"Pump-probe" atom-centered density matrix propagation studies to gauge anharmonicity and energy repartitioning in atmospheric reactive adducts: case study of the OH + isoprene and OH + butadiene reaction intermediates

Time-resolved "pump-probe" ab initio molecular dynamics studies are constructed to probe the stability of reaction intermediates, the mechanism of energy transfer, and energy repartitioning, for moieties involved during the interaction of volatile organic compunds with hydroxyl radical. These systems are of prime importance in the atmosphere. Specifically, the stability of reaction intermediates of hydroxyl radical adducts to isoprene and butadiene molecules is used as a case study to develop novel computational techniques involving "pump-probe" ab initio molecular dynamics. Starting with the various possible hydroxyl radical adducts to isoprene and butadiene, select vibrational modes of each of the adducts are populated with excess energy to mimic the initial conditions of an experiment. The flow of energy into the remaining modes is then probed by subjecting the excited adducts to ab initio molecular dynamics simulations. It is found that the stability of the adducts arises directly due to the anhormonically driven coupling of the modes to facilitate repartitioning of the excess vibrational energy. This kind of vibrational repartitioning has a critical influence on the energy density.     

Direct ab initio dynamics study of the OH + HOCO reaction

The reaction between OH and HOCO has been examined using the coupled-cluster method to locate and optimize the critical points on the ground-state potential energy surface. The energetics are refined using the coupled-cluster method with basis set extrapolation to the complete basis set (CBS) limit. Results show that the OH + HOCO reaction produces H2O + CO2 as final products and the reaction passes through an HOC(O)OH intermediate. In addition, the OH + HOCO reaction has been studied using a direct dynamics method with a dual-level ab initio theory. Dynamics calculations show that hydrogen bonding plays an important role during the initial stages of the reaction. The thermal rate constant is estimated over the temperature range 250-800 K. The OH + HOCO reaction is found to be nearly temperature-independent at lower temperatures, and at 300 K, the thermal rate constant is predicted to be 1.03 x 10(-11) cm3 molecule(-1) s(-1). In addition, there may be an indication of a small peak in the rate constant at a temperature between 300 and 400 K.     

Quantum dynamics of the H + O2 --> O + OH reaction on an accurate ab initio potential energy surface

We report exact time-dependent and time-independent quantum mechanical studies of the title reaction on an accurate ab initio potential energy surface of Xu et al. (J. Chem. Phys. 2005, 122, 24305). The J = 0 reaction probabilities for several reactant states show sharp resonance structures superimposed on relatively low backgrounds, and they are remarkably different from existing quantum results on an earlier potential energy surface (DMBE-IV). The new findings reported here suggest that our current understanding of this important reaction might require significant revision.     

Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study

Using quantum chemistry plus ab initio molecular dynamics and classical molecular dynamics methods, we address the relationship between molecular conformation and the biomedical function of arylamide polymers. Specifically, we have developed new torsional parameters for a class of these polymers and applied them in a study of the interaction between a representative arylamide and one of its biomedical targets, the anticoagulant drug heparin. Our main finding is that the torsional barrier of a C(aromatic)-C(carbonyl) bond increases significantly upon addition of an o-OCH2CH2NH3+ substituent on the benzene ring. Our molecular dynamics studies that are based on the original general AMBER force field (GAFF) and GAFF modified to include our newly developed torsional parameters show that the binding mechanism between the arylamide and heparin is very sensitive to the choice of torsional potentials. Ab initio molecular dynamics simulation of the arylamide independently confirms the degree of flexibility we obtain by classical molecular dynamics when newly developed torsional potentials are used.     

Application of a kinetic energy partitioning scheme for ab initio molecular dynamics to reactions associated with ionization in water tetramers

We analyze the short-time dynamics of 'cyclic' and 'branched' water tetramers after an ionization event, with the aid of a scheme that partitions the kinetic energy of a solute plus solvent system into separate solute and solvent (or bath) contributions, using instantaneous internal coordinates and atomic velocities. The analysis supports the partitioning of the tetrameric systems into two subsystems, a 'reactive trimer' and a 'solvent' molecule. The partitioned kinetic energy exhibits two features, a broad peak assigned to the interaction between the two sub-systems and a sharper peak arising from the proton transfer that occurs upon ionization. It is found that the stability of the hydroxyl radical formed upon ionization is sensitive to the configuration of the water molecules around the ionized water at the moment of the ionization event.     

Kinetic study on the H + SiH4 abstraction reaction using an ab initio potential energy surface

Variational transition state theory calculations with the correction of multidimensional tunneling are performed on a 12-dimensional ab initio potential energy surface for the H + SiH(4) abstraction reaction. The surface is constructed using a dual-level strategy. For the temperature range 200-1600 K, thermal rate constants are calculated and kinetic isotope effects for various isotopic species of the title reaction are investigated. The results are in very good agreement with available experimental data.     

Hyperfine interactions in aqueous solution of Cr3+: an ab initio molecular dynamics study

We performed an ab initio molecular dynamics simulation of the paramagnetic transition metal ion Cr³⁺ in aqueous solution. Isotropic hyperfine coupling constants between the electron spin of the chromium ion and nuclear spins of all water molecules have been determined for instantaneous snapshots extracted from the trajectory. The coupling constant of first sphere oxygen, A _iso(¹⁷O_I)=1.9±0.3 MHz, is independent on Cr–O_I distance but increases with the tilt angle for the water molecule approaching 180°. First sphere hydrogen spins have A _iso(¹ H_I)=2.1±0.2 MHz which decreases with increasing tilt angle and shows a Cr–H_I distance dependence. The hyperfine coupling constants for second sphere ¹⁷O is negative and an order of magnitude smaller (−0.20±0.02 MHz) compared to first sphere.     

Quasiclassical trajectory study of the collision-induced dissociation dynamics of Ar + CH3SH+ using an ab initio interpolated potential energy surface

Classical trajectory calculations have been performed to investigate the collision-induced dissociation (CID) of the CH(3)SH(+) cation with Ar atoms. A new intramolecular potential energy surface for the CH(3)SH(+) cation is evaluated by interpolation of 3000 ab initio data points calculated at the MP2/6-311G(d,p) level of theory. The new potential energy surface includes seven accessible dissociation channels of the cation. The present QCT calculations show that migration of hydrogen atoms, leading to the rearrangement CH(3)SH(+) <--> CH(2)SH(2)(+), is significant at the collision energies considered (6.5-34.7 eV) and that the formation of CH(3)(+), CH(3)S(+), and CH(2)(+) cations takes place primarily by a "shattering" mechanism in which the products are formed just after the collision. The theoretical product abundances are found to be in qualitative agreement with the experimental data. However, at high collision energies, the calculated total cross sections for the formation of CH(3)(+) and CH(2)SH(+) cations are noticeably larger than the experimental determinations. Several features of the dynamics of the CID processes are discussed.     

Ab initio study of the potential energy surface for the OH+CO-->H+CO2 reaction

Potential energy surface for the reaction OH+CO-->H+CO2 has been calculated using the complete active space self-consistent-field and multireference configuration interaction methods with the correlation consistent triple-, quadruple-, and quintuple-zeta basis sets. A specific- reaction-parameters density functional theory has been suggested, in which the B3LYP functional is reoptimized to give the highly accurate potential energy surface with less computational efforts.     

An ab initio chemical kinetic study on the reactions of H,OH, and Cl with HOClO3

The mechanisms for reactions of H, HO, and Cl with HOClO₃, important elementary processes in the early stages of the ammonium perchlorate (AP) combustion reaction, have been investigated at the CCSD(T)/6‐311+G(3df,2p)//PW91PW91/6‐311+G(3df) level of theory. The rate constants for the low‐energy channels have been calculated by statistical theory. For the reaction of H and HOClO₃, the main channels are the production of H₂ + ClO₄ (k_1a) and HO + HOClO₂ (k_1b); k_1a and k_1b can be represented as 1.07 × 10^?17 T^1.97 exp(?7484/T) and 6.08 × 10^?17T^1.96 exp(?7729/T) cm³ molecule^?1 s^?1, respectively. For the HO + HOClO₃ reaction, the main pathway is the H₂O + ClO₄ (k_2a) production process, with the predicted rate constant k_2a = 1.24 × 10 ^?8 T^?2.99 exp(1664/T) for 300–500 K and k_2a = 1.27×10^?19 T^2.12 exp(?1474/T) for 500–3000 K. For the Cl + HOClO₃ reaction, the formation of HOCl + ClO₃ (k_3a) and HCl + ClO₄ (k_3b) is dominant, with k_3a = 1.33×10^?12 T^0.67 exp(?9658/T) and k_3b = 1.75×10¹⁶ T^1.63 exp(?11156/T) cm³ molecules^?1 in the range of 300–3000 K. In addition, the heats of formation of ClO₃ and HOClO₃ have been predicted based on several isodesmic and/or isogyric reactions with Δ_fH^o₀ (ClO₃) = 47.0 ± 1.0 and Δ_fH^o₀ (HOClO₃) = 5.5 ± 1.5 kcal/mol, respectively. These data may be used for kinetic simulation of the AP decomposition and combustion reaction. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 253–261, 2010     

Accurate quantum mechanical calculations of differential and integral cross sections and rate constant for the O+OH reaction using an ab initio potential energy surface

The authors report accurate quantum mechanical studies of the O+OH reaction on the improved Xu-Xie-Zhang-Lin-Guo potential energy surface. The differential cross section was obtained at several energies near the reaction threshold using a time-independent method. The dominant forward and backward peaks in the angular distribution are consistent with a complex-forming mechanism, which is also confirmed by the extensive rotational excitation in the O2 product. However, the asymmetry of these peaks suggests a significant nonstatistical component. The initial state (upsilon i=0, j i=0) specified integral cross section, which was calculated up to 1.15 eV of collision energy using the Chebyshev wave packet method, shows no energy threshold and decreases with the increasing collision energy, consistent with the barrierless nature of the reaction. The resulting rate constant exhibits a negative temperature dependence for T>100 K and decays as the temperature is lowered, in qualitative agreement with available experimental data.     

Intramolecular SN2 reaction caused by photoionization of benzene chloride-NH3 complex: direct ab initio molecular dynamics study

Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.     

A global ab initio potential energy surface for HNO (a3A") and quantum mechanical studies of vibrational states and reaction dynamics

A new global potential energy surface for the lowest triplet electronic state (a(3)A") of HNO has been developed by a three-dimensional cubic spline interpolation of more than 13,000 ab initio points, which were calculated at the multireference configuration interaction level with Davidson correction using the augmented correlation-consistent polarized valence quintuple zeta basis set. Two minima and five saddle points were found on the potential energy surface. Low-lying vibrational states were obtained in this new potential using the Lanczos method and assigned. In addition, thermal rate constants for the N + OH → H + NO reactions were obtained using an exact wave packet method. Reasonably good agreement with experimental data was obtained.     

Interconversion behavior of the C-H bond in the CH4+ radical cation: ab initio molecular dynamics study

Thermal motion of CH4+ is investigated by performing an ab initio molecular dynamics method with the second-order M?ller-Plesset (MP2)/6-311G** force field. In the trajectories obtained at 400 K, we have observed rapid interconversion behavior of the geometrical parameters of CH4+ with the frequency of 0.6/ps, where the C-H pair forming the small angle around 55 degrees is switched to another pair on subpicosecond time scale. The switching patterns are found to be classified into the following two types. Type 1: one C-H of the small angled C-H pair is switched to one C-H of the other C-H pair. Type 2: the small angled C-H pair is switched to the other C-H pair, which has been newly observed in the present ab initio MD calculation. The four C-H bonds of CH4+ are characterized by the long and short C-H bonds in a time region of the trajectories, and also for the time-evolution of C-H bonds such interconversion behavior is observed. The switching patterns of the geometrical parameters are compared with those in the interconversion scheme between six equivalent C2v symmetry structures of CH4+ [Paddon-Row, M. N. et al., J Am Chem Soc 1985, 107, 7696]. We have also investigated the electronic energy fluctuation due to thermal motion of CH4+. The standard deviation of total electronic energy at 400 K is evaluated to be 1.2 kcal/mol.     

Location of energy barriers. VI. The dynamics of endothermic reactions,ab + c

A systematic 3D classical-trajectory study has been made of the effect of reagent energy distribution and mass combination on the dynamics of endothermic reaction. The potential-energy hypersurface was endothermic by 35.7 kcal mole^?1. Reagent translation, T′, and vibration, V′, was varied in the range up to T′ + V′ = 90 kcal mole^?. Among the principal findings for the equal-mass case were the following. (i) There is an orders-of-magnitude increase in reaction cross section when energy is transferred from T′ to V′, until an optimal distribution over T′ and V′ is achieved at V′ ?, T′. There is a qualitative difference between the forms of the reactive cross section dependences S(T′) V′ and S(V′)_T′. (ii) The greater efficacy of V′ than T′ in promoting endothermic reaction is marked even at total reagent energies ≈ 3 x the endothermic barrier height. (iii) The total reactive cross section for endothermic reaction increases to large values (≈ gas kinetic) as V′ increased to several times the barrier height. (iv) Reagent energy in excess of that required to cross the endothermic barrier is subject to the same “adiabatic” transformation into product energy as was previously observed for exothermic reactions: ΔT′ → ΔT + ΔR (where R is enhanced product rotational energy), and ΔV′ → ΔV. This is explained in terms of induced repulsive energy release in the former case, and induced attractive energy release in the latter. (v) The molecular product is backwards or sideways scattered. Enhanced V′ at constant T′ diminishes product repulsion, giving rise to more-forward scattering. (vi) These findings remain qualitatively unchanged when extreme mass combinations H H + L and L H + H (L = 1 amu, H = 80 amu) are substituted for the equal-mass combination, L L + L. Effects ascribable to a “late” barrier are accentuated for HH + L. and diminished for L H + H. (vii) The total reactive cross section at a given reagent energy increases in the sequence H H + L, L L + L, L H + H, for simple kinematic reasons. (viii) The dynamics on this endothermic potential-energy surface resemble, in all the points listed above, the dynamics on a thermoneutral surface which has its barrier crest in the coordinate of separation (surface II of part I of this series).     

Stability of nucleic acid base pairs in organic solvents: molecular dynamics, molecular dynamics/quenching, and correlated ab initio study

The dynamic structure and potential energy surface of adenine...thymine and guanine...cytosine base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of organic solvents (methanol, dimethylsulfoxide, and chloroform) were investigated by various theoretical approaches starting from simple empirical methods employing the Cornell et al. force field to highly accurate ab initio quantum chemical calculations (MP2 and particularly CCSD(T) methods). After the simple molecular dynamics simulation, the molecular dynamics in combination with quenching technique was also used. The molecular dynamics simulations presented here have confirmed previous experimental and theoretical results from the bulk solvents showing that, whereas in chloroform the base pairs create hydrogen-bonded structures, in methanol, stacked structures are preferred. While methanol (like water) can stabilize the stacked structures of the base pairs by a higher number of hydrogen bonds than is possible in hydrogen-bonded pairs, the chloroform molecule lacks such a property, and the hydrogen-bonded structures are preferred in this solvent. The large volume of the dimethylsulfoxide molecule is an obstacle for the creation of very stable hydrogen-bonded and stacked systems, and a preference for T-shaped structures, especially for complexes of methylated adenine...thymine base pairs, was observed. These results provide clear evidence that the preference of either the stacked or the hydrogen-bonded structures of the base pairs in the solvent is not determined only by bulk properties or the solvent polarity but rather by specific interactions of the base pair with a small number of the solvent molecules. These conclusions obtained at the empirical level were verified also by high-level ab initio correlated calculations.     

Highlevel ab initio and hybrid density functional theory study of the energy profile for the CO+CO reaction

Two complete basis set and three hybrid density functional computational studies were applied in the exploration of the ¹CO+²CO⁺ reaction potential energy surface. One molecular carbon monoxide–carbon monoxide cation molecular associate was elucidated as the structure with the lowest energy on the potential energy surface. Ionization energies, bond dissociation energies, and enthalpies of formation for every di and tri-atomic molecule on the potential energy surface were estimated with the two complete basis sets and the three hybrid density functional theory methods. Six different endothermic channels for the ¹CO+²CO⁺ reaction were evaluated with ab initio and DFT methods. The computed energies and structural parameters are compared with experimental values where available. Some new energies for this reaction system were suggested.