Computational studies on the thermal decomposition and isomerization of CHBr2O radical

The unimolecular decomposition study of dibromomethoxy radical, CHBr₂O, and its isomeric hydroxy dibromomethyl radical, CBr₂OH, is carried out using ab initio electronic molecular structure methods. Three kinds of reaction pathways are examined, C–H and C–Br bond scissions, intramolecular three-center HBr elimination and isomerization. Based on the ab initio results, energy-specific rate coefficients k(E) and thermal rate constants k(T,P) are evaluated using RRKM theory and master equation numerical analysis. Relevance to existing experimental evidence is discussed.     

过氧硝酸乙酰酯分解反应的速率常数

在G3MP2B3结构优化和能量计算的基础上, 采用RRKM理论和疏松过渡态模型重新估算了过氧硝酸乙酰酯(PAN)的热分解反应PAN→CH₃C(O)OO+NO₂(R1)的反应速率常数, 得到与实验值吻合的结果.用同样的模型计算了PAN→CH₃C(O)O+NO₃(R2)的反应速率常数. 结果表明, 在相同的反应条件下, R1是主要的分解通道, R2是次要通道, R2的反应速率常数比R1的小两个数量级.     

Ab initio CI study of the reaction between NH2 and NO

Using ab initio CI calculations we have evaluated the structural, energetic and kinetic parameters of the reaction between NH₂ and NO. In light of the results obtained, it appears that while the formation of molecular nitrogen is highly probable, the reaction pathway leading to N₂H+OH cannot be thermodynamically excluded. The kinetic model based on the RRKM and TST methods leads to a calculated rate constant at 298 K (k = 1.64×10⁻¹¹ cm³ molecule⁻¹ s⁻¹) which is comparable to that determined experimentally and which decreases with temperature in the range 200–700 K.     

Ab initio quantum chemical studies of reaction mechanism for CH2CO with NCO

An extensive quantum chemical study of the potential energy surface (PES) for all possible isomerization and dissociation reactions of CH₂CO with NCO is reported at the DFT (B3LYP/6-311++G(d,p)) and CCSD(T)/cc-pVDZ//B3LYP/6-311++G(d,p) levels of theory. For the CH₂CO+NCO reaction, the formation of CO+CH₂NCO via an addition–elimination mechanism is the dominant channel on the doublet surface. While the formation of CO+CH₂OCN via bimolecular substitution reaction is in the secondary. Meanwhile, the isomerization and dissociation reactions of the products, CH₂NCO and CH₂OCN, also have been investigated using the same theoretical approach. It can be concluded that these reaction channels are not feasible kinetically at low or fairly high temperatures. On the basis of the ab initio data, the total rate constants for the CH₂CO+NCO reaction in the T=296–560 K range have been computed using conventional transition state theory with Wigner tunneling correction and fitted by a rate expression as k=2.14×10⁻¹² (cm³ molecule⁻¹ s⁻¹) exp(654.29/T). The calculated total rate constants with Wigner tunneling correction for the CH₂CO+NCO reaction are in good agreement with the available experimental values.     

Ab initio analysis of the conformational changes of the prolyl-proline model peptide

For- -Pro- -Pro-NH₂ is an ab initio model of the prolyl-proline sequence unit present in numerous peptides and proteins. Cis–trans isomerization of the peptide linkage is a crucial step in accessing the active conformation of several proline containing macromolecules.

The present study focuses on the flexibility of the five-membered pyrrolidine ring, which is considered to help other conformational changes as well as cis–trans isomerization. Ring flexibility is characterized by the pseudorotational amplitude, A, and the phase angle, P. Calculations are carried out at the RHF/6-31+G(d) level of theory. The choice of method and level of theory is further supported by single point DFT calculations.

In the course of NMR structure determination of peptides or proteins, proline residues present in the sequences need special attention. Because of the lack of an amide hydrogen, sequential assignment of proline is rather complicated. Furthermore, in solution state, peptide cis–trans isomers are almost always present. Ab initio study on the For- -Pro- -Pro-NH₂ model is a useful tool to discover the structural characteristics of the prolyl-proline sequence unit.     

Quantitative analysis of photoisomerization rates in trans-stilbene and 4-methyl-trans-stilbene

Recent measurements of isomerization rates of electronically excited trans-stilbene in supersonic beams and in thermal gases are analyzed in terms of the RRKM theory. It is shown that statistical unimolecular rate theory can quantitatively account for the experimental results. The absence of a major methyl-substitution effect is well reproduced. A comparison of isolated-molecule and liquid-phase isomerization rates indicates so far not understood solvent effects.     

Ab Initio Kinetics for Thermal Decomposition of CH(3)N(•)NH(2), cis-CH(3)NHN(•)H, trans-CH(3)NHN(•)H, and C(•)H(2)NNH(2) Radicals

The thermal decomposition of the CH(3)N(?)NH(2), cis-CH(3)NHN(?)H, trans-CH(3)NHN(?)H, and C(?)H(2)NNH(2) radicals, which are the four radical products from the H-abstraction reactions of monomethylhydrazine, were theoretically studied by using ab initio Rice-Ramsperger-Kassel-Marcus (RRKM) transition-state theory and master equation analysis. Various decomposition pathways were identified by using either the QCISD(T)/cc-pV∞Z//CASPT2/aug-cc-pVTZ or the QCISD(T)/cc-pV∞Z//B3LYP/6-311++G(d,p) quantum chemistry methods. The results reveal that the β-scission of NH(2) to form methyleneimine is the predominant channel for the decomposition of the C(?)H(2)NNH(2) radical due to its small energy barrier of 13.8 kcal mol(-1). The high pressure limit rate coefficient for the reaction is fitted by 3.88 × 10(19)T(-1.672) exp(-9665.13/T) s(-1). In addition, the pressure dependent rate coefficients exhibit slight temperature dependence at temperatures of 1000-2500 K. The cis-CH(3)NHN(?)H and trans-CH(3)NHN(?)H radicals are the two distinct spatial isomers with an energy barrier of 26 kcal mol(-1) for their isomerization. The β-scission of CH(3) from the cis-CH(3)NHN(?)H radical to form trans-diazene has an energy barrier of 35.2 kcal mol(-1), and the β-scission of CH(3) from the trans-CH(3)NHN(?)H radical to form cis-diazene has an energy barrier of 39.8 kcal mol(-1). The CH(3)N(?)NH(2) radical undergoes the β-scission of methyl hydrogen and amine hydrogen to form CH(2)═NNH(2), trans-CH(3)N═NH, and cis-CH(3)N═NH products, with the energy barriers of 42.8, 46.0, and 50.2 kcal mol(-1), respectively. The dissociation and isomerization rate coefficients for the reactions were calculated via the E/J resolved RRKM theory and multiple-well master equation analysis at temperatures of 300-2500 K and pressures of 0.01-100 atm. The calculated rate coefficients associated with updated thermochemical property data are essential components in the development of kinetic mechanisms for the pyrolysis and oxidation of MMH and its derivatives.     

Hydroxy peroxy nitrites and nitrates from OH initiated reactions of isoprene

The reaction of hydroxy peroxy radicals (RO(2)) with NO represents one of the most crucial tropospheric processes, leading to terrestrial ozone formation or NO(x)() removal and chain termination. We investigate the formation of hydroxy peroxy nitrites (ROONO) and nitrates (RONO(2)) from the OH-isoprene reactions using DFT and ab initio theories and variational RRKM/master equation (vRRKM/ME) formalism. The binding energies of ROONO from NO addition to RO(2) are determined to be in the range of 20-22 kcal mol(-)(1), and the bond dissociation energies of ROONO to form an alkoxy radical (RO) and NO(2) range from 6 to 9 kcal mol(-)(1). Isomerization of ROONO to RONO(2) is exothermic by 22-28 kcal mol(-)(1). The entrance and exit channels of the RO(2)-NO reaction are found to be barrierless, and the rate constants to form ROONO are calculated to be 3 x 10(-)(12) to 2 x 10(-)(11) cm(3) molecule(-)(1) s(-)(1) using the canonical variational transition state theory. The vRRKM/ME analysis reveals negligible stabilization of excited ROONO and provides an assessment of ROONO isomerization to RONO(2).     

Dissociation dynamics of the trifluoromethoxy radical

Trifluoromethoxy radical formation (by O-atom addition to trifluoromethyl) and dissociation (by F-atom elimination) are studied by ab initio molecular-orbital theory. The activation enthalpy (298 K) for F-atom elimination is 35.3 kcal mol⁻¹ at the UMP4SDQ/6-31 G¹//UHF/6-31 G¹+ΔZPE+Δ(H-E₀ level. The implication of calculated RRKM dissociation rate constants is discussed.     

An electronic structure investigation of the BNO-BON-NBO system

The potential energy hypersurface of the ground triplet states of the BNO-BON-NBO system has been investigated using traditional ab initio electronic structure theory. The molecules studied have the molecular formula BON and include three linear and three angular species, and two transition states for the isomerization of an angular N-B-O to an angular B-O-N and a linear B-NO, respectively. All stationary points on the BNO-BON-NBO isomerization potential energy surface have been characterized employing UMP2, UMP4, and Gaussian-2 (G2) theory with the 6-311G(d), 6-311G(2d), and TZ2P basis sets. The isomerization for an angular N-BO to the linear B-NO has a lower energy barrier than that of the former to an angular B-ON. Energetics are presented with G2 energies. Two sets of resonance structures for both bent B-NO (boron nitrosyl) and B-ON (boron isonitrosyl) were proposed and the bonding in the two species was analyzed. For the purpose of comparison, the density functional theory based hybrid methods B3LYP/6-311G(d) and B3LYP/TZ2P have also been applied to both geometry optimization and single-point calculations. It is found that the B3LYP prediction of the nature of the linear B-O is contradictory to that made by all MPn(n = 2 and 4) calculations. The cause for this contradiction is discussed.     

Theoretical studies of the reactions of O(~3p) with halogenated methyl (Ⅰ)——Reaction mechanism of the O(~3p) CH_2Cl reaction

The reaction of O(~3P) with CH_2Cl radical has been studied using ab initio molecular orbital theory. G2 (MP2) method is used to calculate the geometrical parameters, vibrational frequencies and energies of various stationary points on the potential energy surface. The reaction mechanism is revealed. The addition of O(~3P) with CH_2Cl leads to the formation of an energy rich intermediate OCH_2Cl which can subsequently undergo decomposition or isomerization to the final products. The calculated heat of reaction for each channel is in agreement with the experimental value. The production of H CHClO and Cl CH_2O are predicted to be the major channels. The overall rate constants are calculated using transition state theory on the basis of ab initio data. The rate constant is pressure independent and exhibits negative temperature dependence at lower temperatures, in accordance with the experimental results.     

Experimental and theoretical investigation of the reaction CF3 + NO + M → CF3NO + M from 0.5 to 12 Torr and from 253 to 373 K

The kinetics of the association reaction of CF₃ with NO was studied as a function of temperature near the low-pressure limit, using pulsed laser photolysis and time-resolved mass spectrometry. CF₃ radicals were generated by photolysis of CF₃I at 248 nm and the kinetics was determined by monitoring the time-resolved formation of CF₃NO. The bimolecular rate constants were measured from 0.5 to 12 Torr, using nitrogen as the buffer gas. The results are in very good agreement with recent data published by Vakhtin and Petrov, obtained at room temperature in a higher pressure range and, therefore, the two studies are quite complementary. A RRKM model was developed for fitting all the data, including those of Vakhtin and Petrov and for extrapolating the experimental results to the low- and high-pressure limits. The rate expressions obtained are the following: k₁(0) = (3.2 ± 0.8) × 10⁻²⁹ (T/298)^{−(3.4±0.6)} cm⁶ molecule⁻² s⁻¹ for nitrogen used as the bath gas and k₁(∞) = (2.0 ± 0.4) × 10⁻¹¹ (T/298)^(0±1) cm³ molecule⁻¹ s⁻¹. RRKM calculations also help to understand the differences in reactivity between CF₃ and other radicals, for the same association reaction with NO.     

Influence of vibrational energy flow on isomerization of flexible molecules: incorporating non-Rice-Ramsperger-Kassel-Marcus kinetics in the simulation of dipeptide isomerization

The conformational isomerization of a dipeptide, N-acetyl-tryptophan methyl amide (NATMA), is studied computationally by including important dynamical corrections to Rice-Ramsperger-Kassel-Marcus (RRKM) theory for the transition rate between pairs of isomers. The dynamical corrections arise from incomplete or sluggish vibrational energy flow in the dipeptide, a property suggested by the mode-selective chemistry that has been observed by Dian et al. [J. Chem. Phys. 120, 133 (2004)]. We compute the extent and rate of vibrational energy flow in NATMA quantum mechanically using local random matrix theory, which we then use to correct the RRKM theory rates. The latter rates are then introduced into a master equation to study the population dynamics of the dipeptide. Incomplete or slow vibrational energy flow is found to enhance the conformational selectivity of NATMA over RRKM estimates.     

A dual-level ab initio and hybrid density functional theory dynamics study on the unimolecular decomposition reaction C2H5O-->CH2O + CH3

We present a direct ab initio and hybrid density functional theory dynamics study of the thermal rate constants of the unimolecular decomposition reaction of C2H5O-->CH2O + CH3 at a high-pressure limit. MPW1K/6-31+G(d,p), MP2/6-31+G(d,p), and MP2(full)/6-31G(d) methods were employed to optimize the geometries of all stationary points and to calculate the minimum energy path (MEP). The energies of all the stationary points were refined at a series of multicoefficient and multilevel methods. Among all methods, the QCISD(T)/aug-cc-pVTZ energies are in good agreement with the available experimental data. The rate constants were evaluated based on the energetics from the QCISD(T)/aug-cc-pVTZ//MPW1K/6-31+G(d,p) level of theory using both microcanonical variational transition state theory (microVT) and RRKM theory with the Eckart tunneling correction in the temperature range of 300-2500 K. The calculated rate constants at the QCISD(T)/aug-cc-pVTZ/MPW1K/6-31+G(d,p) level of theory are in good consistent with experimental data. The fitted three-parameter Arrhenius expression from the microVT/Eckart rate constants in the temperature range 200-2500 K is k = 2.52 x 10(12)T(0.41)e(-8894.0/T) s(-1). The falloff curves of pressure-dependent rate constants are performed using master-equation method within the temperature range of 391-471 K. The calculated results are in good agreement with the available experimental data.     

Theoretical study for the HNSi–HSiN isomerization: ab initio and DFT calculations

Ab initio and density functional theory (DFT) calculations using the GAUSSIAN 94 program have been performed to investigate the molecular structures of HNSi and HSiN in the ground state as well as the transition state for the HNSi–HSiN isomerization reaction at the 6-311G(d,p), 6-311+G(2d,p) and 6-311+G(2df,p) basis sets. The results show that DFT calculations at higher levels of theory reproduce experimental vibrational frequencies of both HNSi and HSiN better than ab initio methods including electron correlation effects. Those calculated geometries are accurate enough to predict the rotational constant of HNSi. The barrier height for the isomerization reaction is found to be about 10 kcal/mol.     

Dynamical theory of proton tunneling transfer rates in solution: general formulation

A general dynamical theory is presented for the rate constant of weak coupling, nonadiabatic proton-tunneling reactions in solution. The theory incorporates the critical role of the solvent and the vibration of the separation of the heavy particles between which the proton transfers, including their dynamics. The formulation which allows the computation of the quantum rate constant k via classical molecular dynamics simulation techniques is presented, as are a number of approximate analytic results for k in a variety of different important regimes. The frequent appearance of (nearly) classical Arrhenius behavior for k — even though the intrinsic reactive event is quantum proton tunneling — is discussed, together with the solvent and vibrational contributions to the apparent activation energy. In certain weak solvation limits, however, non-Arrhenius behavior for k is found and is related to vibrational Franck-Condon features in the reaction.     

Ab initio studies of conformational properties of dimethyl diphosphate dianion and its complex with magnesium

The conformational properties of the diphosphate linkage have been studied with ab initio methods using the dimethyl diphosphate dianion (1) and magnesium dimethyl diphosphate (2) as models. The ab initio energy and geometry of the conformers around the P-O bonds have been determined at the self-consistent-field (SCF) using the 6-31G* and the tzp basis sets; whereas, the 6-31G* basis set alone has been used for 2. In addition, the adiabatic connection method (ACM) of density functional theory (DFT) using the dzvp basis set has been employed for 1. The optimization of all possible staggered conformers assumed for the four P-O bonds, led to nine minima for 1. In agreement with the general anomeric effect, the sc conformation about the P-O bonds is clearly preferred over the ap one. Vibrational frequencies were calculated at the SCF level using the 6-31G* basis set and used to evaluate zero-point energies, thermal energies, and entropies for all minima of 1. The effect of zero-point energies and thermal energies is quite small. However, the effect of entropies, mainly resulting from a multiplicity contribution, changes the stability of the conformers. For each minimum of 1, up to six different arrangements of the Mg²⁺ were used to determine minima of 2. This procedure led to 21 distinct minima. The presence of the magnesium counter-ion appeared to completely change the structure and relative energy of the conformers. The preferred structures of the complex exhibit the (sc, ap) orientation around the two central P–O bonds and an arrangement in which the magnesium cation is coordinated by three phosphoryl oxygen atoms. The results of this work clearly demonstrate that interactions with the metal counter-ion can induce conformational changes in the overall 3D-shape adopted by molecules containing diphosphate linkages. The PM3 and MNDO quantum semi-empirical methods and molecular mechanics methods using the CVFF force field were tested and large differences in the minimum structures, as well as in the conformational energies between these and ab initio methods, are discussed.     

Effect of intramolecular energy transfer on the rate of unimolecular isomerization: HCN --HNC

This paper reports calculations of the rate of isomerization of HCN - HCN based on the theory of Gary and Rice as extended by Zhao and Rice. The major task is to determine the effect of intramolecular energy transfer on the prediction of the rate of isomerization. Both the full three-dimensional (3D) system and the reduced two-dimensional (2D) system obtained from freezing CN bond at 1.159 A are analyzed to check the validity of the freezing bond approximation. Meanwhile, RRKM rates are calculated to test RRKM choice of the transition state by comparing to Gary-Rice three-state model. The comparison shows that the rates from 2D model and 3D model are differing up to 20% with 2D rates consistently larger. The intramolecular energy transfer modifies the isomerization rate for HCN system up to 30% that is modestly small by the expectation. The isomerization rate predicted from RRKM theory is greater than those of Gary-Rice three-state model theory up to 65%, and it overstimates the rates under all consider     

Implementation of a microcanonical variational transition state theory for direct dynamics calculations of rate constants

Calculation of microcanonical rate constants has been an important field in chemical dy-namic studies for many years because it can be used not only to give good prediction of rate con-stants in microcanonical assembly, but also to calculate rate constants with certain conserved quantum numbers such as the total angular momentum, and in turn, can be easily converted into thermal rate constants[1—3]. The widely used method for calculating microcanonical rate constants of unimolecular reac-tions…     

The rate enhancement for prolyl cis-to-trans isomerization of cyclic CPFC peptide is caused by an increase in the vibrational entropy of the transition state

The conformational preferences and prolyl cis-trans isomerization of oxidized and reduced Ac-Cys-Pro-Phe-Cys-NH2 (CPFC peptides) have been carried out using the ab initio HF/6-31+G(d) and hybrid density functional B3LYP/6-311++G(d,p) levels of theory. The most preferred conformations of oxidized and reduced CPFC peptides with the trans prolyl peptide bond have a type-I beta-turn for the Pro-Phe sequence in common. In particular, the transition states for both forms are stabilized by the intramolecular hydrogen bonds between the prolyl nitrogen and the N-H group of the Phe3 residue. The rotational barrier DeltaGct to the cis-to-trans isomerization for the oxidized CPFC peptide is calculated to be 19.37 kcal/mol at the B3LYP/6-311++G(d,p)//HF/6-31+G(d) level of theory, which is lower by 0.88 kcal/mol than that of the reduced CPFC peptide. This may indicate that the rate constant kc-->t of the prolyl cis-to-trans isomerization for the oxidized form is about 4 times larger than that of the reduced form, which is reasonably consistent with the value deduced from NMR experiments. In particular, the increase in vibrational entropy for the transition state of the oxidized form over that of the reduced form contributes to enhance the rate constant for the prolyl cis-to-trans isomerization of the oxidized form.