation, which is a source of intense stochastic fluctuation in protein numbers, suppresses the destructive effects of the finite leakage rate of protein production and thus plays a constructive role for the persistent oscillation. When multiple repressilators are coupled to each other, the cooperative interactions among repressilators enhance the coherence in oscillation but the dephasing fluctuation among multiple repressilators induces the amplitude fluctuation in the collective oscillation. [ABSTRACT FROM AUTHOR]

Leap methods are very promising for accelerating stochastic simulation of a well stirred chemically reacting system, while providing acceptable simulation accuracy. In Gillespie’s τ-leap method [D. Gillespie, J. Phys. Chem. 115, 1716 (2001)], the number of firings of each reaction channel during a leap is a Poisson random variable, whose sample values are unbounded. This may cause large changes in the populations of certain molecular species during a leap, thereby violating the leap condition. In this paper, we develop an alternative leap method called the K-leap method, in which we constrain the total number of reactions occurring during a leap to be a number K calculated from the leap condition. As the number of firings of each reaction channel during a leap is upper bounded by a properly chosen number, our K-leap method can better satisfy the leap condition, thereby improving simulation accuracy. Since the exact stochastic simulation algorithm (SSA) is a special case of our K-leap method when K=1, our K-leap method can naturally change from the exact SSA to an approximate leap method during simulation, whenever the leap condition allows to do so. [ABSTRACT FROM AUTHOR]

This paper is aimed at understanding what happens to the propensity functions (rates) of bimolecular chemical reactions when the volume occupied by the reactant molecules is not negligible compared to the containing volume of the system. For simplicity our analysis focuses on a one-dimensional gas of N hard-rod molecules, each of length l. Assuming these molecules are distributed randomly and uniformly inside the real interval [0,L] in a nonoverlapping way, and that they have Maxwellian distributed velocities, the authors derive an expression for the probability that two rods will collide in the next infinitesimal time dt. This probability controls the rate of any chemical reaction whose occurrence is initiated by such a collision. The result turns out to be a simple generalization of the well-known result for the point molecule case l=0: the system volume L in the formula for the propensity function in the point molecule case gets replaced by the “free volume” L-Nl. They confirm the result in a series of one-dimensional molecular dynamics simulations. Some possible wider implications of this result are discussed. [ABSTRACT FROM AUTHOR]

Transition path sampling is an innovative method for focusing a molecular dynamics simulation on a reactive event. Although transition path sampling methods can generate an ensemble of reactive trajectories, an initial reactive trajectory must be generated by some other means. In this paper, the authors have evaluated three methods for generating initial reactive trajectories for transition path sampling with ab initio molecular dynamics. The authors have tested each of these methods on a set of chemical reactions involving the breaking and making of covalent bonds: the 1,2-hydrogen elimination in the borane-ammonia adduct, a tautomerization, and the Claisen rearrangement. The first method is to initiate trajectories from the potential energy transition state, which was effective for all reactions in the test set. Assigning atomic velocities found using normal mode analysis greatly improved the success of this method. The second method uses a high temperature molecular dynamics simulation and then iteratively reduces the total energy of the simulation until a low temperature reactive trajectory is found. This was effective in generating a low temperature trajectory from an initial trajectory run at 3000 K of the tautomerization reaction, although it failed for the other two. The third uses an orbital based bias potential to find a reactive trajectory and uses this trajectory to initiate an unbiased trajectory. The authors found that a highest occupied molecular orbital–lowest unoccupied molecular orbital bias could be used to find a reactive trajectory for the Claisen rearrangement, although it failed for the other two reactions. These techniques will help make it practical to use transition path sampling to study chemical reaction mechanisms that involve bond breaking and forming. [ABSTRACT FROM AUTHOR]

The activation energy and ligand reorganization energy for nonadiabatic electron transfer reactions in chemical and biological systems are investigated in this paper. The free energy surfaces and the activation energy are derived exactly in the general case in which the ligand vibration frequencies are not equal. The activation energy is derived by free energy minimization at the transition state. Our formulation leads to the Marcus-Hush [J. Chem. Phys. 24, 979 (1956); 98, 7170 (1994); 28, 962 (1958)] results in the equal-frequency limit and also generalizes the Marcus-Sumi [J. Chem. Phys. 84, 4894 (1986)] model in the context of studying the solvent dynamic effect on electron transfer reactions. It is found that when the ligand vibration frequencies are different, the activation energy derived from the Marcus-Hush formula deviates by 5%–10% from the exact value. If the reduced reorganization energy approximation is introduced in the Marcus-Hush formula, the result is almost exact. [ABSTRACT FROM AUTHOR]

We present a detailed experimental and theoretical investigation of formaldehyde photodissociation to H2 and CO following excitation to the 2141 and 2143 transitions in S1. The CO velocity distributions were obtained using dc slice imaging of single CO rotational states (v=0, jCO=5–45). These high-resolution measurements reveal the correlated internal state distribution in the H2 cofragments. The results show that rotationally hot CO (jCO∼45) is produced in conjunction with vibrationally “cold” H2 fragments (v=0–5): these products are formed through the well-known skewed transition state and described in detail in the accompanying paper. After excitation of formaldehyde above the threshold for the radical channel (H2CO→H+HCO) we also find formation of rotationally cold CO (jCO=5–28) correlated to highly vibrationally excited H2 (v=6–8). These products are formed through a novel mechanism that involves near dissociation followed by intramolecular H abstraction [D. Townsend et al., Science 306, 1158 (2004)], and that avoids the region of the transition state entirely. The dynamics of this “roaming” mechanism are the focus of this paper. The correlations between the vibrational states of H2 and rotational states of CO formed following excitation on the 2143 transition allow us to determine the relative contribution to molecular products from the roaming atom channel versus the conventional molecular channel. [ABSTRACT FROM AUTHOR]

In this paper we present a theoretical study using time-dependent nonadiabatic reactant-product decoupling method for the state-to-state reactive scattering calculation of F(2P1/2)+H2 (ν=j=0) reaction on the Alexander-Stark-Werner potential energy surface. In this nonadiabatic state-to-state calculation, the full wave function is partitioned into reactant component and a sum of all product components. The reactant and product components of the wave function are solved independently. For the excited state reaction, the state-to-state reaction probabilities for J=0.5 are calculated. Comparing the state-to-state reaction probabilities, it is found that the vibrational population of the HF product is dominated by vibrational levels ν=2 and 3. The rotation specific reaction probabilities of HF product in j=1 and 2 are larger than those in other rotational levels. As the rotation quantum number j increases, the positions of the peak in the rotational reaction probability of HF product in ν=3 shift to higher collision energy. [ABSTRACT FROM AUTHOR]

In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing modes, a free diffusion and a DNA-sliding mode, to search for its specific binding site in the center of the cell. There is no need for a straightforward simulation of this process. Instead, an alternative and exact approach is shown to be essentially faster than explicit random walk simulations. The speed-up of this novel simulation technique is rapidly growing with system size. [ABSTRACT FROM AUTHOR]

Semilocal density functional approximations (DFAs) for the exchange-correlation energy suffer from self-interaction error, which is believed to be the cause of many of the failures of common DFAs, such as poor description of charge transfer and transition states of chemical reactions. The standard self-interaction correction (SIC) of Perdew and Zunger mends some of these failures but spoils such essential properties as thermochemistry and equilibrium bond lengths. The Perdew-Zunger SIC seems to overcorrect many-electron systems. In this paper, we propose a modified SIC, which is scaled down in many-electron regions. The new SIC has an improved performance for many molecular properties, including total energies, atomization energies, barrier heights of chemical reactions, ionization potentials, electron affinities, and bond lengths. The local spin-density approximation (LSDA) benefits from SIC more than higher-level functionals do. The scaled-down SIC has only one adjustable parameter. Rationalization of the optimal value of this parameter enables us to construct an almost-nonempirical version of the scaled-down SIC-LSDA, which is significantly better than uncorrected LSDA and even better than the uncorrected generalized gradient approximation. We present an analysis of the formal properties of the scaled-down SIC and define possible directions for further improvements. In particular, we find that exactness for all one-electron densities does not guarantee correct asymptotics for the exchange-correlation potential of a many-electron system. [ABSTRACT FROM AUTHOR]

Large-amplitude motions, particularly internal rotations, are known to affect substantially thermodynamic functions and rate constants of reactions in which flexible molecules are involved. Up to now all methods for computing the partition functions of these motions rely on the Pitzer approximation of more than 50 years ago, in which the large-amplitude motion is treated in complete independence of the other (vibrational) degrees of freedom. In this paper an extended hindered-rotor model (EHR) is developed in which the vibrational modes, treated harmonically, are correctly separated from the large-amplitude motion and in which relaxation effects (the changes in the kinetic-energy matrix and potential curvature) are taken into account as one moves along the large-amplitude path. The model also relies on a specific coordinate system in which the Coriolis terms vanish at all times in the Hamiltonian. In this way an increased level of consistency between the various internal modes is achieved, as compared with the more usual hindered-rotor (HR) description. The method is illustrated by calculating the entropies and heat capacities on 1,3-butadiene and 1-butene (with, respectively, one and two internal rotors) and the rate constant for the addition reaction of a vinyl radical to ethene. We also discuss various variants of the one-dimensional hindered-rotor scheme existing in the literature and its relation with the EHR model. It is argued why in most cases the HR approach is already quite successful. [ABSTRACT FROM AUTHOR]

In this paper a perturbation-theory study of vibrational lifetimes for the bending and stretching modes of hydrogen adsorbed on a Si(100) surface is presented. The hydrogen-silicon interaction is treated with a semiempirical bond-order potential. Calculations are performed for H–Si clusters of different sizes. The finite lifetime is due to vibration-phonon coupling, which is assumed to be linear or bilinear in the phonon and nonlinear in the H–Si stretching and bending modes. Lifetimes and vibrational transition rates are evaluated with one- and two-phonon processes taken into account. Temperature effects are also discussed. In agreement with the experiment and previous theoretical treatment it is found that the H–Si (υs=1) stretching vibration decays on a nanosecond timescale, whereas for the H–Si (υb=1) bending mode a picosecond decay is predicted. For higher-excited vibrations, simple scaling laws are found if the excitation energies are not too large. The relaxation mechanisms for the excited H–Si stretching and the H–Si bending modes are analyzed in detail. [ABSTRACT FROM AUTHOR]

Control of the chaotic behavior of a chemical system can be achieved perturbing periodically some control parameters of the system. This procedure based on external forcing, which is based on the phenomenon of resonance, can change a chaotic behavior into a periodical one by means of the application of a sinusoidal perturbation. In this paper, the influence of a periodical modulation added to the parameter controlling the oxygen adsorption rate in a cellular automaton (CA) model studying CO oxidation is analyzed. This CA model considers the oxidation reaction of CO on a catalytic surface, taking into account the catalyst temperature variation in order to analyze the reaction time oscillatory behavior. Simulations of the CA model exhibit chaotic and quasiperiodical behaviors, and it can be shown that the periodical forcing strategy can suppress the chaotic dynamics by means of the stabilization of periodical solutions. [ABSTRACT FROM AUTHOR]

In this paper, we investigate the effects of using inverse analyses developed for monodisperse particles to extract particle-particle and particle-surface potentials from simulated interfacial colloidal configurations having finite-size polydispersity. Forward Monte Carlo simulations are used to generate three-dimensional equilibrium configurations of log normal-distributed polydisperse particles confined by gravity near an underlying surface. Particles remain levitated above the substrate and stabilized against aggregation by repulsive electrostatic Derjaguin-Landau-Verwey-Overbeck pair potentials. An inverse Ornstein-Zernike analysis and an inverse Monte Carlo simulation method are used to obtain interactions from simulated distribution functions as a function of polydispersity (σ), relative range of repulsion (κ...), and projected interfacial concentration (ρ). Both inverse analyses successfully recover input potentials for all monodisperse cases, but fail for polydispersities often encountered in experiments. For different conditions (σ, κ..., and ρ, our results indicate softened short-range repulsion, anomalous long-range attraction, and apparent particle overlaps, which are similar to commonly reported observations in optical microscopy measurements of quasi-two-dimensional interfacial colloidal ensembles. By demonstrating signatures of, and limitations due to, polydispersity when extracting pair potentials from measured distribution functions, our specific goal is to provide a basis to objectively interpret and resolve the effects of polydispersity in optical microscopy experiments. [ABSTRACT FROM AUTHOR]

In this paper we report a combined experimental and theoretical study on the dynamics of the insertion reaction C(1D)+D2 at 15.5 kJ mol-1 collision energy. Product angular and velocity distributions have been obtained in crossed beam experiments and quasiclassical trajectory (QCT) and rigorous statistical calculations have been performed on the recent and accurate ab initio potential energy surface of Bussery-Honvault, Honvault, and Launay at the energy of the experiment. The molecular-beam results have been simulated using the theoretical calculations. Good agreement between experiment and both QCT and statistical predictions is found. [ABSTRACT FROM AUTHOR]

This paper discusses different routes to gaining insight from closed loop learning control experiments. We focus on the role of the basis in which pulse shapes are encoded and the algorithmic search is performed. We demonstrate that a physically motivated, nonlinear basis change can reduce the dimensionality of the phase space to one or two degrees of freedom. The dependence of the control goal on the most important degrees of freedom can then be mapped out in detail, leading toward a better understanding of the control mechanism. We discuss simulations and experiments in selective molecular fragmentation using shaped ultrafast laser pulses.© 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Reactions in real chemical systems often take place on vastly different time scales, with “fast” reaction channels firing very much more frequently than “slow” ones. These firings will be interdependent if, as is usually the case, the fast and slow reactions involve some of the same species. An exact stochastic simulation of such a system will necessarily spend most of its time simulating the more numerous fast reaction events. This is a frustratingly inefficient allocation of computational effort when dynamical stiffness is present, since in that case a fast reaction event will be of much less importance to the system’s evolution than will a slow reaction event. For such situations, this paper develops a systematic approximate theory that allows one to stochastically advance the system in time by simulating the firings of only the slow reaction events. Developing an effective strategy to implement this theory poses some challenges, but as is illustrated here for two simple systems, when those challenges can be overcome, very substantial increases in simulation speed can be realized. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

This paper discusses efficient simulation methods for stochastic chemical kinetics. Based on the τ-leap and midpoint τ-leap methods of Gillespie [D. T. Gillespie, J. Chem. Phys. 115, 1716 (2001)], binomial random variables are used in these leap methods rather than Poisson random variables. The motivation for this approach is to improve the efficiency of the Poisson leap methods by using larger stepsizes. Unlike Poisson random variables whose range of sample values is from zero to infinity, binomial random variables have a finite range of sample values. This probabilistic property has been used to restrict possible reaction numbers and to avoid negative molecular numbers in stochastic simulations when larger stepsize is used. In this approach a binomial random variable is defined for a single reaction channel in order to keep the reaction number of this channel below the numbers of molecules that undergo this reaction channel. A sampling technique is also designed for the total reaction number of a reactant species that undergoes two or more reaction channels. Samples for the total reaction number are not greater than the molecular number of this species. In addition, probability properties of the binomial random variables provide stepsize conditions for restricting reaction numbers in a chosen time interval. These stepsize conditions are important properties of robust leap control strategies. Numerical results indicate that the proposed binomial leap methods can be applied to a wide range of chemical reaction systems with very good accuracy and significant improvement on efficiency over existing approaches. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Competitive interactions within diverse mixed populations of chemically active sites are prevalent throughout nature, science, and engineering. Their effects are readily seen in the distribution of dead and surviving aerobic cells within a thick biofilm and particle shape changes during the growth and coarsening of crystals. Even in the most dilute case, competition for a reactant requires at least two spheres/cells, and the solution of the two-spherical sink problem is of interest for several reasons. The solution accurately describes lower cell concentration behavior (108 cells/l), and like the Smoluchowski diffusion-reaction treatment for a single sphere, the analysis is extremely helpful in understanding the fundamental phenomena of the effect on the first spherical sink of the presence of a second different spherical sink. In addition these exact solutions are required for the systematic extension to higher density behavior by rigorous expansions in the spherical sink densities. The method of the twin spherical expansion is used with a formal matrix elimination scheme to generate an exact solution for two distinct spherical sinks of differing sizes and kinetics. The two sinks exist in a medium, which supplies a reactant to the sinks via Fickian diffusion. The two sinks compete for the same reactant with different first-order reactions occurring at the surface of each sink. Earlier work focused on two spherical sinks of the same size with identical surface reaction kinetics. This work has been advanced to allow for diversity in the theory of cellular or reactive sink competition. A number of interesting higher order interactive phenomena are observed in this paper when the different reactive sinks are in close proximity. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

It is now widely accepted that there is a class of enzymatic proton transfer reactions, which proceed through quantum tunneling. In a series of papers we have argued that some experimental features of these reactions can be explained by assuming the presence of a "rate-promoting" vibration which brings donor and acceptor closer together, thus leading to rate enhancement. There has never been a study of this effect for classical systems. We used transition path sampling to study the equivalent classical problem and found a complicated dynamical behavior that cannot he captured by transition state theory. Slow promoting vibrations lead to reactive trajectories that overshoot the saddle point, hut on the other hand the short period of fast oscillations allows the reactants to stay only briefly in a low-barrier regime. There is a competition between these effects, which results to an intermediate value for the frequency of the rate-promoting vibration that is optimal for enhancing the rate. [ABSTRACT FROM AUTHOR]

We perform a Monte Carlo simulation of irreversible template copolymerization near a chemically heterogeneous surface with a regular distribution of discrete adsorption sites that selectively adsorb from solution one of the two polymerizing monomers and the corresponding chain segments. In the polymerization model, the chain propagation process is simulated by adding individual monomers to the end of growing macroradical. We focus in this paper on the influence of polymerization rate, adsorption energy, and the distance between adsorption sites on the chain conformation and the primary sequence of the resulting two-letter (AB) copolymers and, specifically, on the coupling between polymerization and adsorption. The conditions for the realization of conformation-dependent copolymerization are formulated. For this regime, we observe the formation of a quasiregular copolymer with two types of alternating sections. One of them contains randomly distributed A and B segments. The second one consists mainly of strongly adsorbed A segments. It is found that the average length of the random sections is proportional to the distance between the nearest neighbor adsorption sites. The average length of the A-rich sections is determined by the “adsorption capacity” of adsorption site. By varying the strength of the effective monomer-substrate interaction and the distribution of adsorption sites on the substrate, the copolymers with different surface-induced primary sequences can be designed and synthesized in a controlled fashion. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In this paper we examine the different formulations of Gillespie’s stochastic simulation algorithm (SSA) [D. Gillespie, J. Phys. Chem. 81, 2340 (1977)] with respect to computational efficiency, and propose an optimization to improve the efficiency of the direct method. Based on careful timing studies and an analysis of the time-consuming operations, we conclude that for most practical problems the optimized direct method is the most efficient formulation of SSA. This is in contrast to the widely held belief that Gibson and Bruck’s next reaction method [M. Gibson and J. Bruck, J. Phys. Chem. A 104, 1876 (2000)] is the best way to implement the SSA for large systems. Our analysis explains the source of the discrepancy. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The authors obtain, in the Laplace transform space, the exact analytic solution for the Green function and survival probabilities for the excited-state diffusion-influenced reversible geminate reaction, A*+B⇋C*+D, with two different lifetimes and in the presence of an added quenching process. This extends a previous investigation by Popov and Agmon [J. Chem. Phys. 117, 5770 (2002)] of the ground-state reaction without quenching. The long-time asymptotic behavior of the survival probabilities is obtained in the time domain. It is found to be different from the equal-lifetime case. This paper also provides a useful short-time approximation for the kinetics. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The Sm+O chemiionization reaction has been investigated theoretically using a method that allows for correlation and relativistic effects. Potential energy curves have been calculated for several electronic states of SmO and SmO+. Comparison with available spectroscopic and thermodynamic values for these species is reported and a mechanism for the chemiionization reaction Sm+O is proposed. The importance of spin–orbit coupling in the excited states of SmO, in allowing this chemiionization reaction to take place, has been revealed by these calculations. This paper shows the metal-plus-oxidant chemiionization reaction. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The interaction of Na atoms with CH3OH films was studied with metastable impact electron spectroscopy (MIES) under UHV conditions. The films were grown at 90(+/-10) K on tungsten substrates and exposed to Na. Na-induced formation of methoxy (CH3O) species takes place, and Na atoms become ionized. At small Na exposures the outermost solvent layer remains largely intact as concluded from the absence of MIES signals caused by the reaction products. However, emission from CH3O, located at the film surface, occurs at larger exposures. In the same exposure range also Na species can be detected at the surface. The spectral feature from 3s Na ionization occurs at an energetic position different from that found for metals or semiconductors. The results are compared with density functional theory calculations [see Y. Ferro, A. Allouche, and V. Kempter, J. Chem. Phys. 120, 8683 (2004), preceding paper]. Experiment and theory agree in the energetic positions of the main spectral features from the methanol and sodium ionization. The calculations suggest that the 3s Na emission observed experimentally originates from solvated 3s electrons which are located far from the Na core and become stabilized by solvent molecules. The simultaneous emergence of emission from CH3O and from solvated 3s electrons suggests that the delocalization and, consequently, the solvation play an important role in the Na-induced formation of CH3O from CH3OH. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]