Reactant Configuration Research Articles

Modeling Intermediate Temperature Protonic Ceramic Fuel Cells

Protonic ceramics fuel cells (PCFC) have emerged as a promising candidate for distributed power generation and synthetic fuel production. The cells offer the potential for reduced temperature operation (~500°C) which enables faster startup times, longer life, and lower material cost components to be used compared to their oxygen ion conducting counterparts. The development of a protonic ceramic fuel cell computational modeling tool is imperative to the design and implementation of systems. A framework is presented for a predictive cell-level, interface charge transfer PCFC model capturing the mixed conducting nature of the protonic ceramic materials. The model employs a 1-D channel-level modeling strategy (Fig. 1) where fuel depletion and flow configuration effects are resolved and coupled to a semi-empirical electrochemical model. Modeling results calibrated against experimental data of a state-of-the-art PCFC composition are presented. The lower cell temperature and hydrogen removal from the anode channel present unique operational features which are considered in the present work. In particular, a thermodynamic analysis is presented for operating regimes where solid carbon formation is not thermodynamically favorable. Simulation results are presented for the operation of the cell over a variety of operational regimes. Model predicted distributions of gas phase species, temperature, and local current density are resolved. The model predicted cell performance when operating on a humidified methane fuel source with steam-to-carbon ratio (S/C) of 2.4 at 500oC and 80% utilization indicates a power density greater than 0.100 W/cm2 is attainable at an average current density of 0.15 A/cm2. Model-predicted cell performance is explored under various operating conditions (Temperature, utilization, S/C) and an evaluation of reactant flow configuration (co- vs. counter-flow) is also presented. Figure 1

On the Efficiency of Solar H2 and CO Production via the Thermochemical Cerium Oxide Redox Cycle: The Option of Inert-Swept Reduction

A thermodynamic model of the ceria-based solar thermochemical redox cycle is presented with the objective of resolving the widely varying predictions of the solar-to-fuel efficiency possible with reduction carried out in a flow of inert sweep gas. The implications of the treatment of the gas–solid interaction are explored through comparison of mixed flow and countercurrent flow configurations of reactants. The mixed flow model is applied for the first time to both reduction and oxidation reactions. The mechanical work to produce sweep gas of varying purity, separate the products, and pump gases is included. The results identify the conditions necessary for efficient operation. The two models lead to substantially different predictions of the usage of sweep gas and oxidizer and process efficiency. Efficiencies predicted with the conservative mixed flow model reach a maximum of 11% for water splitting at 1073 K, assuming reduction at 1773 K, heat recovery of 80% of the sensible heat of the gases, and an optimistic 75% heat recovery of the sensible heat of the solid ceria. Without solid phase heat recovery, the maximum efficiency is 4%. With the countercurrent model, the predicted solar-to-fuel efficiency reaches 41% for water splitting at 1563 K without solid phase heat recovery. Though theoretically attractive, the countercurrent flow model predicts unattainable efficiencies due to the assumption of chemical equilibrium at both the inlet and outlet of the reduction and oxidation reactors and yields nonphysical results for oxidation temperatures less than 1563 K. Thus, we urge caution in drawing conclusions about the promise of metal oxide cycles on the basis of the countercurrent flow model. Nonetheless, it is reasonable to anticipate that the ceria cycle with inert-swept reduction and a temperature swing between reduction and oxidation may achieve commercially viable solar-to-fuel efficiencies, in between the predictions of the mixed and countercurrent models, through the careful design of reactors to provide gas and solid phase heat recovery and favorable gas–solid flow configurations.

Silicon-based Micro Direct Methanol Fuel Cell Stack to Power Portable Devices Using MEMS Technology

A design configuration is presented for integrated series connection of micro direct methanol fuel cells in a planar array. The series path is oriented in a “flip-flop” configuration with electrical interconnections made by thin-film metal layers that coat the flow channels etched on the silicon substrate, presenting the unique advantage of small connection space and low connecting resistance. To overcome the disadvantage of “flip-flop” interconnection that reactant chambers must alternate between fuel and oxidant, an innovative reactant feeding configuration was designed, providing a uniform reactant feeder and reliable hermetic seals for a multitude of unit cavities per cell. The MEMS fabrication process was adopted to fabricate the silicon plates. The elements of reactant feeder were mechanically carved from PMMA and were assembled with the cells by agglutinant. Application of μDMFC stacks as portable power sources were demonstrated using small electric devices powered by this stack.

The entropic origin of solvent effects on the single bond cZt-tZt isomerization rate constant of 1,3,5-cis-hexatriene in alkane and alcohol solvents: a molecular dynamics study.

The single-bond cZt-tZt isomerization rate constants of 1,3,5-cis-hexatriene dissolved in a series of explicit alkane (cyclohexane, n-heptane, and cycloheptane) and alcohol (methanol, ethanol, and n-propanol) solvents were calculated via reactive flux theory, from classical molecular dynamics simulations, at different temperatures (275-325 K). We find that the isomerization rate constants in alcohol solvents are slower than those in alkane solvents, in accord with the observed experimental trend (Harris, D. A.; Orozco, M. B.; Sension, R. J. J. Phys. Chem. A 2006, 110, 9325-9333). We also find that the same trend is obtained when the transition state theory limit of the reactive flux expression for the reaction rate constant is employed. The solvent dependence of the reaction rate constant is then traced back to the fundamentally different structure of the solvation shell in alcohol and alkane solvents. Whereas in alcohol solvents, hexatriene fits inside a rigid cavity formed by the hydrogen-bonded network, which is relatively insensitive to conformational dynamics, alkane solvents form a cavity around hexatriene that adjusts to the conformational state of hexatriene, thereby increasing the entropy of transition state configurations relative to reactant configurations and giving rise to faster isomerization.

Theoretical study on intramolecular hydrogen transfer of 1-methylbutyl peroxide radical

The density functional theory method has been used to study the mechanism for the intramolecular hydrogen transfer (IHT) reaction of 1-methylbutly peroxide radical [n-C3H7CH(CH3)OO·]. The B3LYP method was used in conjunction with 6-31+G**, 6-311++G** and aug-cc-pVDZ basis sets. The geometrical configurations of reactants, productions and transition states were fully optimized on the potential energy surfaces. The results suggest that the IHT reactions involve the formation of transition states with five-, six- and seven-member rings when the transferring hydrogen atoms are at different initial positions related to the peroxide oxygen. The activation energies for the IHT reactions of β-, γ- and α-H migrations are 90.0, 100.8, and 140–152 kJ/mol at the B3LYP/6-311++G** level, respectively. The α-H is easier to transfer than the α- and γ-H. Both the activation energy and rate constant for β-H migrations at the B3LYP/6-31+G** level are basically in agreement with the experimental values. The methyl substituent on β-position slightly lowers the activation energy, which is consistent with the experimental fact. All the IHT reactions are endothermic. The β-H transferring is the most favorable process in view of both thermodynamics and kinetics. The predicted rate constants indicate that only the β-H and γ-H transfer reactions occur when the temperature is not high enough.

Structure of FC(O)O2 and the mechanism of its reaction with NO

Density functional theory was performed to study the reaction mechanism of the reaction of FC(O)O2 with NO. The geometric configurations of reactants, intermediates, transition states and products were optimized by B3LYP method at 6-311G(d) level. The energies of stationary points along the pathway were also calculated. Intermediates and transition states were confirmed by the results of vibrational analysis. From the results of the mechanism of the reaction of FC(O)O2 with NO, we found that the reaction of FC(O)O2+NO has four pathways and several steps. Comparing the four pathways activation energies, we can find that the pathway FC(O)O2+NO→bM→bT→FC(O)O+NO2 is the main reaction pathway and the main products are FC(O)O radical and NO2, which is in good agreement with the result reported in the literature.

Energy-based formalism for the mapping analysis of concerted reactions

A multiconfigurational mapping formalism is developed, by which the states of a set of reaction products are described in terms of the configurations of the original reactant system. Each reactant configuration is mapped into a wave function of the products, and an optimum mix of the mapped functions is obtained by configuration interaction. The principle governing the mapping is that the topology of bonding and antibonding in the system cannot be altered, although the shapes of the bonding and antibonding regions can be distorted by bends, twists, and stretches. Results of the calculation allow predictions of allowed or forbidden nature of reactions similar to those of Woodward and Hoffmann [1], but the new analysis is fully automated and independent of point group symmetry. Identification of the particular excited state(s) leading to certain products in thermally forbidden reactions is considerably simplified by this analysis. Calculations on relatively well-understood systems, the pyrolysis of cyclobutane and the closure of both a symmetric and chiral butadiene, illustrate this approach to the study of concerted reactions.

Role of the orientation angles of reacting nuclei in evaporation residue production

The influence of the orientation angles of the projectile- and target-nucleus symmetry axes relative to the beam direction on the production of the evaporation residues (ERs) is investigated for the 48Ca+154Sm reaction as a function of the beam energy. The measured yields of ERs by massive nuclei reactions have been well reproduced by using the partial fusion and quasi-fission cross-sections obtained in the dinuclear system model. At lower beam energies, only the orientation angles close to αP=30° (projectile) to αP=0°–15°(target) can contribute to the ER formation. At large beam energies (about E c.m.=140–180 MeV), all αP−αT configurations of reactants can contribute to the ER cross-section, which ranges between 10 and 100 mb, while at E c.m.>185 MeV, the ER cross-section ranges between 1 and 0.1 mb because the fission barrier for the compound nucleus decreases by increasing its excitation energy and angular momentum.

Nuclear Quantum Tunneling in the Light-activated Enzyme Protochlorophyllide Oxidoreductase

In chlorophyll biosynthesis, the light-activated enzyme protochlorophyllide oxidoreductase catalyzes trans addition of hydrogen across the C-17-C-18 double bond of the chlorophyll precursor protochlorophyllide (Pchlide). This unique light-driven reaction plays a key role in the assembly of the photosynthetic apparatus, but despite its biological importance, the mechanism of light-activated catalysis is unknown. In this study, we show that Pchlide reduction occurs by dynamically coupled nuclear quantum tunneling of a hydride anion followed by a proton on the microsecond time scale in the Pchlide excited and ground states, respectively. We demonstrate the need for fast dynamic searches to form degenerate "tunneling-ready" configurations within the lifetime of the Pchlide excited state from which hydride transfer occurs. Moreover, we have found a breakpoint at -27 degrees C in the temperature dependence of the hydride transfer rate, which suggests that motions/vibrations that are important for promoting light-activated hydride tunneling are quenched below -27 degrees C. We observed no such breakpoint for the proton-tunneling reaction, indicating a reliance on different promoting modes for this reaction in the enzyme-substrate complex. Our studies indicate that the overall photoreduction of Pchlide is endothermic and that rapid dynamic searches are required to form distinct tunneling-ready configurations within the lifetime of the photoexcited state. Consequently, we have established the first important link between photochemical and nuclear quantum tunneling reactions, linked to protein dynamics, in a biologically significant system.

Mechanism for the CuX-Catalyzed (X=I, Br) Intramolecular <em>O</em>-Arylation Reaction of <em>N</em>-(<em>ortho</em>-chlorophenyl)benzamide

采用密度泛函理论（DFT）中的B3LYP方法,在6-31＋G^＊基组水平上研究了N-（邻氯苯基）苯甲酰胺在CuX（X=I,Br）催化下发生分子内O-芳基化的反应机理.优化了反应过程中的反应物、中间体、过渡态和产物,通过能量和振动分析证实了中间体和过渡态的真实性.并且在相同基组水平上应用自然键轨道（NBO）理论和分子中的原子（AIM）理论分析了这些化合物的成键特征和轨道间的相互作用.比较了两种不同铜盐催化剂的催化活性,计算结果表明两种催化剂的反应路径和反应的控制步骤完全相同,在CuBr催化下标题化合物控制步骤的活化能比在CuI催化下的低,证明了CuBr的催化活性要比CuI的高一些,与实验结果一致.

Theoretical study on the reaction mechanism of the reaction of FC(O)O with NO

Density functional theory was used to study the mechanism of the reaction of FC(O)O with NO. The geometric configurations of reactants, intermediates, transition states and products were optimized by B3LYP method at 6-311G(d,p) level. The energies of stationary points along the pathway were calculated at CCSD(T) level. Intermediates and transition states were confirmed by the results of vibrational analysis. From the results of the reaction mechanism of the reaction of FC(O)O with NO, one can see that the reaction of FC(O)O+NO has four pathways and several steps. Comparing the four pathways’activation energies, one can find that the pathway FC(O)O+NO→M3→TS6→M5→FNO+CO2 is the main reaction pathway and FNO radical and CO2 are the main products, which is in good agreement with the result reported in the literature.

Influence of Reactant Mixing in a Laminar Flow Reactor: The Case of Gas Reburning. 2. Modelling Study

A theoretical study of the influence of mixing on reburning under laminar flow non-premixed conditions has been performed. Two models with a different level of detail of the fluid dynamics description have been developed and adapted. Models have been validated against experimental results. The models are able to reproduce the experimental trends of the influence of the studied variables: temperature, stoichiometry, velocity ratio between the streams, and reactant feeding configuration. Modeling and experimental results have been compared with plug-flow reactor (PFR) results, showing significant differences. Reactant injection mode involves a change in local stoichiometry and residence time distribution in the reactor, which seems to be the main influencing factor. For low temperatures, a higher NO reduction is obtained when local fuel-lean conditions have a longer residence time. For high temperatures, a higher NO reduction is obtained when local fuel-rich conditions have a longer residence time.

Computing tunneling paths with the Hamilton–Jacobi equation and the fast marching method

We present a new method for computing the most probable tunneling paths based on the minimum imaginary action principle. Unlike many conventional methods, the paths are calculated without resorting to an optimization (minimization) scheme. Instead, a fast marching method coupled with a back-propagation scheme is used to efficiently compute the tunneling paths. The fast marching method solves a Hamilton–Jacobi equation for the imaginary action on a discrete grid where the action value at an initial point (usually the reactant state configuration) is known in the beginning. Subsequently, a back-propagation scheme uses a steepest descent method on the imaginary action surface to compute a path connecting an arbitrary point on the potential energy surface (usually a state in the product valley) to the initial state. The proposed method is demonstrated for the tunneling paths of two different systems: a model 2D potential surface and the collinear reaction. Unlike existing methods, where the tunneling path is based on a presumed reaction coordinate and a correction is made with respect to the reaction coordinate within an ‘adiabatic’ approximation, the proposed method is very general and makes no assumptions about the relationship between the reaction coordinate and tunneling path.

Mechanism of Cysteine Oxidation by a Hydroxyl Radical: A Theoretical Study

Cysteine oxidation by HO(.) was studied at a high level of ab initio theory in both gas phase and aqueous solution. Potential energy surface scans in the gas phase performed for the model system methanethiol+HO(.) indicate that the reactants can form two intermediate states: a sulfur-oxygen adduct and a hydrogen bound reactant complex. However these states appear to play a minor role in the reaction mechanism as long as they are fast dissociating states. Thus the main reaction channel predicted at the QCISD(T)/6-311+G(2df,2pd) level of theory is the direct hydrogen atom abstraction. The reaction mechanism is not perturbed by solvation which was found to induce only small variations in the Gibbs free energy of different reactant configurations. The larger size reactant system cysteine+HO* was treated by the integrated molecular orbital+molecular orbital (IMOMO) hybrid method mixing the QCISD(T)/6-311+G(2df,2pd) and the UMP2/6-311+G(d,p) levels of theory. The calculated potential energy, enthalpy, and Gibbs free energy barriers are slightly different from those of methanethiol. The method gave a rate constant for cysteine oxidation in aqueous solution, k=2.4 x 10(9) mol(-1) dm(3) s(-1), which is in good agreement with the experimental rate constant. Further analysis showed that the reaction is not very sensitive to hydrogen bonding and electrical polarity of the molecular environment.

A Hamilton–Jacobi type equation for computing minimum potential energy paths

A new method for computing minimum-energy reaction paths is presented. Unlike existing approaches (e.g. intrinsic reaction coordinate methods), our approach works for any reactant configuration: the structure of the transition state, reactive intermediates and product will be determined by the algorithm, and so need not be known beforehand. The method we have developed is based on solving a Hamilton–Jacobi type equation. Specifically, we introduce a speed function so that the ‘first arrival times’ from the Hamilton–Jacobi equation correspond to least-potentials. Then, adopting a back-tracing method, we can use the first arrival times to determine the minimum-energy path between any classically allowed molecular conformation and the initial (reactant) conformation. The method is illustrated by applying it to six different systems: (1) a model system with four different minima in the potential energy surface, (2) a model Muller–Brown potential, (3) the isomerization reaction of malonaldehyde using a fitting potential energy surface, (4) a model Minyaev–Quapp potential representative of con- and dis-rotations of two BH2 groups in the BH2–CH2–BH2 molecule, (5) the F + H2→FH + H reaction and (6) the H + FH → HF + H reaction. Our results demonstrate that the proposed method represents a robust alternative to existing techniques for finding chemical reaction paths.

Quantum study on the electrocyclic reactions of CH2CHCHCHX (XH, F, Cl)

AbstractThe microscopic mechanisms of the electrocyclic reactions for cis‐1,3‐butadiene and its monofluoro‐, monochloroderivatives have been studied by density functional theory (DFT), using the B3LYP method and 6‐311++G** basis sets. We optimized the geometric configurations of reactants, transition states, and products; verified all the probable transition states through vibrational analysis; and calculated the relative single‐point energies at the QCISD(T)/6‐311++G**//B3LYP/6‐311++G**. The results show that the monofluoro‐, monochloroderivatives of cis‐1,3‐butadiene both have two conformers; the reactant favors the electrocyclic reaction when one outboard hydrogen atom of the CH2 groups is substituted by the fluorine or chlorine atom. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004

Theoretical study of reaction mechanism for CH2CHX(XH, F, Cl) with ozone

AbstractIn this work, we study the reaction mechanism of the CH2CHX(XH, F, Cl) with ozone reactions, using ab initio MP2 method at 6‐311++g** basis set level. The geometric configurations of reactants, intermediates, transition states, and products were optimized, and the energies were obtained at the QCISD(T)/6‐311++G** level. The transition states and intermediates of the reactions were verified by the vibrational analysis. The results show that the ozonolysis of ethylene and its derivatives is reasonable and believable along the Criegee mechanism. The results also show that the activation energies of the controlling steps along the fluoroethylene and chloroethylene with ozone reaction pathways were lower than that along the ethylene with ozone reaction pathway. That is to say, the derivatives of ethylene have the higher activity to react with ozone and deplete the ozone layer. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004

Construction and assessment of models of CYP2E1: predictions of metabolism from docking, molecular dynamics, and density functional theoretical calculations.

3D models of CYP2E1 were constructed for the purpose of structure-based prediction of 2E1 metabolism of diverse substrates based on configuration sampling of ligand-atom-oxyferryl center distances and quantum chemical criteria. Models were constructed on the basis of sequence alignments of 2E1 with templates of known structure, including rabbit CYP2C5 (3LVdH) and bacterial CYP450s. Following geometric and energetic assessments, the utility of the model was tested in structure-based predictions of metabolism. Autodock was used to dock chlorzoxazone, p-nitrophenol, N-nitrosodimethylamine, acetominophen, caffeine, theophylline, and methoxyflurane into the model CYP2E1 employing a model oxyferryl heme with charges based on density functional theoretical parametrization. In all cases, the lowest energy bound docked configurations corresponded to ones with the substrate intimately associated with the oxyferryl center. Configurations among the lowest energy docked forms of each of the ligands had orientations relative to the oxyferryl center consistent with the experimentally observed metabolites. Docking of long-chain dialkylnitrosoamines revealed no heme binding site bound configurations, in agreement with the negligible metabolism of these ligands. The lowest energy docked configurations of chlorzoxazone, p-nitrophenol, and N-nitrosodimethylamine, high-affinity substrates of 2E1, were used to initiate 300 ps molecular dynamics (MD) trajectories. The MD-sampled ligand-oxyferryl heme reactant configurations were in good accord with density functional theoretical (DFT) optimized oxyferryl-heme-ligand geometries. Analysis of the MD-sampled ligand-2E1 configurations from multiple docked orientations indicates the configurations with closest exposure of reactive centers to the oxyferryl heme to be correlated with observed metabolites with proper consideration of H-abstraction energetics. DFT assessment of relative radical energetics is directly compared with differential H-abstraction activation energetics by compound I and by a p-nitrosophenoxy radical compound I surrogate for the specific case of methoxyflurane and is shown to be in good agreement.

A study on the reaction mechanism and kinetic of mercury oxidation by chlorine species

Ab initio MP2 method was performed to study the reaction mechanism and kinetic of mercury oxidation by chlorine species during the process of coal combustion. Seven channels were detected by calculations, the geometric configurations of reactants, products, intermediates and transition states were optimized and energies were computed at QCISD(T)/SDD level. Besides, we used the classic transition state theory to compute the rate constants of the seven channels. Compared with the experimental values, the results show that the rate constants are in good agreement with experimental datum. So our study is believable.

Efficient thermal rate constant calculation for rare event systems

We present an efficient method for computing thermal reaction rate constants that can be applied to systems in which transitions from reactant to product are infrequent. The method can be applied to high-dimensional, disordered systems which exhibit too many transition states to be identified, and for which useful reaction coordinates cannot be easily defined. The focus of our method is the time correlation function C(t), the normalized partition function for trajectories that begin in the reactant region and end in the product region after a time t; the time derivative of C(t) is the reaction rate constant, k(t). We use an umbrella potential to select initial positions from improbable regions of the reactant configuration space. We then compute C(t) directly by choosing random thermal momenta and asking if the resulting dynamical trajectory reaches the product region in time t. Since dynamical trajectories are run on the true potential energy surface, without the umbrella, re-crossing effects are included correctly. The initial condition bias introduced by the umbrella is removed by a weighting factor. We test the method on a simple two dimensional model potential and on a model for the isomerization of a diatomic in a Weeks–Chandler–Andersen fluid, and show that it gives accurate and precise rates with substantial reduction in computer time.