Direct Ab Initio Dynamics Calculations Research Articles

C-C Bond Formation Reaction Catalyzed by a Lithium Atom: Benzene-to-Biphenyl Coupling.

Transition-metal-catalyzed carbon-carbon (C-C) bond formation is an important reaction in pharmaceutical and organic chemistry. However, the reaction process is composed of multiple steps and is expensive owing to the presence of transition metals. This study proposes a lithium-catalyzed C-C coupling reaction of two benzene molecules (Bz) to form a biphenyl molecule, which is a transition-metal-free reaction, based on ab initio and direct ab initio molecular dynamics (AIMD) calculations. The static ab initio calculations indicate that the reaction of two Bz molecules with Li- ions (reactant state, RC) can form a stable sandwiched complex (precomplex), where the Li- ion is sandwiched by two Bz molecules. The complex formation reaction can be expressed as 2Bz + Li - → Bz(Li -)Bz, where the C-C distance between the Bz rings is 2.449 Å. This complex moves to the transition state (TS) via the structural deformation of Bz(Li-)Bz, where the C-C distance is shortened to 2.118 Å. The barrier height was calculated to be -9.9 kcal/mol (relative to RC) at the MP2/6-311++G(d,p) level. After TS, the C(sp3)-C(sp3) single bond was completely formed between the Bz rings (the C-C bond distance was 1.635 Å) (late complex). After the dissociation of H2 from the late complex, a biphenyl molecule was formed: the C(sp2)-C(sp2) bond. The calculations suggest that the C-C bond coupling of Bz occurred spontaneously from 2Bz + Li-, and biphenyl molecules were directly formed without an activation barrier. Direct AIMD calculations show that the C-C coupling reaction also takes place under electron attachment to Li(Bz)2: Li(Bz)2 + e- → [Li-(Bz)2]ver → precomplex → TS → late complex, where [Li-(Bz)2]ver is the vertical electron capture species of Li(Bz)2. Namely, the C-C coupling reaction spontaneously occurred in Li(Bz)2 owing to electron attachment. Similar C-C coupling reactions were also observed for halogen-substituted benzene molecules (Bz-X, X = F and Cl). Furthermore, this study discusses the mechanism of C-C bond formation in electron capture based on the theoretical results.

Reactions of Photoionization-Induced CO-H2O Cluster: Direct Ab Initio Molecular Dynamics Study.

The hydrocarboxyl radical (HOCO) is an important species in combustion and astrochemistry because it is easily converted to CO2 after hydrogen reduction. In this study, the formation mechanism of the HOCO radical in a CO–H2O system was investigated by direct ab initio molecular dynamics calculations. Two reactions were examined for HOCO formation. First, the reaction dynamics of the CO–H2O cluster cation, following the ionization of the neutral parent cluster CO(H2O)n (n = 1–4), were investigated. Second, the bimolecular collision reaction between CO and (H2O)n+ was studied. In the ionization of the CO(H2O)n clusters (n = 3 and 4), proton transfer, expressed as CO(H2O)n+ → CO–(OH)H3O+(H2O)n–2, occurred within the (H2O)n+ cluster cation, and the HOCO radical was yielded as a product upon addition of CO and OH. This reaction proceeds under zero-point energy. Also, this radical was effectively formed from the collision reaction of CO with water cluster cation (H2O)n+, expressed as CO + OH(H3O+)(H2O)n–2 → HOCO–H3O+ + (H2O)n–2. If the intermolecular vibrational stretching mode is excited in the CO(H2O)n cluster (vibrational stretching between CO and the water cluster), the HOCO radical was detected after ionization when n = 2. The reaction mechanism was discussed based on the theoretical results.

Formation of Hydrogen Peroxide from O-(H2O)n Clusters.

Hydrogen peroxide (H2O2) has recently received much attention as a safe and clean energy carrier for hydrogen molecules. In this study, based on direct ab initio molecular dynamics (AIMD) calculations, we demonstrated that H2O2 is directly formed via the photoelectron detachment of O-(H2O)n (n = 1-6) (water clusters of an oxygen radical anion). Three electronic states of oxygen atoms were examined in the calculations: O(X)(H2O)n (X = 3P, 1D, and 1S states). After the photoelectron detachment of O-(H2O)n (n = 1) to the 1S state, a complex comprising O(1S) and H2O, O(1S)-OH2, was formed. A hydrogen atom of H2O immediately transferred to O(1S) during an intracluster reaction to form H2O2 as the final product. Simulations were run to obtain a total of 33 trajectories for n = 1 that all led to the formation of H2O2. The average reaction time of H2O2 formation was calculated to be 57.7 fs in the case of n = 1, indicating that the reaction was completed within 100 fs of electron detachment. All the reaction systems O(1S)(H2O)n (n = 1-6) indicated the formation of H2O2 by the same mechanism. The reaction times for n = 2-6 were calculated to range between 80 and 180 fs, indicating that the reaction for n = 1 is faster than that of the larger clusters, that is, the larger the cluster size, the slower the reaction is. The reaction dynamics of the triplet O(3P) and singlet O(1D) potential energy surfaces were calculated for comparison. All calculations yielded the dissociation product O(X)(H2O)n → O(X) + (H2O)n (X = 3P and 1D), indicating that the O(1S) state contributes to the formation of H2O2. The reaction mechanism was discussed based on the theoretical results.

Molecular Design of a Reversible Hydrogen Storage Device Composed of the Graphene Nanoflake-Magnesium-H2 System.

Carbon materials such as graphene nanoflakes (GRs), carbon nanotubes, and fullerene can be widely used for hydrogen storage. In general, metal doping of these materials leads to an increase in their H2 storage density. In the present study, the binding energies of H2 to Mg species on GRs, GR–Mgm+ (m = 0–2), were calculated using density functional theory calculations. Mg has a wide range of atomic charges. In the case of GR–Mg (m = 0, Mg atom), the binding energy of one H2 molecule is close to 0, whereas those for m = 1 (Mg+) and 2 (Mg2+) are 0.23 and 13.2 kcal/mol (n = 1), respectively. These features suggest that GR–Mg2+ has a strong binding affinity toward H2, whereas GR–Mg+ has a weak binding energy. In addition, it was found that the first coordination shell is saturated by four H2 molecules, GR–Mg2+–(H2)n (n = 4). Next, direct ab initio molecular dynamics calculations were carried out for the electron-capture process of GR–Mg2+–(H2)n and a hole-capture process of GR–Mg+–(H2)n (n = 4). After electron capture, the H2 molecules left and dissociated from GR–Mg+: GR–Mg2+–(H2)n + e– → GR–Mg+ + (H2)n (H2 is released into the gas phase). In contrast, the H2 molecules were bound again to GR–Mg2+ after the hole capture of GR–Mg+: GR–Mg+ + (H2)n (gas phase) + hole → GR–Mg2+–(H2)n. On the basis of these calculations, a model device with reversible H2 adsorption–desorption properties was designed. These results strongly suggest that the GR–Mg system is capable of H2 adsorption–desorption reversible storage.

Electronic states of hydrogen atom trapped in diamond lattice

Density functional theory (DFT) and direct ab initio molecular dynamics (MD) calculations have been applied to a hydrogen atom trapped in diamond cluster. The DFT calculation showed that spin density of hydrogen atom in diamond (hyperfine coupling constant, hfcc) is lower than that of free hydrogen atom in vacuo. This result was in good agreement with that of muon-spin-rotation experiment. The MD calculation showed that the hfcc of hydrogen atom decreases with increasing temperature because the hydrogen atom behaves as electron donor in diamond lattice. The electronic states of hydrogen atom trapped in the diamond were discussed on the basis of theoretical results.

Electronic state dependence of the ion–molecule reaction CH3CN+ + CH3CN → CH4CN+ + CH2CN: threshold electron–secondary ion coincidence (TESICO) and direct ab initio molecular dynamics study

The ion-molecule reaction, CH(3)CN(+) + CH(3)CN → CH(3)CNH(+) + CH(2)CN, has been investigated using the threshold electron-secondary ion coincidence (TESICO) technique. Relative reaction cross sections for two microscopic reaction mechanisms, i.e., proton transfer (PT) from the acetonitrile ion CH(3)CN(+) to neutral acetonitrile CH(3)CN and hydrogen atom abstraction (HA) by CH(3)CN(+) from CH(3)CN, have been determined for two low-lying electronic states, (2)E and (2)A(1) of the CH(3)CN(+) primary ion. The cross section for PT of the (2)A(1) state was smaller than that of the (2)E state, whereas that of HA are almost the same in the two states. Ab initio calculations showed that the dissociation of the C-H(+) bond of CH(3)CN(+) is easier in the (2)E state than that in the (2)A(1) state. The direct ab initio molecular dynamics (MD) calculations showed that two mechanisms, direct proton transfer and complex formation, contribute the reaction dynamics.

Theoretical Study of the Reaction of CH3 with HOCO Radicals

The reaction of HOCO radicals with CH3 radicals is examined using the coupled cluster method to locate and optimize the critical points on the ground-state potential energy surface. The results show that the CH3 + HOCO reaction can produce both the H2O + CH2CO and the CH4 + CO2 products through acetic acid and enediol intermediates. Direct ab initio dynamics calculations determine the thermal rate coefficients to be k(T/K) = 3.24 x 10(-11)T0.1024 in cm3 x molec(-1) x s(-1) at T </= 1000 K for the overall reaction. In addition, the product branching ratio of (H2O + CH2CO) to (CH4 + CO2) is predicted to be RH2O/CH4(T/K) = 1.52 + (1.95 x 10(-4))T using RRKM theory. Both the thermal rate coefficients and the product branching ratios are weakly temperature dependent.

Direct ab initio dynamics calculations of the reaction rate for the hydrogen abstraction reaction of NCO with CH4 and C2H6

The kinetics of the hydrogen abstraction reactions NCO + CH4 (R1) and NCO + C2H6 (R2) have been studied over a wide temperature range. The minimum energy paths (MEPs) were calculated at the MP2/cc-pVDZ level and single-point calculations were refined at the G3MP2 level. The rate constants for the title reactions were calculated using canonical variational transition state theory (CVT) with small-curvature tunneling (SCT) contributions. The fitted three-parameter formulae are k 1 = 2.52 × 10−22 T 3.46 exp(2466/T) and k 2 = 9.8 × 10−22 T 3.2 exp(411.8/T) cm3 molecule−1 s−1 for (R1) and (R2), respectively. The calculated rate constants were found to be in good agreement with the available experimental data. Deuterium kinetic isotope effects were also investigated. Both reactions show a significant kinetic isotope effect in the low-temperature range.

Energetics and kinetics of the reaction of HOCO with hydrogen atoms

The potential energy surface for the reaction of HOCO radicals with hydrogen atoms has been explored using the CCSD(T)/aug-cc-pVQZ ab initio method. Results show that the reaction occurs via a formic acid (HOC(O)H) intermediate, and produces two types of products: H(2)O+CO and H(2)+CO(2). Reaction enthalpies (0 K) are obtained as -102.0 kcalmol for the H(2)+CO(2) products, and -92.7 kcalmol for H(2)O+CO. Along the reaction pathways, there exists a nearly late transition state for each product channel. However, the transition states locate noticeably below the reactant asymptote. Direct ab initio dynamics calculations are also carried out for studying the kinetics of the H+HOCO reaction. At room temperature, the rate coefficient is predicted to be 1.07x10(-10)cm(3) molec(-1) s(-1) with a negligible activation energy E(a)=0.06 kcalmol, and the branching ratios are estimated to be 0.87 for H(2)+CO(2), and 0.13 for H(2)O+CO. In contrast, the product branching ratios have a strong T dependence. The branching ratio for H(2)O+CO could increase to 0.72 at T=1000 K.

Isotope effects on the spin-density distribution in the [formula omitted] clusters: Direct ab initio molecular dynamics study

Direct ab initio molecular dynamics calculations have been carried out for the H 6 + cluster and its isotopic analogues: [H 2(H 2)H 2] +, [H 2(H 2)D 2] +, and [H 2(HD)H 2] +. The calculations predict that the average geometry over the trajectories is asymmetric in both the deuterated clusters [H 2(H 2)D 2] + and [H 2(HD)H 2] +, causing disproportion in the spin density determining hyperfine coupling constants (HFCCs). This prediction agrees well with our recent ESR study of the isotope effects on the HFCCs for these clusters that are considered present in γ-irradiated solid p-H 2. The present result thus provides supportive theoretical evidence for the H 6 + cluster formation in the solid p-H 2.

Direct ab initio dynamics calculations of the rate constants for the reaction of CHF2CF2OCH3 with Cl

AbstractA dual‐level direct dynamics method is employed to reveal the dynamical properties of the reaction of CHF2CF2OCH3 (HFE‐254pc) with Cl atoms. The optimized geometries and frequencies of the stationary points and the minimum energy path (MEP) are calculated at the B3LYP/6‐311G(d,p) level by using GAUSSIAN 98 program package, and energetic information is further refined by the G3(MP2) method. Two H‐abstraction channels have been identified. For the reactant CHF2CF2OCH3 and the two products, CHF2CF2OCH2 and CF2CF2OCH3, the standard enthalpies of formation are evaluated with the values of −256.71 ± 0.88, −207.79 ± 0.12, and −233.43 ± 0.88 kcal/mol, respectively, via group‐balanced isodesmic reactions. The rate constants of the two reaction channels are evaluated by means of canonical variational transition‐state theory (CVT) including the small‐curvature tunneling (SCT) correction over a wide range of temperature from 200 to 2000 K. The calculated rate constants agree well with the experimental data, and the Arrhenius expressions for the title reaction are fitted and can be expressed as k1 = 9.22 × 10−19 T2.06 exp(219/T), k2 = 4.45 × 10−14 T0.90 exp(−2220/T), and k = 4.71 × 10−22 T3.20) exp(543/T) cm3 molecule−1 s−1. Our results indicate that H‐abstraction from CH3 group is the main reaction pathway in the lower temperature range, while H‐abstraction from CHF2 group becomes more competitive in the higher temperature range. © 2007 Wiley Periodicals, Inc. 39: 221–230, 2007

Energy-Flow Dynamics in the Molecular Channel of Propanal Photodissociation, C2H5CHO → C2H6 + CO: Direct ab Initio Molecular Dynamics Study

Direct ab initio molecular dynamics calculations have been carried out for the molecular channel of the photodissociation of propanal, C2H5CHO --> C2H6 + CO, at the RMP2(full)/cc-pVDZ level of ab initio molecular orbital theory. The initial conditions were generated using the microcanonical sampling to put the excess energy randomly into all vibrational modes of the TS. Starting from the TS, a total of approximately 700 trajectories were numerically integrated for 100 fs. The obtained final energy distributions for the C2H6 and CO fragments and their relative translational motion were found to be quite similar to those obtained for the acetaldehyde reaction, CH3CHO --> CH4 + CO, in our previous study (Chem. Phys. Lett. 2006, 421, 549) despite the fact that the number of degree of freedom for C2H6 is larger than that for CH4. The coupling between the intrinsic reaction coordinate and one of the generalized normal modes orthogonal to it was predicted substantially strong around s = 1.4 amu(1/2) bohr, and it is expected that the energy flow out of C2H6 proceeds through this coupling. However, the obtained energy distributions strongly suggest that the coupling among the modes in C2H6 is quite small and the intramolecular energy redistribution does not occur efficiently in this molecule.

Direct ab initio molecular dynamics study on a S N2 reaction OH − + CH 3Cl → CH 3OH + Cl −: Effect of non-zero impact parameter on the reaction dynamics

Direct ab initio molecular dynamics (MD) calculations have been applied to a S N2 reaction OH − + CH 3Cl → CH 3OH + Cl −. The collision dynamics with non-zero impact parameters were treated in the present study, and the results are compared with the near collinear collision dynamics previously reported by us [H. Tachikawa, M. Igarashi, T. Ishibashi, J. Phys. Chem. A 106 (2002) 10977]. The collision energy was fixed to 25 kcal/mol. The product state distribution obtained for the non-zero impact parameter collision dynamics was slightly different from that of the collinear collision. The distribution of relative translational energy between products Cl − and CH 3OH in the non-zero impact parameter collision dynamics was shifted to higher energy region from that of collinear collision. Also, it was found that the mean translational energy of the product has a maximum at non-zero impact parameter ( b = 0.6–1.2 Å). The reaction mechanism is discussed on the basis of theoretical results.

Dynamics of the Concerted Triple Proton Transfer in Cyclic Water Trimer Using the Multiconfiguration Molecular Mechanics Algorithm

Cyclic water clusters are important molecular species to understand the nature of hydrogen bonded networks. Theoretical studies for the dynamics of triple proton transfer in the cyclic water trimer were performed. The potential energy surface (PES) of triple proton transfer is generated by the multiconfiguration molecular mechanics (MCMM) algorithm. We have used the MP2/6-31G(d,p) level for high-level ab initio data (energies, gradients, and Hessians), which are used in the Shepard interpolation. Eight high-level reference points were added step by step, including two points for the critical configurations of the large curvature tunneling paths. The more high-level points are used, the better the potential energy surfaces become. The rate constant and kinetic isotope effect (KIE) for the triple proton transfer at 300 K, which have been calculated by the canonical variational transition-state theory with microcanonical optimized multidimensional semiclassical tunneling approximation, are 1.6 x 10(-3) s(-1) and 230, respectively. Tunneling is very important not only for the triple proton transfer but also for the triple deuterium transfer. The MCMM results show good agreement with those from the direct ab initio dynamics calculations.

SN2 and SN2′ reaction dynamics of cyclopropenyl chloride with halide ion — A direct ab initio molecular dynamics (MD) study

Direct ab initio molecular dynamics (MD) calculations have been carried out for the reaction of cyclopropenyl chloride with halide ion (F–) (F– + (CH)3Cl → F(CH)3 + Cl–) in gas phase. Both SN2 and SN2′ channels were found as product channels. These channels are strongly dependent on the collision angle of F– to the target (CH)3Cl molecule. The collision at one of the carbon atoms of the C=C double bond leads to the SN2′ reaction channel; whereas the collision at the methylene carbon atom leads to the SN2 reaction channel. The reactions proceed via a direct mechanism without long-lived complexes. The reaction mechanism is discussed on the basis of the theoretical results.Key words: SN2 reaction, direct ab initio molecular dynamics, halogen exchange, reaction mechanism.

DFT and direct ab initio MD calculations of the gas hydrate: Hydrogen molecule trapped in water cluster (H2O)12

AbstractDensity Functional Theory (DFT) and direct ab initio molecular dynamics (MD) calculations were applied to the hydrogen molecule trapped in a water cluster composed of 12 water molecules (H2O)12. The static DFT calculation showed that the H2 molecule is trapped in the center of mass of (H2O)12. The vibrational frequency of the H–H stretching mode of the H2 molecule trapped in the water cluster was blueshifted from that in vacuo. On the other hand, the vibrational frequency of H2 in water‐hydrogen 1:1 complex (H2O–H2) was redshifted. A direct ab initio MD calculation of H2(H2O)12 at 50 K indicated that the H2 molecule is rotated freely around the center of mass of the water cluster. The origin of the spectral shift of H2 in water ice is discussed on the basis of the theoretical results. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

A Direct ab Initio Trajectory Study on the Gas-Phase SN2 Reaction OH- + CH3Cl → CH3OH + Cl-

Direct ab initio trajectory calculations have been applied to a SN2 reaction, OH- + CH3Cl → CH3OH + Cl-. First, static ab initio molecular orbital (MO) calculations with several basis sets were examined to select the most convenient and best fit basis set to that of high-quality calculations. As a result of the static ab initio calculations, it was found that the Hartree−Fock (HF)/3-21+G(d) calculation reasonably represents a potential energy surface calculated at the MP2/6-311++G(2df,2pd) level. Next, direct ab initio dynamics calculations using the 3-21+G(d) basis set were carried out for the SN2 reaction. A full dimensional potential energy surface including all degrees of freedom was used in the dynamics calculation. The collision energies chosen were Ecoll = 5 and 25 kcal/mol. In the collisions at Ecoll = 5 and 25 kcal/mol, 48% and 63% of the total available energies were, respectively, partitioned into the relative translational mode between CH3OH and Cl-. Also, it was predicted that the C−H stretching mode of the product CH3OH is excited after the SN2 reaction, which is not detected in the case of the halogen-atom exchange SN2 reaction. The reaction mechanism was discussed on the basis of theoretical results.

Direct ab initio dynamics calculations on the rate constants for the hydrogen-abstraction reaction of C 2 H 5 F with O ( 3 P)

The hydrogen-abstraction reaction C2H5F+O → C2H4F+OH has been studied by a dual-level direct dynamics method. For the reaction, three reaction channels, one for α-abstraction and two for β-abstraction, have been identified. The potential-energy surface information is obtained at the MP2(full)/6-311G(d,p) and PMP2(full)/6-311G(3df,3pd) (single-point) levels. By canonical variational transition-state theory, rate constants for each reaction channel are calculated with a small-curvature tunneling correction. The total rate constant is calculated from the sum of the individual rate constants and the temperature dependence of the branching ratios is obtained over a wide range of temperatures from 300 to 5,000 K. The agreement of the rate constants with experiment is good in the experimental temperature range from 1,000 to 1,250 K. The calculated results indicate that at low temperatures α-abstraction is most likely to be the major reaction channel, while β-abstraction channels will significantly contribute to the whole reaction rate as the temperature increases.

Direct ab initio dynamics calculations of the reaction rates for the hydrogen abstraction reaction Cl + HC(O)F → HCl + CFO

A direct dynamics method is employed to study the kinetics of the Cl + HC(O)F hydrogen abstraction reaction. The potential energy surface (PES) information is explored from ab initio calculations. Optimized geometries and frequencies of the stationary points as well as the extra points along the minimum energy path (MEP) are calculated at the MP2/6-311+G(d,p) level of theory. In order to improve the energetics along the MEP, single-point calculations are carried out at the QCISD(T)/6-311+G(3df,2p) level of theory. Furthermore, the initial potential information is used to evaluate the rate constants using canonical variational transition-state theory (CVT) with the inclusion of small-curvature tunneling (SCT) corrections over a range of temperatures 220–1500 K. The calculated CVT/SCT rate constants are found to be in good agreement with the available experimental data. Our results show that for the title reaction the variational effect is small at all temperatures, while the tunneling effect plays an important role in the lower temperature range.

Direct ab initio dynamics study on the largest methylgermane reaction GeH(CH 3) 3+H→Ge(CH 3) 3+H 2

Direct ab initio dynamics calculations have been performed on the reaction of atomic hydrogen with the largest methylgermane GeH(CH 3) 3 over a wide temperature range 200–2000 K. The minimum energy path (MEP) for the reaction is calculated at the MP2/6-31+G(d) level, and the energies along the MEP are further refined using the G2 method. The obtained CVT/SCT thermal constants are in reasonable agreement with available experimental values within 298–510 K. For the title reaction, the variational effect should not be neglected over the whole considered temperature range, while the small curvature tunneling effect is only important in the lower temperature range.