Transition State Theory Analysis Research Articles

The Effect of the Surrounding Matrix on Spin Transition Nanoparticles: How Shell Characteristics Alter Core Elastic Properties in Core‐Shell Particles

A surrounding matrix is known to alter nanoparticle spin transitions, the solid state structural phase changes associated with transitions between high spin (HS) and low spin(LS) states. To better quantify how the spin transition solid and surrounding matrix interact, several series of core‐shell particles were prepared based on RbxCo[Fe(CN)6]z∙nH2O, RbCoFe‐PBA, as spin transition core with isostructural shells of different compositions and thicknesses. Synchrotron PXRD through the thermal high HS to LS, the LS to photoexcited high spin (PXHS), and thermal PXHS to LS transitions, show the activation energy is lowered as shells become thicker and stiffer. Calorimetry data coupled with transition state theory analysis indicate the core stiffens in the core‐shell particles relative to the uncoated particles. The conclusion is supported by microstrain analysis that shows stiffer shells limit the extent to which the core distorts as individual sites transition, leading to the lower activation energy. Finally, differences in lattice mismatch with different shell materials are shown to alter the mechanism by which the transition progresses.

Theoretical Revelation of HNCO Formation during Coal Pyrolysis: Mechanism, Formation Pathway and DFT Calculation

ABSTRACT Pyridine is one of the main nitrogen-containing compounds that produce NOx precursors (HNCO, HCN, NH3) in coal during pyrolysis, which can be converted into 2-pyridone (2-Py) in the presence of H2O. HNCO is a NOx precursor during coal and coal tar pyrolysis. In this study, the possible paths for the pyrolysis of 2-pyridone to generate HNCO and HCN were studied using density functional theory (DFT). This was the first theoretical revelation of the source of HNCO generation during coal pyrolysis. At the same time, the formation path of HCN was also calculated and compared with the formation of HNCO. Through the transition state theory analysis, the behavior characteristics of NOx precursors produced during the pyrolysis of 2-pyridone were theoretically explained.

Density Functional Theory Based Micro- and Macro-Kinetic Studies of Ni-Catalyzed Methanol Steam Reforming

The intrinsic mechanism of Ni-catalyzed methanol steam reforming (MSR) is examined by considering 54 elementary reaction steps involved in MSR over Ni(111). Density functional theory computations and transition state theory analyses are performed on the elementary reaction network. A microkinetic model is constructed by combining the quantum chemical results with a continuous stirring tank reactor model. MSR rates deduced from the microkinetic model agree with the available experimental data. The microkinetic model is used to identify the main reaction pathway, the rate determining step, and the coverages of surface species. An analytical expression of MSR rate is derived based on the dominant reaction pathway and the coverages of surface species. The analytical rate equation is easy to use and should be very helpful for the design and optimization of the operating conditions of MSR.

Theoretical Study of the Formation of Naphthalene from the Radical/π-Bond Addition between Single-Ring Aromatic Hydrocarbons

The experimental investigations performed in the 1960s on the o-benzyne + benzene reaction as well as the more recent studies on reactions involving π-electrons highlight the importance of π-bonding for different combustion processes related to PAH's and soot formation. In the present investigation radical/π-bond addition reactions between single-ring aromatic compounds have been proposed and computationally investigated as possible pathways for the formation of two-ring fused compounds, such as naphthalene, which serve as precursors to soot formation. The computationally generated optimized structures for the stationary points were obtained with uB3LYP/6-311+G(d,p) calculations, while the energies of the optimized complexes were refined using the uCCSD(T) method and the cc-pVDZ basis set. The computations have addressed the relevance of a number of radical/π-bond addition reactions including the singlet benzene + o-benzyne reaction, which leads to formation of naphthalene and acetylene through fragmentation of the benzobicyclo[2,2,2]octatriene intermediate. For this reaction, the high-pressure limit rate constants for the individual elementary reactions involved in the overall process were evaluated using transition state theory analysis. Other radical/π-bond addition reactions studied were between benzene and triplet o-benzyne, between benzene and phenyl radical, and between phenyl radicals, for all of which potential energy surfaces were produced. On the basis of the results of these reaction studies, it was found necessary to propose and subsequently confirm additional, alternative pathways for the formation of the types of PAH compounds found in combustion systems. The potential energy surface for one reaction in particular, the phenyl + phenyl addition, is shown to contain a low-energy channel leading to formation of naphthalene that is energetically comparable to the other examined conventional pathways leading to formation of biphenyl compounds. This channel is the first evidence of a reaction which involves an aromatic radical adding to the nonradical π-bond site of another aromatic radical which leads directly to a fused ring structure.

Ab initio kinetics for the decomposition of monomethylhydrazine (CH3NHNH2)

The decomposition kinetics of CH3NHNH2 (monomethylhydrazine) is studied with ab initio transition state theory-based master equation analyses. The simple NN and CN bond fissions to produce the radicals CH3NH+NH2 or CH3+NHNH2 are expected to dominate the decomposition kinetics. The transition states for these two bond fissions are studied with variable reaction coordinate transition state theory employing directly determined CASPT2/aug-cc-pVDZ interaction energies. Orientation independent corrections for limitations in the basis set and for the effects of conserved mode geometry relaxation are included. The bond dissociation energies are evaluated at the QCISD(T)/CBS//B3LYP/6-311++G(d,p) level. The transition state theory analysis directly provides high pressure dissociation and recombination rate coefficients. Predictions for the pressure dependence and product branching in the dissociation of CH3NHNH2 are obtained by solving the master equation.

Rate Constants and Hydrogen Isotope Substitution Effects in the CH3 + HCl and CH3 + Cl2 Reactions

The kinetics of the CH3 + Cl2 (k2a) and CD3 + Cl2 (k2b) reactions were studied over the temperature range 188-500 K using laser photolysis-photoionization mass spectrometry. The rate constants of these reactions are independent of the bath gas pressure within the experimental range, 0.6-5.1 Torr (He). The rate constants were fitted by the modified Arrhenius expression, k2a = 1.7 x 10(-13)(T/300 K)(2.52)exp(5520 J mol(-1)/RT) and k2b = 2.9 x 10(-13)(T/300 K)(1.84)exp(4770 J mol(-1)/RT) cm(3) molecule(-1) s(-1). The results for reaction 2a are in good agreement with the previous determinations performed at and above ambient temperature. Rate constants of the CH3 + Cl2 and CD3 + Cl2 reactions obtained in this work exhibit minima at about 270-300 K. The rate constants have positive temperature dependences above the minima, and negative below. Deuterium substitution increases the rate constant, in particular at low temperatures, where the effect reaches ca. 45% at 188 K. These observations are quantitatively rationalized in terms of stationary points on a potential energy surface based on QCISD/6-311G(d,p) geometries and frequencies, combined with CCSD(T) energies extrapolated to the complete basis set limit. 1D tunneling as well as the possibility of the negative energies of the transition state are incorporated into a transition state theory analysis, an approach which also accounts for prior experiments on the CH3 + HCl system and its various deuterated isotopic substitutions [Eskola, A. J.; Seetula, J. A.; Timonen, R. S. Chem. Phys. 2006, 331, 26].

Possibility of Long-Term Preservation of Freeze-Dried Mouse Spermatozoa1

Freeze-dried mouse spermatozoa are capable of participating in normal embryonic development after injection into oocytes. When the freeze-dried spermatozoa are used as a method for storage of genetic materials, however, it is essential to assure the relevance of long-term preservation over several decades or centuries. Thus, we applied the theory of accelerated degradation kinetics to freeze-dried mouse spermatozoa. Thermal denaturation kinetics were determined based on Arrhenius plots derived from transition-state theory analysis at three elevated temperatures: 30, 40, and 50 degrees C. Accelerated degradation kinetics were calculated by extrapolation of Arrhenius plots. This theory also is being applied to the long-term stability of drugs. The estimated rate of development to the blastocyst stage at 3 and 6 mo and at 1, 10, and 100 yr of sperm storage at 4 degrees C were 21.60%, 7.91%, 1.00%, 0%, and 0%, respectively. At -80 degrees C, estimated development rates to the blastocyst stage that would be expected after 100 yr of storage did not decline significantly. In addition, after 3 or 6 mo of storage at 4 or -80 degrees C, preimplantation development of the embryos derived from intracytoplasmic sperm injection (ICSI) was examined. The actual developmental rates to the blastocyst stage from ICSI by freeze-dried sperm stored for 3 mo at 4 and -80 degrees C were 21% and 62%, respectively, and the rates for such sperm stored for 6 mo were 13% and 59%, respectively. These results indicate that the determination of accelerated degradation kinetics can be applied to the preservation of freeze-dried mouse spermatozoa. Furthermore, for long-term preservation, freeze-dried mouse spermatozoa appear to require being kept at lower than -80 degrees C.

A direct transition state theory based analysis of the branching in NH2 + NO.

A combination of high-level quantum-chemical simulations and sophisticated transition state theory analyses is employed in a study of the temperature dependence of the N2H + OH-->HNNOH recombination reaction. The implications for the branching between N2H + OH and N2 + H2O in the NH2 + NO reaction are also explored. The transition state partition function for the N2H + OH recombination reaction is evaluated with a direct implementation of variable reaction coordinate (VRC) transition state theory (TST). The orientation dependent interaction energies are directly determined at the CAS + 1 + 2/cc-pvdz level. Corrections for basis set limitations are obtained via calculations along the cis and trans minimum energy paths employing an approximately aug-pvtz basis set. The calculated rate constant for the N2H + OH-->HNNOH recombination is found to decrease significantly with increasing temperature, in agreement with the predictions of our earlier theoretical study. Conventional transition state theory analyses, employing new coupled cluster estimates for the vibrational frequencies and energies at the saddlepoints along the NH2 + NO reaction pathway, are coupled with the VRC-TST analyses for the N2H + OH channels to provide estimates for the branching in the NH2 + NO reaction. Modest variations in the exothermicity of the reaction (1-2 kcal mol-1), and in a few of the saddlepoint energies (2-4 kcal mol-1), yield TST based predictions for the branching fraction that are in satisfactory agreement with related experimental results. The unmodified results are in reasonable agreement for higher temperatures, but predict too low a branching ratio near room temperature, as well as too steep an initial rise.

A computational study of the reaction kinetics of methyl radicals with trifluorohalomethanes

Ab initio calculations have been used to characterize the transition states for halogen abstraction by CH3 in reactions with CF4, CF3Cl, CF3Br, and CF3I (1–4). Geometries and frequencies were obtained at the HF/6-31G(d) and MP2=full/6-31G(d) levels of theory. Energy barriers were computed via the Gaussian-2 methodology, and the results were employed in transition state theory analyses to obtain the rate constants over 298–2500 K. There is good accord with literature measurements in the approximate temperature range 360–500 K for reactions (2–4), and the computed activation energies are accurate to within ±6 kJ mol−1. Recommended rate constant expressions for use in combustion modeling are k;1=1.6×10−19 (T/K)2.41 exp(−13150 K/T), k2=8.4×10−20(T/K)2.34 exp(−5000 K/T), k3=4.6×10−19 (T/K)2.05 exp(−3990 K/T), and k4=8.3×10−19 (T/K)2.18 exp(−1870 K/T) cm3 molecule−1 s−1. The results are discussed in the context of flame suppression chemistry. © 1998 John Wiley & Sons, Inc. Int J Chem Kinet 30: 179–184, 1998.

Ab Initio Study of RDX Decomposition Mechanisms

The mechanism of the gas phase unimolecular decomposition of hexahydro-1,3,5,-trinitro-1,3,5,-triazine (RDX) has been investigated using first principles gradient-corrected density functional theory. We have calculated the potential energy profile for two previously suggested dissociation channels: (I) N−NO2 bond rupture, and (II) concerted ring fission to three methylenenitramine molecules. The activation barriers for channels I and II are predicted to be 34.2 and 52.5 kcal/mol at the B-PW91/cc-pVDZ level, respectively. We have performed a simple transition state theory analysis which indicates that the prefactors for channel I and II are roughly 7 × 1017 and 1 × 1017 s-1, respectively. Thus, our results suggest that path I is the dominant channel in gas phase thermal RDX decomposition.

Thermodynamic analysis of the stabilisation of pig heart mitochondrial malate dehydrogenase and maize leaf phospho enolpyruvate carboxylase by different salts, amino acids and polyols

As part of our investigations into the inactivation of pig heart mitochondrial malate dehydrogenase ( phm-MDH) and maize leaf phospho enolpyruvate carboxylase ( ml-PEPC) in the presence of various cosolvents, the denaturation kinetics as a function of temperature have been determined based on Arrhenius plots derived from transition state theory analysis over the temperature range from 3.5°C to 65°C. The experimental data for phm-MDH were obtained in the presence of 1 M concentrations of various salts of monovalent and polyvalent anions, 1 M amino acids or 1 M sucrose and 6.1 M glycerol. Similarly, Arrhenius plot data were obtained for ml-PEPC in the presence of 2.5 M NaOAc and 0.8 M sodium glutamate. Distinct regimes of inactivation corresponding to high and low values of inactivation enthalpy were identified for the phm-MDH in the presence of all cosolvents and for the ml-PEPC in the presence of 2.5 M NaOAc, but not in the presence of 0.8 M sodium glutamate. A significant temperature-dependent effect dominated the inactivation of phm-MDH and ml-PEPC at elevated temperatures (e.g., ≥45°C), whilst the inactivation of these enzymes over a lower temperature range (≤25°C) was dominated by temperature-independent phenomenon. The corresponding thermodynamic activation parameters ( Δ G ‡, Δ H ‡ and Δ S ‡) associated with the transition state complexes involved in the inactivation of phm-MDH and ml-PEPC in the presence of the various cosolvents have been determined. The results indicate that the transition states associated with the inactivation of these two enzymes at elevated temperatures are characterised by large, positive enthalpic and entropic changes. In contrast, the inactivation process observed for phm-MDH at low temperatures in the presence of various cosolvents was marked by a large, negative entropic contribution and a small, positive enthalpic contribution. The results obtained in this study indicate that more than one mechanism of inactivation can occur with these two multimeric enzymes depending on the selected temperature range and the type of cosolvent. The relationship of these results to stabilisation models for phm-MDH and ml-PEPC in the presence of various cosolvents, as well as the application of Arrhenius plot data to extrapolate the long term solution stability of these enzymes at lower temperatures from the pseudo-first order rate constants of inactivation experimentally derived over a range of temperatures, are discussed.

Computational studies of the reactions of CH 3I with H and OH

Transition states for attack by H and OH at the CH and CI bonds of CH 3I have been characterized at the Gaussian-2 level of theory. The results are employed in transition state theory analyses to obtain ab initio rate constants and product branching ratios. For the H reaction the major pathway is predicted to be I-atom abstraction, while for OH attack H-atom abstraction is faster than HOI formation. The rate constants agree well with measurements at around room temperature and are extrapolated to combustion conditions. The contributions of the title reactions to the flame chemistry of CH 3I are assessed.

A shock tube study of reactions of CN with HCN, OH, and H2 using CN and OH laser absorption

Quantitative, narrow-line laser absorption measurements of CN time-histories at 388.444 nm were acquired in high-temperature pyrolysis and laser photolysis shock tube experiments. The data were analyzed using a detailed kinetics mechanism to determine the rate coefficients of the reactions for temperatures between 940 and 1860 K. Two independent experimental approaches were utilized: laser photolysis (at 193 nm) of dilute C2N2/HCN/argon and C2N2/H2/argon mixtures in reflected shock wave experiments, and shock heating of HNO3/HCN/argon mixtures in incident and reflected shock wave experiments. Laser absorption measurements of OH at 306.687 nm were also taken in the HNO3/HCN/argon experiments The results are in good agreement with rate coefficient determinations from previous studies at different temperatures. The expression derived by Yang et al (1992) from their k2 measurements in combination with those of Szekely et al (1983), is recommended for the broad temperature range 300–3000 K. The uncertainty factors f and F give the limiting values of the rate coefficient kmin = f kbest fit, kmax = Fkbest fit. The recommended expression for the rate coefficient of reaction (3) also valid for temperatures 300–3000 K, is taken from the transition state theory analysis of the CN + H2 reaction by Wagner and Bair (1986). The rate coefficient for reaction (1) was measured to be 4.0 × 1013cm3mol−1 s−1(f = 0.61, F = 1.40) for the temperature range 1250–1860 K. © 1996 John Wiley & Sons, Inc.

Computational studies of the potential energy surface for O(3P)+H2S: Characterization of transition states and the enthalpy of formation of HSO and HOS

Structures and vibrational frequencies for minima and 11 transition states on the O(3P)+H2S potential energy surface have been characterized at the MP2=FULL/6-31G(d) level. GAUSSIAN-2 theory was employed to calculate ΔHf,298 for HSO and HOS of −19.9 and −5.5 kJ mol−1, respectively. The kinetics of HSO=HOS isomerization are analyzed by Rice–Ramsperger–Kassel–Marcus theory. Transition state theory analysis for O+H2S suggests OH+HS is the dominant product channel, with a rate constant given by 1.24×10−16 (T/K)1.746 exp(−1457 K/T) cm3 molecule−1 s−1. Kinetic isotope effects and the branching ratio for H+HSO production are also analyzed. The other possible products H2+SO and H2O+S do not appear to be formed in single elementary steps, but low-barrier pathways to these species via secondary reactions are identified. No bound adducts of O+H2S were found, but results for weakly bound triplet HOSH are presented. The likely kinetics for the reactions OH+SH→S(3P)+H2O, OH+SH→cis and trans 3HOSH, cis 3HOSH→HOS+H, and HSO and HOS+H→H2+3SO are discussed.

Experimental and theoretical studies of the reaction of atomic hydrogen with silane

The kinetics of the reaction H(1 2S)+SiH 4 have been measured from 290 to 660 K by the flash photolysis-resonance fluorescence technique. The results are summarized by k=(1.78±0.11)×10 −10 exp[−(16.0±0.2) kJ mol −1/ RT] cm 3 s −1 with a confidence interval of about ±10%. The transition state for direct H-atom abstraction was investigated theoretically, at up to the GAUSSIAN 2 ab initio level. A transition state theory analysis of the abstraction channel gives excellent accord with the measurements, which suggests that H 2+SiH 3 are the dominant products. An expression for the reverse reaction is given. An extrapolated k from 290 up to 2000 K, which includes a Wigner tunneling correction, is k=2.44×10 16 ( T/K) 1.903 exp(−1102 K/ T) cm 3 s −1.

Experimental and theoretical studies of the reaction of atomic oxygen with silane

The flash-photolysis resonance-fluorescence technique has been employed to measure the rate constant for O+SiH4→products from 295–565 K, and yielded k1=1.23×10−10 exp(−14.6 kJ mol−1/RT) cm3 s−1 with an accuracy of about ±15%. The transition state for direct H-atom abstraction has been characterized at up to the Gaussian-2 ab initio level of theory. With small adjustments it is possible to model kinetic data for O+SiH4 in terms of an abstraction channel leading to OH+SiH3. This agreement does not rule out minor participation by addition or insertion channels, but there is no theoretical evidence for bound triplet intermediates in the potential energy surface. A transition state theory analysis suggests that k1 at 1000 K is 16 times larger than previously thought.

Kinematics and dynamical effects in the total and differential excitation functions. A variational transition state theory analysis

A variational transition state theory, previously developed to account for the kinetic energy dependence of the reaction cross section, has been extended to include the effect of the curvature of the reaction coordinate as well as to calculate the energy disposal of elementary reactions. A systematic study of the influence of kinematics and dynamical factors in the kinetic energy dependence of both the energy disposal and reaction cross section has been made. The theory was applied to ideal systems with different mass combinations as well as to the M + RX → MX + R reaction family (M = Na, K, Rb; R = CH 3; X = Cl, Br, I). One of the most important findings of the present study is that for a given potential energy surface there is a correlation between the energy disposal as well as the excitation function, with the actual location of the maximum in the curvature of the reaction coordinate. Those systems for which the location of the maximum of the curvature along the reaction coordinate lies close to that of maximum gradient in the potential energy showed a clear non-adiabatic behaviour, i.e. there is a significant flux between the (translational) energy along the reaction coordinate and the (vibrational) energy perpendicular to it. Therefore they showed the higher fraction in vibrational energy of the products as well as the higher collision energy dependence of the reaction cross section (i.e. higher slope of σ R versus E T.

The temperature coefficient of the rates in the system Cl + CH4 ⇆ CH3 + HCl, thermochemistry of the methyl radical

AbstractThe bimolecular rate constant for the title reaction has been measured by very‐low‐pressure reactor techniques at 233 < T K < 338. The equilibrium constant has also been measured between 253 and 338 K. Our rate constants are in excellent agreement with recent measurements using very different techniques and reaction conditions, and the general agreement probably makes this one of the most accurately measured rateconstants. Transition state models of the reaction rule out a bent TS in favor of a TS with colinear Cl···H···C bonds. The curvature at higher temperatures (>350 K) is quantitatively accounted for by transition state theory analysis. Tunneling is shown not to play a role. The measured values of K1 allow an experimental value of S° (CH3) to be fixed to only ±2.4 e.u. However, using known values of S° for all species gives ΔH°f298(CH3.) = 35.1 plusmn; 0.1 kcal/mol in excellent agreement with other measured values.