Dissociation of carbonic acid: gas phase energetics and mechanism from ab initio metadynamics simulations

A comprehensive metadynamics study of the energetics, stability, conformational changes, and mechanism of dissociation of gas phase carbonic acid, H2CO3, yields significant new insight into these reactions. The equilibrium geometries, vibrational frequencies, and conformer energies calculated using the density functional theory are in good agreement with the previous theoretical predictions. At 315 K, the cis-cis conformer has a very short life time and transforms easily to the cis-trans conformer through a change in the O=C-O-H dihedral angle. The energy difference between the trans-trans and cis-trans conformers is very small (approximately 1 kcal/mol), but the trans-trans conformer is resistant to dissociation to carbon dioxide and water. The cis-trans conformer has a relatively short path for one of its hydroxyl groups to accept the proton from the other end of the molecule, resulting in a lower activation barrier for dissociation. Comparison of the free and potential energies of dissociation shows that the entropic contribution to the dissociation energy is less than 10%. The potential energy barrier for dissociation of H2CO3 to CO2 and H2O from the metadynamics calculations is 5-6 kcal/mol lower than in previous 0 K studies, possibly due to a combination of a finite temperature and more efficient sampling of the energy landscape in the metadynamics calculations. Gas phase carbonic acid dissociation is triggered by the dehydroxylation of one of the hydroxyl groups, which reorients as it approaches the proton on the other end of the molecule, thus facilitating a favorable H-O-H angle for the formation of a product H2O molecule. The major atomic reorganization of the other part of the molecule is a gradual straightening of the O=C=O bond. The metadynamics results provide a basis for future simulation of the more challenging carbonic acid-water system.     

Spectroscopic investigations and ab initio computations of the dye Chromotrope 2R

Detailed analysis of the NIR FT-Raman, FT-IR and UV–visible spectra of the dye Chromotrope 2R (C2R) has been performed. The optimized geometry of the dye is theoretically computed with the HF and DFT levels using the standard 6-31G(d) and LANL2DZ basis sets. Optimized geometry and vibrational spectra indicate that the major species in the solid state are the trans form of hydrogen bonded hydrazone tautomer. The effect of H-bonding in stabilizing a particular type of structure is also discussed. The most preferred trans-configuration for its photochemical activity has been demonstrated on the basis of torsional potential energy surface (PES) scan studies. The optimized geometries and calculated vibrational wavenumbers are evaluated via comparison with experimental values. Electronic spectra are in accordance with the nature of the electronic transitions predicted by time-dependent B3LYP/DZ calculations.     

Electronic state of push-pull alkenes: an experimental dynamic NMR and theoretical ab initio MO study

The (1)H and (13)C NMR spectra of a number of push-pull alkenes were recorded and the (13)C chemical shifts calculated employing the GIAO perturbation method. Of the various levels of theory tried, MP2 calculations with a triple-zeta-valence basis set were found to be the most effective for providing reliable results. The effect of the solvent was also considered but only by single-point calculations. Generally, the agreement between the experimental and theoretically calculated (13)C chemical shifts was good with only the carbons of the carbonyl, thiocarbonyl, and cyano groups deviating significantly. The substituents on the different sides of the central C=C partial double bond were classified qualitatively with respect to their donor (S,S < S,N < N,N) and acceptor properties (C identical with N < C=O < C=S) and according to the ring size on the donor side (6 < 7 < 5). The geometries of both the ground (GS) and transition states (TS) of the restricted rotation about the central C=C partial double bond were also calculated at the HF and MP2 levels of theory and the free energy differences compared with the barriers to rotation determined experimentally by dynamic NMR spectroscopy. Structural differences between the various push-pull alkenes were reproduced well, but the barriers to rotation were generally overestimated theoretically. Nevertheless, by correlating the barriers to rotation and the length of the central C=C partial double bonds, the push-pull alkenes could be classified with respect to the amount of hydrogen bonding present, the extent of donor-acceptor interactions (the push-pull effect), and the level of steric hindrance within the molecules. Finally, by means of NBO analysis of a set of model push-pull alkenes (acceptors: -C identical with N, -CH=O, and -CH=S; donors: S, O, and NH), the occupation numbers of the bonding pi orbitals of the central C=C partial double bond were shown to quantitatively describe the acceptor powers of the substituents and the corresponding occupation numbers of the antibonding pi orbital the donor powers of the substituents. Thus, for the first time an estimation of both the acceptor and the donor properties of the substituents attached to the push-pull double bond have been separately quantified. Furthermore, both the balance between strong donor/weak acceptor substituents (and vice versa) and the additional influences on the barriers to rotation (hydrogen bonding and steric hindrance in the GSs and TSs) could be differentiated.     

All electron ab initio investigations of the electronic states of the MoN molecule

The low lying electronic states of the molecule MoN were investigated by performing all electron ab initio multi-configuration self-consistent-field (CASSCF) calculations. The relativistic corrections for the one electron Darwin contact term and the relativistic mass-velocity correction were determined in perturbation calculations. The electronic ground state is confirmed as being ⁴∑⁻. The chemical bond of MoN has a triple bond character because of the approximately fully occupied delocalized bonding π and σ orbitals. The spectroscopic constants for the ground state and ten excited states were derived. The excited doublet states ²∑⁻, ²Γ, ²Δ, and ²∑⁺ are found to be lower lying than the ⁴Π state that was investigated experimentally. Elaborate multi-configuration configuration-interaction (MRCI) calculations were carried out for the states ⁴∑⁻ and ⁴∏ using various basis sets. The spectroscopic constants for the ⁴∑⁻ ground state were determined as r_e=1.636 Å and ω_e=1109 cm⁻¹, and for the ⁴∏ state as r_e=1.662 Å and ω_e=941 cm⁻¹. The values for the ground state are in excellent agreement with available experimental data. The MoN molecule is polar with a charge transfer from Mo to N. The dipole moment was determined as 2.11 D in the ⁴∑⁻ state and as 4.60 D in the ⁴∏ state. These values agree well with the revised experimental values determined from molecular Stark spectroscopic measurements. The dissociation energy, D_e, is determined as 5.17 eV, and D₀ as 5.10 eV.     

The structure of the phenol-nitrogen cluster: a joint experimental and ab initio study

The rotationally resolved LIF spectra of four different isotopomers of the phenol--nitrogen cluster have been measured to elucidate the structural parameters of the cluster in ground and electronically excited (S1) state. The fit of the rotational constants has been performed by a genetic algorithm and by an assigned fit to the line frequencies. The results of both methods are compared. The intermolecular structures are fit to the inertial parameters and are compared to the results of ab initio calculations for both states. This fit was performed under the restriction that the geometry of the monomer moieties do not change upon complexation. Of the remaining five intermolecular parameters two dihedral angles were fixed due to the planarity of the complex, which was inferred from the inertial defects of all isotopomers. The distance of the nearest nitrogen atom to the hydrogen atom of the phenolic hydroxy group is found to decrease upon electronic excitation of the chromophore considerably more than predicted from ab initio calculations. This deviation between theory and experiment can be traced back to the absence of electron-electron correlation in the performed complete active space self-consistent field calculations. The shortening of the OH...NN "hydrogen" bond upon electronic excitation is in agreement with the increased dipole moment of phenol in the S1-state.     

An ab initio approach to the mechanism of the Grignard reaction

The mechanism of the Grignard reaction is investigated for the first time in the light of ab initio SCF MO theory. The possible advantage of a single-electron transfer over a polar mechanism is discussed.     

A crossed beam and ab initio study of the reaction of atomic boron with ethylene

The reaction of atomic boron, B(2P), with the simplest alkene, C2H4, has been investigated under single collision conditions in crossed beam experiments with mass spectrometric detection. Our experimental data clearly showed that the atomic boron versus hydrogen exchange reaction led to molecule(s) of gross formula C2H3B via bound intermediate(s). According to the experimentally derived fraction of the available energy released as product translational energy, we propose that an important reaction pathways is the one leading to the borirene plus atomic hydrogen and/or the one leading to ethynylborane plus atomic hydrogen. The experimental results are accompanied by electronic structure calculations of the relevant potential energy surface and RRKM estimates of the product branching ratio. According to RRKM calculations, within the limit of complete energy randomization, the three isomers borirene, BH=C=CH2 and BH2-CCH, are all formed, with BH2-CCH being the dominant one. The discrepancies between the trend of the product translational energy distributions and the picture emerging from RRKM estimates are a symptom that a statistical treatment is not warranted for this system.     

Multireference ab initio calculations on reaction intermediates of the multicopper oxidases

The multicopper oxidases (MCOs) couple the four-electron reduction of dioxygen to water with four one-electron oxidations of various substrates. Extensive spectroscopic studies have identified several intermediates in the MCO catalytic cycle, but they have not been able to settle the structures of three of the intermediates, viz. the native intermediate (NI), the peroxy intermediate (PI), and the peroxy adduct (PA). The suggested structures have been further refined and characterized by quantum mechanical/molecular mechanical (QM/MM) calculations. In this paper, we try to establish a direct link between theory and experiment, by calculating spectroscopic parameters for these intermediates using multireference wave functions from the multistate CASPT2 and MRDDCI2 methods. Thereby, we have been able to reproduce low-spin ground states (S = 0 or S = 1/2) for all the MCO intermediates, as well as a low-lying (approximately 150 cm-1) doublet state and a doublet-quartet energy gap of approximately 780 cm-1 for the NI. Moreover, we reproduce the zero-field splitting (approximately 70 cm-1) of the ground 2E state in a D3 symmetric hydroxy-bridged trinuclear Cu(II) model of the NI and obtain a quantitatively correct quartet-doublet splitting (164 cm-1) for a mu3-oxo-bridged trinuclear Cu(II) cluster. All results support the suggestion that the NI has an O2- atom in the center of the trinuclear cluster, whereas both the PI and PA have an O22- ion in the center of the cluster, in agreement with the QM/MM results and spectroscopic measurements.     

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.     

Solvent-dependent stereoselectivity in a Still-Wittig rearrangement: an experimental and ab initio study

[see reaction]. The Still-Wittig rearrangement gave opposite selectivities for (Z:E)-alkenes in THF (3:1) vs toluene (1:3) in the synthesis of serine-proline dipeptide amide isosteres. Four transition states leading to (Z)-and (E)-alkenes with THF and without (representing toluene) were identified by ab initio calculations at the 3-21G* level. The calculated (Z:E)-ratios with THF (4.7:1) and without THF (1:3.2) suggested that the transition state geometries and energies were well-represented by the calculations.     

A simple treatment of intermolecular interactions: Synthesis of ab initio calculations and combination rules

A new technique for a simple and efficient treatment of intermolecular interactions is proposed and tested. The method is based on an approximation of the first order SCF term E_SCF⁽¹⁾ which is the most structured contribution to the total interaction. E_SCF⁽¹⁾ is represented by a site–site potential V of (exp, 1/R)-type, which accounts for the exchange plus penetration and the long range Coulomb forces (by means of a point charge model). The individual contributions to V are obtained by means of combination rules from corresponding site parameters of interacting molecules. The site parameters are consequently molecular and not intermolecular properties and can conveniently be determined by probing a molecule with appropriate test particles. Site parameters are reported for He, Ne, Ar, N₂, CO, CO₂, CS₂, and HCl. Comprisons show close agreement of V with E which in turn is close to ΔE_SCF if polarization and charge transfer effects are small.     

Comparison of ab initio calculated and experimental methyl-top moments of inertia

The methyl-top moments of inertia and planar moments of inertia of a large number of compounds have been obtained from rotational spectroscopic data and are compared with the corresponding quantities obtained from ab initio geometries. Ab initio geometry refinements have been performed with the 4-21G basis set using standard gradient techniques. High correlation is found between the spectroscopic and calculated values, indicating the possibility of using experimental methyl-top moments of inertia as a source of structural information on methyl groups.     

Pd-N to Pd-O rearrangement for a carbamate synthesis from carbon dioxide and methane: a density functional and ab initio molecular dynamics metadynamics study

We investigated the key step of Pd-N to Pd-O rearrangement from a model catalytic cycle for the activation of carbon dioxide and methane with static quantum chemical calculations and metadynamics simulation. Our calculations show that different bottlenecks appear in the catalytic cycle but that the investigated rearrangement of the Pd-N to Pd-O bounded complex has a barrier ΔG(#)/ΔF(#) of approximately 20 kJ mol?1 and is therefore accessible at ambient reaction conditions.     

Comparison of nitroaldol reaction mechanisms using accurate ab initio calculations

In the nitroaldol reaction, condensation between a nitroalkane and an aldehyde yields a nitroalcohol that can undergo dehydration to yield a nitroalkene. Amine-functionalized, MCM-41-type mesoporous silica nanosphere (MSN) materials have been shown to selectively catalyze this reaction. Gas-phase reaction paths for the several competing mechanisms for the nitroaldol reaction have been mapped out using second-order perturbation theory (MP2). Improved relative energies were determined using singles and doubles coupled cluster theory with perturbative triples, CCSD(T). The mechanism in the absence of a catalyst was used to provide a baseline against which to assess the impact of the catalyst on both the mechanism and the related energetics. Catalyzed mechanisms can either pass through a nitroalcohol intermediate as in the classical mechanism or an imine intermediate.     

Mechanisms of methanol decomposition on platinum: A combined experimental and ab initio approach

The dual path mechanism for methanol decomposition on well-defined low Miller index platinum single crystal planes, Pt(111), Pt(110), and Pt(100), was studied using a combination of chronoamperometry, fast scan cyclic voltammetry, and theoretical methods. The main focus was on the electrode potential range when the adsorbed intermediate, CO(ad), is stable. At such "CO stability" potentials, the decomposition proceeds through a pure dehydrogenation reaction, and the dual path mechanism is then independent of the electrode-substrate surface structure. However, the threshold potential where the decomposition of methanol proceeds via parallel pathways, forming other than CO(ad) products, depends on the surface structure. This is rationalized theoretically. To gain insights into the controlling surface chemistry, density functional theory calculations for the energy of dehydrogenation were used to approximate the potential-dependent methanol dehydrogenation pathways over aqueous-solvated platinum interfaces.     

Molecular dynamics investigations of chlorine peroxide dissociation on a neural network ab initio potential energy surface

Molecular dissociation of chlorine peroxide (ClOOCl), which consists of two elementary dissociation channels (of Cl–O and O–O), is investigated using molecular dynamics simulations on a neural network-fitted potential energy surface constructed by MP2 calculations with the 6-311G(d,p) basis set. When relaxed scans of the surface are executed, we observe that Cl–O dissociation is extremely reactive with a low barrier height of 0.1928 eV (18.602 kJ/mol), while O–O bond scission is less reactive (0.7164 eV or 69.122 kJ/mol). By utilizing the “novelty sampling” method, 35,006 data points in the ClOOCl configuration hyperspace are collected, and a 40-neuron feed-forward neural network is employed to fit approximately 90% of the data to produce an analytic potential energy function. The mean absolute error and root mean squared error of this fit are reported as 0.0078 eV (0.753 kJ/mol) and 0.0137 eV (1.322 kJ/mol), respectively. Finally, quasi-classical molecular dynamics is executed at various levels of internal energy (from 0.8 to 1.3 eV) to examine the bond ruptures. The two first-order rate coefficients are computed statistically, and the results range from 5.20 to 22.67 ps⁻¹ for Cl–O dissociation and 3.72–8.35 ps⁻¹ for O–O dissociation. Rice-Ramsperger-Kassel theory is utilized to classically correlate internal energies to rate coefficients in both cases, and the plots exhibit very good linearity, thus can be employed to predict rate coefficients at other internal energy levels with good reliability.     

Catalytic reaction mechanism of L-lactate dehydrogenase: an ab initio study

Studies on the catalytic reaction mechanism of L-lactate dehydrogenase have been carried out by using quantum chemical ab initio calculation at HF/6-31G* level. It is found that the interconversion reaction of pyruvate to L-lactate is dominated by the hydride ion HR- transfer, and the transfers of the hydride ion HR and proton HR are a quasi-coupled process, in which the energy barrier of the transition state is about 168.37 kJ/mol. It is shown that the reactant complex is 87.61 kJ/mol lower, in energy, than the product complex. The most striking features in our calculated results are that pyridine ring of the model cofactor is a quasi-boat-like configuration in the transited state, which differs from a planar conformation in some previous semiempirical quantum chemical studies. On the other hand, the similarity in the structure and charge between the HR transfer process and the hydrogen bonding with lower barrier indicates that the HR transfer process occurs by means of an unusual manner. In addition,     

Infrared experimental and ab initio quantum mechanical studies of 2-mercaptopyrimidine tautomers

Results are presented from ab initio SCF(3-21G*) calculations for the geometries and vibrational spectra (wavenumbers and absolute intensifies) of the thiol and thione tautomers of 2-mercaptopyrimidine. The results of calculations are compared with available experimental data, particularly with the reported vibrational spectra of the molecule isolated in inert gas matrices (Ar, N₂) and in crystalline state. The calculations of the normal modes predicted the experimental spectrum close enough to allow reliable assignment of most of the bands. The thiol⇌⇌thione tautomerism of the molecule is discussed. Matrix isolated monomers were observed in the thiol form only. That agrees with the results of ab initio calculations of internal energies of the tautomers [SCF(6-31Gu*) + MBPT(2)(6-31G*) + vib(0)(3-21G*); at the SCF(3-21G*) geometries] which predict the energy of thiol form to be ≈33 kJ mol⁻¹ lower than that of thione form. In the crystalline state the hydrogen-bonded associations in the thione form dominate while in disordered amorphous layers, in matrices with a high guest-to-host ratio and in annealed matrices the associations both in thiol and thione form were observed.