Direct Ab Initio Dynamics Study Research Articles

Direct ab initio molecular dynamics study on the reactions of multi-valence ionized states of water dimer

We investigated the reaction of multi-valence (+2) ionization states of water dimer (H2O)2 using direct ab initio molecular dynamics method. The following multi-valence ionization states were considered. In the direct two-electron ionization state, (H2O)2 was ionized to form (H2O)2 2+ in one step; in the stepwise two-electron ionization state, (H2O)2 was first converted to (H2O)2 + and further ionized after structural relaxation. The (H2O)2 2+ from direct ionization dissociated into two H2O+ ions, while (H2O)2 2+ in stepwise ionization generated H3O+ and OH+ ions from H3O+–OH radical-ion pairs. Additionally, we performed dynamics calculations for the excited state of (H2O)2 2+ generated through direct ionization. The excited (H2O)2 2+ ions also dissociated to form H3O+ and OH+ ions. The reaction mechanism of multi-valence ionization states of (H2O)2 is discussed on the basis of calculation results.

Direct ab initio dynamics study of rate constants and kinetic isotope effects for C2(A3Π u ) + CH3OH reaction

The hydrogen abstraction of CH3OH by C2 (A3Π u ) has been investigated by direct ab initio dynamics over a wide temperature range 200–3000 K. The potential energy surfaces (PESs) have been constructed at the UCCSD(T)/aug-cc-pVTZ//UMP2/6-311++G(d,p) levels of theory. Two different hydrogen abstractions on the methyl and hydroxyl sites of methanol are considered. For the methyl H-abstraction, it is essentially a hydrogen atom transfer (HAT), whereas the hydroxyl site H-abstraction is better described as a proton coupled electron transfer (PCET) according to the Natural Bond Orbital (NBO) analysis. The results suggest that the methyl site reaction is dominant, and the calculated rate constants are roughly consistent with available experimental values. On the other hand, the temperature dependence of deuterium kinetic isotope effects (KIEs) analysis reveals a substantial normal isotope effect in the methyl H-abstraction process, while normal and inverse KIEs coexist in the hydroxyl H-abstraction channel. Furthermore, the three and four–parameter expressions of Arrhenius rate constants are also provided within 200–3000 K.

AB INITIO CALCULATIONS AND KINETICS STUDY FOR THE DIRECT HYDROGEN ABSTRACTION REACTION OF HYDROGEN SELENIDE WITH HYDROGEN ATOM

We present a direct ab initio dynamics study of thermal rate constants of the hydrogen abstraction reaction of H 2 Se + H → SeH + H 2. The QCISD and CCSD(T) methods were employed to optimize the geometries of stationary points and to calculate the harmonic vibrational frequencies. The split-valence 6-311 + G(d,p) and correlation-consistent cc-pVTZ basis sets big enough to describe the geometries and vibrational frequencies of the species involving in the title reaction. The energies obtained at the QCISD(T)/6-311 ++ G(3df,3pd)//QCISD/6-311 + G(d,p) level of theory is able to compare to those calculated at the CCSD(T)/6-311 ++ G(3df,3pd)//CCSD(T)/6-311 + G(d,p) level of theory. The energies of all the selected points along the minimum energy path (MEP) were refined at the QCISD(T)/6-311 ++ G(3df,3pd) level of theory. The barriers were obtained at the both QCISD(T)/6-311 ++ G(3df,3pd)//QCISD/6-311 + G(d,p) and CCSD(T)/6-311 ++ G(3df,3pd)//CCSD(T)/6-311 + G(d,p) levels of theory are in good agreement with experimental one. The forward rate constants were evaluated with both canonical variational transition state theory with small curvature tunneling correction (CVT/SCT) and improved canonical variational transition state theory with small curvature tunneling correction (ICVT/SCT) in the temperature range of 200–2500 K. The calculated forward rate constants of the reaction at the QCISD(T)/6-311 ++ G(3df,3pd)//QCISD/6-311 + G(d,p) level of theory are in good agreement with available experimental data.

An ab initio molecular dynamics study of the roaming mechanism of the H2+HOC+ reaction

We report here a direct ab initio molecular dynamics study of the p-/o-H2+HOC+ reaction on the basis of the accurate SAC-MP2 potential energy surface. The quasi-classical trajectory method was employed. This work largely focuses on the study of reaction mechanisms. A roaming mechanism was identified for this molecular ion–molecule reaction. The driving forces behind the roaming mechanism were thoroughly investigated by using a trajectory dynamics approach. In addition, the thermal rate coefficients of the H2+HOC+ reaction were calculated in the temperature range [25, 300] K and are in good agreement with experiments.

Direct ab initio dynamics study of the reaction of C2(A3Πu) with CH4

AbstractThe reaction of C2(A3Πu) with CH4 has been investigated over a wide temperature range 200–3,000 K by direct ab initio dynamics method at the BMC‐CCSD//BB1K/6‐311+G(2d,2p) level of theory. The optimized geometries and frequencies of the stationary points are calculated at the BB1K/6‐311+G(2d,2p) level, and then the energy profiles of the reactions are refined using the BMC‐CCSD method. The activation barrier height for H‐abstraction reaction was calculated to be 4.44 kcal/mol in temperature range (337–605 K), and the electron transfer behavior was also analyzed by quasi‐restricted molecular orbital method in detail. The canonical variational transition‐state theory (CVT) with the small curvature tunneling (SCT) correction method is used to calculate the rate constants over a wide temperature range 200–3,000 K. The theoretical results shows that variational effect is to some extent large in lower temperature range, and small curvature and tunneling effect play important roles to the H‐atom abstraction only at lower temperatures. The CVT/SCT rate constants are in good agreement with the available experimental results. Our theoretical study is expected to provide a direct insight into the reaction mechanism and may be useful for estimating the kinetics of the title reaction over a wide temperature range where no experimental data are available so far. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

Direct ab initio dynamics study of the reaction of C 2(A 3Π u) radical with C 2H 6

The reaction of C 2 (A 3Π u) with C 2H 6 has been investigated at the BMC–CCSD//BB1K/6-311+G(2d, 2p) level. The classical barrier height for H-abstraction reaction is calculated to be 3.32 kcal/mol and the electron transfer behavior is also analyzed in detail. The rate constants are calculated by TST, CVT, and CVT/SCT over a wide temperature range 50–3000 K. The results indicate: (1) variational effect is small and nonclassical reflection effect is important to the H abstraction in high temperature region; and (2) variational effect is negligible and tunneling effect cooperating with the nonclassical reflection effect makes the rate constant temperature independence in low-temperature range. The CVT/SCT rate constants are in excellent agreement with experimental values.

Further quasi-classical trajectory studies on the C++ H2O reaction

Further trajectory studies on the C+ + H2O reaction have been performed using a potential energy surface described through a finite element method in its p version. In former trajectory studies [Y. Ishikawa, T. Ikegami and R.C. Binning Jr., Direct ab initio molecular dynamics study of C++H2O: angular distribution of products and distribution of product kinetic energies, Chem. Phys. Lett. 370 (2003), pp. 490–495; J.R. Flores, Quasichemical trajectories on a finite element density functional potential energy surface: the C++H2O reaction revisited, J. Chem. Phys. 125 (2006), 164309], tunnelling was not taken into account. The present results together with the analysis of the electronic excited states [J.R. Flores and A.B. González, The role of the excited electronic states in the C++H2O reaction, J. Chem. Phys. 128 (2008), 144310] are useful to interpret the mechanism of the title reaction, which has been the subject of crossed beam experiments [D.M. Sonnenfroh, R.A. Curtiss and J.M. Farrar, Collision complex formation in the reaction of C+ with H2O, J. Chem. Phys. 83 (1985), pp. 3958–3964] and can be considered a prototypical ion–molecule reaction.

Direct ab initio molecular dynamics study of F atom reaction with methane

The dynamics of the F + CH4 → HF + CH3 and F + CD4 → DF + CD3 reactions have been investigated using classical trajectory calculations at the MP2/cc-pvdz level of theory. The trajectories were calculated directly from electronic structure computations, and a Hessian based method with updating was used to integrate the trajectories. Using this method, product rovibrational populations and internal energy distributions were obtained for the F + CH4 and F + CD4 reactions. The theoretical results were compared with the available experimental data and previous calculations results. The state distributions of the reaction F + CH4 in these calculations are in reasonable agreement with the experimental results, which indicates that the experimental behavior of the reaction could be well reproduced by the direct classical trajectory calculations at MP2/cc-pvdz level. As such, the product rovibrational populations and internal energy distributions for the reaction F + CD4 were predicted. The same degree of agreement between theory and experiment as the F + CH4 reaction is expected.

A direct ab initio molecular dynamics (MD) study on the repair reactions of stacked thymine dimer

DNA repair reactions of the thymine dimer (T) 2 following the hole capture have been investigated by means of direct ab initio molecular dynamics (MD) method in order to elucidate the mechanism of repair processes of thymine dimer interacting with a photo-enzyme. The thymine dimer has two C–C single bonds between thymine rings at neutral state expressed by (T T). After the hole capture of (T T), one of the C–C bonds was preferentially broken, while the structure of (T T) + was spontaneously changed to an intermediate having a C–C single bond expressed by (T–T) +. Time scale of the C–C bond breaking and formation of the intermediate was estimated to be 60–180 fs. The mechanism of repair reactions of the thymine dimer was discussed on the basis of theoretical results.

Reaction‐path dynamics and theoretical rate constants for the reaction CH4 + O3 → HOOO + CH3

AbstractWe present a direct ab initio dynamics study of thermal rate constants of the hydrogen abstraction reaction of CH4 + O3 → HOOO +CH3. The geometries of all the stationary points are optimized at MPW1K/6‐31+G(d,p), MPWB1K/6‐31+G(d,p), and BHandHLYP/6‐31+G(d,p) levels of theory. The energies are refined at a multi‐high‐level method. The extended Arrhenius expression fitted from the CVT/SCT and μVT/Eckart rate constants of ozonolysis of methane in the temperature range 200–2500 K are kCVT/SCT(T) = 5.96 × 10−29T4.49e(−17321.3/T) and kμVT/Eckart(T) = 7.92 × 10−29T4.46e(−17301.7/T), respectively. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

Direct dynamics study on the hydrogen abstraction reactions N2H4+R→N2H3+RH (R=NH2,CH3)

We present a direct ab initio dynamics study on the hydrogen abstraction reactions N(2)H(4)+R-->N(2)H(3)+RH (R=NH(2),CH(3)), which are predicted to have six possible reaction channels for NH(2) abstraction and four for CH(3) abstraction caused by the different N(2)H(4) isomers and various attacking orientations of foreign radical to N(2)H(4). The structures and frequencies at the stationary points and the points along the minimum energy paths (MEPs) of all reaction channels are obtained at the UMP2(full)6-31+G(d,p) level of theory. Energetic information of stationary points and the points along the MEPs is further refined by means of MC-QCISD method. The rate constants of these channels are calculated using the improved canonical variational transition-state theory with the small-curvature tunneling correction (ICVT/SCT) method. The calculated results show that the favorable reaction channels are channels (n1) and (n4) as well as (c1) and (c3) (refer to Scheme 1) in the whole temperature range. The total ICVT/SCT rate constants of all channels for the two reactions at the MC-QCISDUMP2(full)6-31+G(d,p) level are both in good agreement with the available experimental data, and corresponding three-parameter expressions of k(ICVTSCT) in 220-3000 K are fitted as 6.46 x 10(-15)(T298)(3.60) exp(-386T) cm(3) mol(-1) s(-1) for NH(2) abstraction and 1.04 x 10(-14)(T298)(4.00) exp(-2037T) cm(3) mol(-1) s(-1) for CH(3) abstraction. Additionally, the long range interaction between the H atom of X-H bond in foreign radicals and the lone pair on the nonreactive N atom of the transition states is further discussed to explain the various transition-state numbers of the two similar hydrogen abstraction reactions.

Direct Ab Initio Dynamics Study for the Hydrogen Abstraction Reaction: CH $$_{2} ({^{3}}B_{1})$$ + H2CO $$\rightarrow $$ CH3 + CHO

We present a direct ab initio dynamics study of thermal rate constants of the hydrogen abstraction reaction of CH \(_{2}(^{3}B_{1})\) + H2CO \(\rightarrow \) CH3 + CHO. The MP2/cc-pVDZ method is employed to optimize the geometries of stationary points as well as the points on the minimum energy path. The energies of all the points were further refined at the CCSD(T)/cc-pVTZ level of theory based on the Moller– Plesset perturbation theory (MP2) optimized geometries. The rate constants were evaluated using the conventional transition state theory, the canonical variational TST, and the improved canonical variational TST, also both including small-curvature tunneling correction in the temperature range of 300–2,500 K. The calculated results show that the rate constants have positive temperature dependence in the calculated temperature range. The calculated results show that the tunneling effect is important at low temperature region.

Direct Dynamics Study on the Hydrogen Abstraction Reaction CH2O + HO2 → CHO + H2O2

We present a direct ab initio dynamics study on the hydrogen abstraction reaction CH2O + HO2 --> CHO + H2O2, which is predicted to have four possible reaction channels caused by different attacking orientations of HO2 radical to CH2O. The structures and frequencies at the stationary points and the points along the minimum energy paths (MEPs) of the four reaction channels are calculated at the B3LYP/cc-pVTZ level of theory. Energetic information of stationary points and the points along the MEPs is further refined by means of some single-point multilevel energy calculations (HL). The rate constants of these channels are calculated using the improved canonical variational transition-state theory with the small-curvature tunneling correction (ICVT/SCT) method. The calculated results show that, in the whole temperature range, the more favorable reaction channels are Channels 1 and 3. The total ICVT/SCT rate constants of the four channels at the HL//B3LYP/cc-pVTZ level of theory are in good agreement with the available experiment data over the measured temperature ranges, and the corresponding three-parameter expression is k(ICVT/SCT) = 3.13 x 10(-20) T(2.70) exp(-11.52/RT) cm3 mole(-1) s(-1) in the temperature range of 250-3000 K. Additionally, the flexibility of the dihedral angle of H2O2 is also discussed to explain the different experimental values.

A DFT and ab initio direct dynamics study on the hydrogen abstract reaction of H 3BNH 3 → H 2 + H 2BNH 2

A direct ab initio dynamics study is presented on the hydrogen abstraction reaction of H 3BNH 3 → H 2 + H2BNH 2. The geometries of all the stationary points are optimized at the B3LYP and MP2 levels of theory with a series of basis sets up to aug-cc-pVTZ. The energies are refined using the G3, G3MP2, G3MP2B3, CBS-Q, CBS-Q//B3, and a combined high-level (HL) method based on the geometries optimized using the B3LYP/aug-cc-pVTZ level of theory. The rate constants are evaluated using the conventional transition-state theory and canonical variational transition-state theory (CVT). The fitted Arrhenius expression calculated from the CVT/SCT method is k ( T ) = 6.86 × 10 6 × T 1.69 × e ( - 1.37 × 10 4 / T ) s - 1 . The estimated apparent activation energy is in accordance with experimental results.

Direct dynamics study on the reaction of O( 3P)+PH 3→PH 2+OH

A direct ab initio dynamics study of thermal rate constants is presented for the hydrogen abstraction reaction of O( 3P)+PH 3→PH 2+OH. The UQCISD/6-311++G(d,p) method was employed to optimize geometry structures and to calculate the minimum energy path (MEP). Frequencies for all stationary points were obtained at the UQCISD/6-311++G(d,p) and UQCISD(T)/6-311++G(2df,2pd) levels of theory, respectively. The energies of the stationary points and 22 points selected along MEP were refined at the UQCISD(T)/6-311++G(2df,2pd)//UQCISD/6-311++G(d,p) level of theory. Reaction rate constants were evaluated by using the conventional transition state theory (TST), the canonical variational transition state theory (CVT) and the CVT with the small curvature tunneling correction method (CVT/SCT) over the temperature range of 200–2000 K, respectively. The results show that the classical potential barrier Δ E ≠ and the reaction enthalpy Δ H 298 0 calculated are 3.35 and −19.44 kcal/mol, respectively, for title reaction. The variational effect is significant in the whole temperature range, while the SCT tunneling correction is important within the temperature range of T≤500 K for the calculation of rate constant.

Direct ab initio dynamics studies of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical

The kinetics of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical were studied using the direct ab initio dynamics approach. BHandHLYP/cc-pVDZ method was employed to optimize the geometries of stationary points as well as the points on the minimum energy path (MEP). The energies of all the points for the two reactions were further refined at the QCISD(T)/cc-pVTZ level of theory. No barrier was found at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory for both reactions. The forward and reverse rate constants were evaluated with both canonical variational transition state theory (CVT) and microcanonical variational transition state theory (mu VT) in the temperature range of 300-2,500 K. The fitted three-parameter Arrhenius expression of the calculated CVT rate constants at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory are k(CVT) (n-C3H7) = 1.68 x 10(-14) T(0.84) e((319.5/T)) cm3 molecule(-1) s(-1) and k(CVT) (iso-C3H7)=4.99 x 10(-14) T(0.90) e((159.5/T)) cm3 molecule(-1) s(-1) for reactions of n-C3H7 + H and iso-C3H7 + H, respectively, which are in good agreement with available literature data. The variational effects were analysed.

Direct ab initio dynamics study on the rate constants and kinetics isotope effects of CH3O+H→CH2O+H2 reaction

We present a direct ab initio dynamics study of thermal rate constants of the hydrogen abstraction reaction of CH(3)O+H-->CH(2)O+H(2). The unrestricted Becke's half-and-half hybrid functional using the Lee-Yang-Parr correlation functional with Dunning's correlation consistent polarized valence double-zeta basis set, the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence double-zeta basis set, and the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set methods were employed to optimize the structures and to calculate frequencies for all stationary points. Minimum energy paths were obtained by the unrestricted Becke's half-and-half hybrid functional using the Lee-Yang-Parr correlation functional and the unrestricted quadratic configuration interaction calculation including single and double substitutions with the same Dunning's correlation consistent polarized valence double-zeta basis set levels of theory. No barrier is found at the unrestricted Becke's half-and-half hybrid functional using the Lee-Yang-Parr correlation functional with Dunning's correlation consistent polarized valence double-zeta basis set level of theory in contrast to a small barrier of 1.43 kcal mol(-1) at the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence double-zeta basis set level of theory. In particular, the barrier vanishes as the energies along the minimum energy path MEP are refined at the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set level of theory. Smaller barriers of 0.47 and 0.17 kcal mol(-1) were obtained at the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set and the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set based on the geometries at the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence triple-zeta basis set levels of theory, respectively. The forward rate constants are evaluated with the canonical variational transition state theory in the temperature range of 300-2500 K. The calculated forward rate constants at the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set based on the geometries at the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence double-zeta basis set level of theory are in good agreement with the available experimental data. The kinetic isotope effects are estimated.

Ab initio calculations and mechanism of two proton migration reactions of ethoxy radical

Abstract We present a direct ab initio and density functional theory dynamics study of the thermal rate constants of the two H-migration reactions of C 2 H 5 O radical. MPW1K/6-31+G(d,p) 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 the QCISD(T)/aug-cc-pVTZ level of theory. The thermal gas phase 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 (μVT) and canonical variational transition state theory (CVT) with the Eckart tunneling correction in the temperature range of 200–2500 K. The extended Arrhenius expression fitted from the μVT/Eckart rate constants of 1,2 H-shift and 1,3 H-shift reactions of C 2 H 5 O radical in the temperature range of 200–2500 K are k = 3.90 × 10 −31 T 12.4 e (−2.13 × 10 3 / T ) and k = 2.83 × 10 −29 T 11.9 e (−2.24 × 10 3 / T ) s −1 , respectively. The two isomerization rate constants exhibited positive temperature dependence in the calculated temperature region. The variational effects for the two isomerizations of ethoxy radical are small and the tunneling effects are important in the low temperature range. The titled reactions are minor and not essential compared to the decomposition pathways of ethoxy radical.

Mechanism of the inner hydrogen atom transfer in free base porphyrazine: a direct ab initio dynamics study

A theoretical study of the mechanism and kinetics of the inner double hydrogen atom-transfer process in free base porphyrazine is presented. The structures and energies of reactant, product, intermediate, transition-state, and second-order saddle-point in the transfer reaction of inner hydrogen atoms in porphyrazine are calculated by using B3LYP/6-31G** method under certain symmetry restriction. The results show that the probability of asynchronous mechanism is larger than that of synchronous mechanism via a second-order saddle-point. Changes from porphyrin to porphyrazine have a less dramatic effect on the mechanism of NH tautomerism. Our analysis reveals that the stepwise mechanism first requires the porphyrazine ring to compress followed by transfer of a H atom with an additional energy requirement of 9.9 kcal mol −1. Meanwhile, the difference of theoretical calculated results between porphyrazine and porphyrin are discussed.

Direct ab initio molecular dynamics study of the two photodissociation channels of formic acid

A total of ∼1200 trajectories have been integrated for the two photodissociation channels of formic acid, HCOOH → H2O + CO (1) and HCOOH → CO2 + H2 (2), which occur with 248 and 193 nm photons, using the direct ab initio molecular dynamics method at the RMP2(full)/cc-pVDZ level of theory. It was found that the percentage of the energy distributed to a relative translational mode in reaction (2) is much larger than that in reaction (1). This is mainly due to the difference in the geometry of transition state (TS); the H2O geometry in the TS of reaction (1) was predicted to significantly deviate from the equilibrium one, whereas the CO2 and H2 geometries in the TS of reaction (2) were found to be more similar to their equilibrium ones. It was also found that the product diatomic molecules, CO and H2, are both vibrationally and rotationally excited. The calculated relative population of the vibrationally excited CO for the 248 nm photodissociation was consistent with experiment.