Ab initio study of the reaction of CHO+ with H2O and NH3

An MP4(full,SDTQ)/6-311++G(d,p)//MP2(full)/6-311++G(d,p) ab initio study was performed of the reactions of formyl and isoformyl cations with H₂O and NH₃, which play an important role in flame and interstellar chemistries. Two different confluent channels were located leading to CO+H₃O⁺/NH. The first one corresponds to the approach of the neutral molecule to the carbon atom of the cations. The second one leads to the direct proton transfer from the cations to the neutrals. At 900 K the separate products CO+H₃O⁺/NH are the most stable species along the Gibbs energy profiles for the processes. For the reaction with H₂O the reaction channel leading to HC(OH) (protonated formic acid) is disfavored with respect to the two CO+H₃O⁺ channels in agreement with the experimental evidence that H₃O⁺ is the major ion observed in hydrocarbon flames. According to our calculations, NH+H₂O are considerably more stable in Gibbs energy than NH₃+H₃O⁺;NH will predominate in the reaction zone when ammonia is added to CH₄+Ar diffusion flame, as experimentally observed. At 100 K the most stable structures are the intermediate complexes CO…HOH/HNH. Particularly the CO…HOH complex has a lifetime large enough to be detected and, therefore, could play a certain role in interstellar chemistry. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1432–1443, 1999     

Interaction in the ternary complexes of HCl-methanol-X, X = H2O or NH3: Ab initio calculations and on-the-fly molecular dynamics

Dynamics, structures, energetics, and vibrational spectra of the ternary complexes of hydrogen chloride with either methanol and water or methanol and ammonia were investigated by on-the-fly molecular dynamics and ab initio and density functional theory (DFT) with aug-cc-pvDZ basis sets. Addition of CH3OH to the HCl-NH3 system catalyzes the proton transfer from HCl to NH3. However, the dynamics of the system show that the proton is not localized on NH3; rather, it is shared between N and Cl.     

Ab initio QM/MM dynamics of H3O+ in water

A molecular dynamics (MD) simulation based on a combined ab initio quantum mechanics/molecular mechanics (QM/MM) method has been performed to investigate the solvation structure and dynamics of H3O+ in water. The QM region is a sphere around the central H3O+ ion, and contains about 6-8 water molecules. It is treated at the Hartree-Fock (HF) level, while the rest of the system is described by means of classical pair potentials. The Eigen complex (H9O4+) is found to be the most prevalent species in the aqueous solution, partly due to the selection scheme of the center of the QM region. The QM/MM results show that the Eigen complex frequently converts back and forth into the Zundel (H5O2+) structure. Besides the three nearest-neighbor water molecules directly hydrogen-bonded to H3O+, other neighbor waters, such as a fourth water molecule which interacts preferentially with the oxygen atom of the hydronium ion, are found occasionally near the ion. Analyses of the water exchange processes and the mean residence times of water molecules in the ion's hydration shell indicate that such next-nearest neighbor water molecules participate in the rearrangement of the hydrogen bond network during fluctuative formation of the Zundel ion and, thus, contribute to the Grotthuss transport of the proton.     

Ab initio calculations and molecular dynamics simulation of H2 adsorption on CN3Be3+ cluster

Hydrogen adsorption properties of the CN₃Be₃⁺ cluster have been studied using density functional theory and MP2 method with a 6–31++G** basis set. Five hydrogen molecules get adsorbed on the CN₃Be₃⁺ cluster with a hydrogen storage capacity of 10.98 wt%. Adsorption of three H₂ molecules on one of the three Be atoms in a cluster is reported for the first time. It is due to the more positive charge on this Be atom than the remaining two. The average value for H₂ adsorption energy in CN₃Be₃⁺ (5H₂) complexes is 0.41 (0.43) eV/H₂ at MP2 (wB97XD) level, which fits well within the ideal range. Adsorption energy from electronic structure calculations plays an important role in retaining the number of H₂ molecules on a cluster during atom-centered density matrix propagation (ADMP) molecular dynamics (MD) simulations. According to ADMP-MD simulations, out of five H₂ adsorbed molecules on CN₃Be₃⁺, four and two H₂ molecules remain absorbed on CN₃Be₃⁺ cluster at 275 K and 350 K, respectively, during the simulation.

     

Proton transfer dynamics of the reaction H3O(+)(NH3,H2O)NH4+ studied using the crossed molecular beam technique

The proton transfer reaction of H3O+ and NH3 was studied using the crossed molecular beam technique at relative energies of 0.41, 0.81, and 1.27 eV. At all three energies, the center-of-mass flux distribution of the product ion NH4+ exhibits sharply asymmetry, and the maximum is close to the velocity and direction of the precursor ammonia beam. The reaction transforms almost all of the 1.69 eV exothermicity into internal excitation of the products at all three collision energies. At the lowest collision energy of 0.41 eV, nearly 77% of the total energy appears in NH4+ internal excitation. However, almost 100% of the incremental translational energy in the two higher-energy experiments appears in the product translational energy. Such an observation provides a classic example of the "induced repulsive energy release" mechanism that is expected to be operative on the highly skewed potential energy surfaces characteristic of the heavy+light-heavy mass combination. These results indicate that the proton transfer proceeds through a direct reaction mechanism; a Rice-Ramsperger-Kassel-Marcus theory calculation shows that the lifetime of the intermediate complex [NH3-H-H2O]+ is about 100 fs. Proton transfer occurs early on the reaction coordinate, when the incipient N-H bond is extended, and results in highly vibrationally excited NH4+ products, with excitation primarily in N-H stretching modes.     

Ab initio study on the reaction of Y+ + NH3 → Y+ NH + H2

The reaction of Y⁺ + NH₃ → Y⁺ NH + H₂ was theoretically investigated by ab initio MO methods. Two possible pathways (1–1 H₂ loss and 1–2 H₂ loss) on the singlet potential energy surface and reaction mechanism were examined and discussed. The singlet and triplet PESs of this reaction system were compared to confirm the correctness of spin conservation concepts. © 1996 John Wiley & Sons, Inc.     

Ab initio molecular dynamics study of glycine intramolecular proton transfer in water

We use ab initio molecular-dynamics simulations to quantify structural and thermodynamic properties of a model proton transfer reaction that converts a neutral glycine molecule, stable in the gas phase, to the zwitterion that predominates in aqueous solution. We compute the potential of mean force associated with the direct intramolecular proton transfer event in glycine. Structural analyses show that the average hydration number (N(w)) of glycine is not constant along the reaction coordinate, but rather progresses from N(w) = 5 in the neutral molecule to N(w) = 8 for the zwitterion. We report the free-energy difference between the neutral and charged glycine molecules, and the free-energy barrier to proton transfer. Finally, we identify the approximations inherent in our method and estimate the corresponding corrections to our reported thermodynamic predictions.     

DFT:B3LYP ab initio molecular dynamics study of the Zundel and Eigen proton complexes, H5O2+ and H9O4+, in the triplet state in gas phase and solution

DFT:B3LYP ab initio molecular dynamics (MD) approach is used to elucidate the properties of the Zundel and Eigen, H5O2+ and H9O4+, proton complexes in the triplet state. The simulation considers the complexes in the gas phase (isolated complexes) and inside the clusters composed of 32, 64, and 128 water molecules, mimicking the behavior of aqueous solutions. MD simulations reveal three distinct periods. For the complex in solutions, the periods are smoothed out. The H5O2+ and H9O4+ complexes in the triplet state undergo structural rearrangements, which eventually result in hydrogen elimination. For the H5O2+, the hydrogen is eliminated from the center of the water cluster, whereas for the H9O4+ it is removed from a near-surface water molecule. The rate of hydrogen elimination decreases with increasing the number of water molecules surrounding the complex.     

Structures, energetics, vibrational spectra of NH4+ (H2O)(n=4,6) clusters: Ab initio calculations and first principles molecular dynamics simulations

Important structural isomers of NH(4) (+)(H(2)O)(n=4,6) have been studied by using density functional theory, Moller-Plesset second order perturbation theory, and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The zero-point energy (ZPE) correction to the complete basis set limit of the CCSD(T) binding energies and free energies is necessary to identify the low energy structures for NH(4) (+)(H(2)O)(n=4,6) because otherwise wrong structures could be assigned for the most probable structures. For NH(4) (+)(H(2)O)(6), the cage-type structure, which is more stable than the previously reported open structure before the ZPE correction, turns out to be less stable after the ZPE correction. In first principles Car-Parrinello molecular dynamics simulations around 100 K, the combined power spectrum of three lowest energy isomers of NH(4) (+)(H(2)O)(4) and two lowest energy isomers of NH(4) (+)(H(2)O)(6) explains each experimental IR spectrum.     

Ab initio molecular dynamics simulation of the structure and proton transport dynamics of methanol-water solutions

Ab initio molecular dynamics simulations are employed to study the structural and proton transport properties of methanol-water mixtures. Structural characteristics analyzed at two different methanol mole fractions (X(M) = 0.25 and X(M) = 0.5) reveal enhanced structuring of water as the methanol mole fraction increases in agreement with recent neutron diffraction experiments. The simulations reveal the existence of separate hydrogen-bonded water and methanol networks, also in agreement with the neutron diffraction data. The addition of a single proton to the X(M) = 0.5 mixture leads to an anomalous structural or Grotthuss-type diffusion mechanism of the charge defect in which water-to-water, methanol-to-water, and water-to-methanol proton transfer reactions play the dominant role with methanol-to-methanol transfers being much less significant. Unlike in bulk water, where coordination number fluctuations drive the proton transport process, suppression of the coordination number of waters in the first solvation shell of the defect diminish the importance of coordination number fluctuations as a driving force in the structural diffusion process. The charge defect is found to reside preferentially at the interface between water and methanol networks. The length of the ab initio molecular dynamics run (approximately 120 ps), allowed the diffusion constant of the charge defect to be computed, yielding a value of D = 4.2 x 10(-5) cm2/s when deuterium masses are assigned to all protons in the system. The relation of this value to excess proton diffusion in bulk water is discussed. Finally, a kinetic theory is introduced to identify the relevant time scales in the proton transfer/transport process.     

Short-time Fourier transform analysis of ab initio molecular dynamics simulation: collision reaction between NH+4 (NH3)2 and NH3

An analyzing technique of the ab initio molecular dynamics simulation is proposed with the use of short-time Fourier transform (ST-FT). The ST-FT analysis demonstrates the dynamical change of the vibrational states in the simulated system. Numerical assessments are preformed for the collision reaction of the ammonia cluster ion NH+(4) (NH3)(2) with the ammonia monomer NH3. Spectrogram obtained by the ST-FT method, which corresponds to the time evolution of vibrational power spectra, clarifies the relationship between the vibrational states and the reaction channels such as nonreactive collision, substitution, and incorporation.     

Ab initio study of C + H3+ reactions

The reaction C + H3+ --> CH(+) + H2 is frequently used in models of dense interstellar cloud chemistry with the assumption that it is fast, i.e. there are no potential energy barriers inhibiting it. Ab initio molecular orbital study of the triplet CH3+ potential energy surface (triplet because the reactant carbon atom is a ground state triplet) supports this hypothesis. The reaction product is 3 pi CH+; the reaction is to exothermic even though the product is not in its electronic ground state. No path has been found on the potential energy surface for C + H3+ --> CH2(+) + H reaction.     

Ab initio static and molecular dynamics study of 4-styrylpyridine.

We report an in‐depth theoretical study of 4‐styrylpyridine in its singlet S₀ ground state. The geometries and the relative stabilities of the trans and cis isomers were investigated within density functional theory (DFT) as well as within Hartree–Fock (HF), second‐order Møller–Plesset (MP2), and coupled cluster (CC) theories. The DFT calculations were performed using the B3LYP and PBE functionals, with basis sets of different qualities, and gave results that are very consistent with each other. The molecular structure is thus predicted to be planar at the energy minimum, which is associated with the trans conformation, and to become markedly twisted at the minimum of higher energy, which is associated with the cis conformation. The results of the calculations performed with the post‐HF methods approach those obtained with the DFT methods, provided that the level of treatment of the electronic correlation is high enough and that sufficiently flexible basis sets are used. Calculations carried out within DFT also allowed the determination of the geometry and the energy of the molecule at the biradicaloid transition state associated with the thermal cis?trans isomerization and at the transition states associated with the enantiomerization of the cis isomer and with the rotations of the pyridinyl and phenyl groups in the trans and cis isomers. Car–Parrinello molecular dynamics simulations were also performed at 50, 150, and 300 K using the PBE functional. The studies allowed us to evidence the highly flexible nature of the molecule in both conformations. In particular, the trans isomer was found to exist mainly in a nonplanar form at finite temperatures, while the rotation of the pyridinyl ring in the cis isomer was incidentally observed to take place within ≈1 ps during the simulation carried out at 150 K on this isomer.     

Ab initio study of NH3 and H2O adsorption on pristine and Na-doped MgO nanotubes

We have investigated, on the basis of density functional theory calculations, the structural and electronic properties of chemical modification of pristine and Na-doped MgONTs with NH₃ and H₂O molecules. We found that the NH₃ and H₂O molecules can be barrierlessly adsorbed on the Mg atom of the tube sidewall along with a charge transfer from the adsorbate to MgONT. The adsorption is chemical in nature with adsorption energies about ?22.3 and ?21.5 kcal/mol for H₂O and NH₃, respectively. The calculated density of state (DOS) shows that the chemical modification of MgONTs with these molecules can be generally classified as certain type of “harmless modification.” In other words, the electronic properties of the MgONT are little changed by the adsorption processes. The substitution of an Mg atom in the tube surface with an Na atom results in a semi-insulator to p-type semiconductor transition based on DOS analysis. It was also found that the doping process reduces the adsorption energies and the electronic properties of Na-doped MgONT is slightly more sensitive toward NH₃ and H₂O molecules, compared with the pristine one.     

Ab initio molecular dynamics simulations of the Li4F4 cluster

Molecular dynamics simulations have been performed directly on the ab initio potential energy surface of Li₄F₄, which was generated within the Hartree-Fock approximation using a Gaussian basis set (split valence contraction). Trajectories at different temperatures yield the temperature dependence of the infrared spectra and the photoelectron spectra. For the infrared spectra comparison is made with MD results using a shell model ion pair potential function.     

Dissociative recombination of NH4+ and ND4+ ions: storage ring experiments and ab initio molecular dynamics

The dissociative recombination (DR) process of NH4+ and ND4+ molecular ions with free electrons has been studied at the heavy-ion storage ring CRYRING (Manne Siegbahn Laboratory, Stockholm University). The absolute cross sections for DR of NH4+ and ND4+ in the collision energy range 0.001-1 eV are reported, and thermal rate coefficients for the temperature interval from 10 to 2000 K are calculated from the experimental data. The absolute cross section for NH4+ agrees well with earlier work and is about a factor of 2 larger than the cross section for ND4+. The dissociative recombination of NH4+ is dominated by the product channels NH3+H (0.85+/-0.04) and NH2+2H (0.13+/-0.01), while the DR of ND4+ mainly results in ND3+D (0.94+/-0.03). Ab initio direct dynamics simulations, based on the assumption that the dissociation dynamics is governed by the neutral ground-state potential energy surface, suggest that the primary product formed in the DR process is NH3+H. The ejection of the H atom is direct and leaves the NH3 molecule highly vibrationally excited. A fraction of the excited ammonia molecules may subsequently undergo secondary fragmentation forming NH2+H. It is concluded that the model results are consistent with gross features of the experimental results, including the sensitivity of the branching ratio for the three-body channel NH2+2H to isotopic exchange.     

Ab initio molecular dynamics study of H2 formation inside POSS compounds

The mechanism and dynamics of the formation of a hydrogen molecule by incorporating two hydrogen atoms in a stepwise manner into the cavity of some POSS (polyhedral oligomeric silsesquioxanes) compounds has been investigated by ab initio molecular orbital and ab initio molecular dynamics (AIMD) methods. The host molecules in the present reactions are two types of POSS, T(8) ([HSiO(1.5)](8)) and T(12)(D(2d)) ([HSiO(1.5)](12)). AIMD simulations were performed at the CASSCF level of theory, in which two electrons and two orbitals of the colliding hydrogen atoms are included in the active space. The trajectories were started by inserting the second hydrogen atom into the hydrogen atom-encapsulated-POSS (H + H@T(n) → H(2)@T(n); n = 8 and 12). In many cases, the gradual formation of a hydrogen molecule has been observed after frequent collisions of two hydrogen atoms within the cages. The effect of the introduction of an argon atom in T(12) is discussed as well.     

Ab initio EOM-CCSD spin-spin coupling constants for hydrogen-bonded formamide complexes: bridging complexes with NH3, (NH3)2, H2O, (H2O)2, FH, and (FH)2

EOM-CCSD spin-spin coupling constants across hydrogen bonds have been computed for complexes in which NH3, H2O, and FH molecules and their hydrogen-bonded dimers form bridging complexes in the amide region of formamide. The formamide one-bond N-H coupling constant [(1)J(N-H)] across N-H...X hydrogen bonds increases in absolute value upon complexation. The signs of the one-bond coupling constants (1h)J(H-X) indicate that these complexes are stabilized by traditional hydrogen bonds. The two-bond coupling constants for hydrogen bonds with N-H as the donor [(2h)J(N-X)] and the carbonyl oxygen as the acceptor [(2h)J(X-O)] increase in absolute value in the formamide/dimer relative to the corresponding formamide/monomer complex as the hydrogen bonds acquire increased proton-shared character. The largest changes in coupling constants are found for complexes of formamide with FH and (FH)2, suggesting that bridging FH monomers and dimers in particular could be useful NMR spectroscopic probes of amide hydrogen bonding.     

Ab initio potential energy surface of CH and reaction dynamics of H + CH+

This work presents a new ground state potential energy surface (PES) for CH. The potential is tested using quasi classical trajectory (QCT) and quantum reactive scattering methods for the H + CH(+) reaction. Cross sections and rate coefficients for all reaction channels up to 300 K are calculated. The abstraction rate coefficients follow the expected slightly decreasing behaviour above 90 K, but have a positive gradient with lower temperatures. The inelastic collision and exchange reaction rate constants are increasing monotonically with temperature. The rate coefficients of the exchange reaction differ significantly between QCT and quantum reactive scattering, due to intrinsic shortcomings of the QCT final state distributions.