Reaction Barrier Heights Research Articles

Revisiting the reaction energetics of the CH3O˙ + O2 (3Σ-) reaction: the crucial role of post-CCSD(T) corrections.

The CH3O˙ + O2 reaction has been studied by means of high level ab initio calculations to predict the reaction energy and barrier height with chemical accuracy. We have employed post-CCSD(T) corrections in terms of partial quadratic excitations at the coupled cluster level, along with relativistic, core, spin-orbit and diagonal Born-Oppenheimer corrections, to estimate the barrier height and energetics for the title reaction. After including all the corrections, the reaction energy and barrier height were found to be -26.86 and 2.59 kcal mol-1, respectively, which is in good agreement with the corresponding experimentally derived values. Using this information, we have also calculated the rate constants for the title reaction employing transition state theory (TST) in conjunction with zero curvature tunneling (ZCT) within a temperature range of 250 to 900 K.

Performance and Scope of Perturbative Corrections to Random-Phase Approximation Energies

It has been suspected since the early days of the random-phase approximation (RPA) that corrections to RPA correlation energies result mostly from short-range correlation effects and are thus amenable to perturbation theory. Here we test this hypothesis by analyzing formal and numerical results for the most common beyond-RPA perturbative corrections, including the bare second-order exchange (SOX), second-order screened exchange (SOSEX), and approximate exchange kernel (AXK) methods. Our analysis is facilitated by efficient and robust algorithms based on the resolution-of-the-identity (RI) approximation and numerical frequency integration, which enable benchmark beyond-RPA calculations on medium- and large-size molecules with size-independent accuracy. The AXK method systematically improves upon RPA, SOX, and SOSEX for reaction barrier heights, reaction energies, and noncovalent interaction energies of main-group compounds. The improved accuracy of AXK compared with SOX and SOSEX is attributed to stronger screening of bare SOX in AXK. For reactions involving transition-metal compounds, particularly 3d transition-metal dimers, the AXK correction is too small and can even have the wrong sign. These observations are rationalized by a measure α̅ of the effective coupling strength for beyond-RPA correlation. When the effective coupling strength increases beyond a critical α̅ value of approximately 0.5, the RPA errors increase rapidly and perturbative corrections become unreliable. Thus, perturbation theory can systematically correct RPA but only for systems and properties qualitatively well captured by RPA, as indicated by small α̅ values.

Describing strong correlation with fractional-spin correction in density functional theory

An effective fractional-spin correction is developed to describe static/strong correlation in density functional theory. Combined with the fractional-charge correction from recently developed localized orbital scaling correction (LOSC), a functional, the fractional-spin LOSC (FSLOSC), is proposed. FSLOSC, a correction to commonly used functional approximations, introduces the explicit derivative discontinuity and largely restores the flat-plane behavior of electronic energy at fractional charges and fractional spins. In addition to improving results from conventional functionals for the prediction of ionization potentials, electron affinities, quasiparticle spectra, and reaction barrier heights, FSLOSC properly describes the dissociation of ionic species, single bonds, and multiple bonds without breaking space or spin symmetry and corrects the spurious fractional-charge dissociation of heteroatom molecules of conventional functionals. Thus, FSLOSC demonstrates success in reducing delocalization error and including strong correlation, within low-cost density functional approximation.

Photoinduced hydrogen-transfer reactions in pyridine-water clusters: Insights from excited-state electronic-structure calculations

Recent experiments have shown that photoexcited pyridine can abstract a hydrogen atom from a water molecule in pyridine-water clusters containing at least four water molecules. To explain these findings, we explored the electron-driven proton-transfer reaction from water to pyridine in pyridine-(H2O)n, n = 1–4, complexes with ab initio methods. It is shown that the photoinduced electron/proton transfer reaction is energetically possible for all clusters. The calculations reveal that the hydrogen bond between pyridine and the adjacent water molecule is weakened (strengthened) in the 1nπ∗ (1ππ∗) excited state, which is unfavorable (favorable) for the H-atom transfer reaction. For pyridine-(H2O)n clusters with n = 1–3, the steepest descent path leads to a local minimum of 1nπ∗ character, while for the pyridine-(H2O)4 cluster, this path leads to a local minimum of 1ππ∗ character. The transition state calculations show the presence of this 1ππ∗ minimum substantially reduces the barrier height for the H-atom transfer reaction. These results provide a tentative explanation of the experimental observations.

Impact of Post-CCSD(T) Corrections on Reaction Energetics and Rate Constants of the OH• + HCl Reaction.

High level ab initio calculations have been performed to predict the reaction energy and barrier height for the OH• + HCl reaction. After including the effect of full quadratic excitations at the coupled cluster level, in addition to core, relativistic, spin-orbit, and diagonal Born-Oppenheimer corrections, we found the values of reaction energy and barrier height to be -15.29 and +2.38 kcal mol-1, respectively. Employing this reaction energy and barrier height, we used variational transition state theory in conjunction with small curvature tunneling to calculate the rate constants within a temperature range from 138 to 1000 K. The calculated rate constants were found to be in good agreement with available experimental results throughout the whole temperature range.

Wavefunction-like Correlation Model for Use in Hybrid Density Functionals.

We present Unsöld-W12 (UW12), an approximation to the correlation energy of molecules that is an explicit functional of the single-particle reduced-density matrix. The approximation resembles one part of modern explicitly correlated second-order Møller-Plesset (MP2) theory and is intended as an alternative to MP2 in double-hybrid exchange-correlation functionals. Orbital optimization with UW12 is straightforward, and the UW12 energy is evaluated without a double summation over unoccupied orbitals, leading to a faster basis-set convergence than is seen in double-hybrid functionals. We suggest a one-parameter hybrid exchange-correlation functional XCH-BLYP-UW12. XCH-BLYP-UW12 is similar to double-hybrid functionals, but contains UW12 correlation instead of MP2 correlation. We find that XCH-BLYP-UW12 is more accurate than the existing double-hybrid functional B2-PLYP for small-molecule main-group reaction barrier heights and has roughly the same accuracy as the existing hybrid functional B3LYP for atomization energies.

QM/MM Molecular Dynamics Investigations of the Substrate Binding of Leucotriene A4 Hydrolase: Implication for the Catalytic Mechanism.

LTA4H is a monozinc bifunctional enzyme which exhibits both aminopeptidase and epoxide hydrolase activities. Its dual functions in anti- and pro-inflammatory roles have attracted wide attention to the inhibitor design. In this work, we tried to construct Michaelis complexes of LTA4H with both a native peptide substrate and LTA4 molecule using combined quantum mechanics and molecular mechanics molecular dynamics simulations. First of all, the zinc ion is coordinated by H295, H299, and E318. For its aminopeptidase activity, similar to conventional peptidases, the fourth ligand to the zinc ion is suggested to be an active site water, which is further hydrogen bonded with a downstream glutamic acid, E296. For the epoxide hydrolase activity, the fourth ligand to the zinc ion is found to be an epoxy oxygen atom. The potential of mean force calculation indicates about an 8.5 kcal/mol activation barrier height for the ring-opening reaction, which will generate a metastable carbenium intermediate. Subsequent frontier molecular orbital analyses suggest that the next step would be the nucleophilic attacking reaction at the C12 atom by a water molecule activated by D375. Our simulations also analyzed functions of several important residues like R563, K565, E271, Y383, and Y378 in the binding of peptide and LTA4.

When Hartree-Fock exchange admixture lowers DFT-predicted barrier heights: Natural bond orbital analyses and implications for catalysis

The conventional wisdom in density functional theory (DFT) is that standard approximations systematically underestimate chemical reaction barrier heights and that exact (Hartree-Fock-like, HF) exchange admixture improves this. This conventional wisdom is inconsistent with the good performance of functionals without HF exchange for many reactions on metal catalyst surfaces. We have studied several "anomalous" gas-phase reactions where this conventional wisdom is upended, and a HF exchange admixture decreases or does not affect the predicted barrier heights [Mahler et al., J. Chem. Phys. 146, 234103 (2017)]. Here we show how natural bond orbital analyses can help identify and explain some factors that produce anomalous barriers. Applications to pnictogen inversion, standard benchmark reaction barrier datasets, and a model Grubbs catalyst illustrate the utility of this approach. This approach is expected to aid DFT users in choosing appropriate functionals, and aid DFT developers in devising DFT approximations generally applicable to catalysis.

Non-empirical exchange-correlation parameterizations based on exact conditions from correlated orbital theory

Some of the exact conditions provided by the correlated orbital theory are employed to propose new non-empirical parameterizations for exchange-correlation functionals from Density Functional Theory (DFT). This reparameterization process is based on range-separated functionals with 100% exact exchange for long-range interelectronic interactions. The functionals developed here, CAM-QTP-02 and LC-QTP, show mitigated self-interaction error, correctly predict vertical ionization potentials as the negative of eigenvalues for occupied orbitals, and provide nice excitation energies, even for challenging charge-transfer excited states. Moreover, some improvements are observed for reaction barrier heights with respect to the other functionals belonging to the quantum theory project (QTP) family. Finally, the most important achievement of these new functionals is an excellent description of vertical electron affinities (EAs) of atoms and molecules as the negative of appropriate virtual orbital eigenvalues. In this case, the mean absolute deviations for EAs in molecules are smaller than 0.10 eV, showing that physical interpretation can indeed be ascribed to some unoccupied orbitals from DFT.

A general range-separated double-hybrid density-functional theory.

A range-separated double-hybrid (RSDH) scheme which generalizes the usual range-separated hybrids and double hybrids is developed. This scheme consistently uses a two-parameter Coulomb-attenuating-method (CAM)-like decomposition of the electron-electron interaction for both exchange and correlation in order to combine Hartree-Fock exchange and second-order Møller-Plesset (MP2) correlation with a density functional. The RSDH scheme relies on an exact theory which is presented in some detail. Several semi-local approximations are developed for the short-range exchange-correlation density functional involved in this scheme. After finding optimal values for the two parameters of the CAM-like decomposition, the RSDH scheme is shown to have a relatively small basis dependence and to provide atomization energies, reaction barrier heights, and weak intermolecular interactions globally more accurate or comparable to range-separated MP2 or standard MP2. The RSDH scheme represents a new family of double hybrids with minimal empiricism which could be useful for general chemical applications.

Simple Modifications of the SCAN Meta-Generalized Gradient Approximation Functional.

We analyzed various possibilities to improve upon the SCAN meta-generalized gradient approximation density functional obeying all known properties of the exact functional that can be satisfied at this level of approximation. We examined the necessity of locally satisfying a strongly tightened lower bound for the exchange energy density in single-orbital regions, the nature of the error cancellation between the exchange and correlation parts in two-electron regions, and the effect of the fourth-order term in the gradient expansion of the correlation energy density. We have concluded that the functional can be modified to separately reproduce the exchange and correlation energies of the helium atom by locally releasing the strongly tightened lower bound for the exchange energy density in single-orbital regions, but this leads to an unbalanced improvement in the single-orbital electron densities. Therefore, we decided to keep the FX ≤ 1.174 exact condition for any single-orbital density, where FX is the exchange enhancement factor. However, we observed a general improvement in the single-orbital electron densities by revising the correlation functional form to follow the second-order gradient expansion in a wider range. Our new revSCAN functional provides more-accurate atomization energies for the systems with multireference character, compared to the SCAN functional. The nonlocal VV10 dispersion-corrected revSCAN functional yields more-accurate noncovalent interaction energies than the VV10-corrected SCAN functional. Furthermore, its global hybrid version with 25% of exact exchange, called revSCAN0, generally performs better than the similar SCAN0 for reaction barrier heights. Here, we also analyzed the possibility of the construction of a local hybrid from the SCAN exchange and a specific locally bounded nonconventional exact exchange energy density. We predict compatibility problems since this nonconventional exact exchange energy density does not really obey the strongly tightened lower bound for the exchange energy density in single-orbital regions.

A computational investigation of the sulphuric acid‐catalysed 1,4‐hydrogen transfer in higher Criegee intermediates

AbstractCriegee intermediates (CIs) are formed during the ozonolysis of unsaturated hydrocarbons in the troposphere. The fate of CIs is of critical importance to tropospheric oxidation chemistry, particularly in the context of radical and secondary organic aerosol formation. Using the high‐level ab initio G4(MP2) method, we investigate the 1,4 hydrogen shift reaction in CIs formed from ozonolysis of two common biogenic hydrocarbons: isoprene and α‐pinene. We consider the uncatalysed reaction, as well as the reaction catalysed by a water molecule and by sulphuric acid. We show that sulphuric acid is a very effective catalyst, leading to a barrierless tautomerization relative to the free reactants and to very low reaction barrier heights relative to the reactant complexes. In particular, we obtain reaction barrier heights of Δ = 24.5 (isoprene CI) and 8.4 (α‐pinene CI) kJ mol−1 relative to the reactant complexes. Given the reaction of OH radicals with SO2 in the troposphere can ultimately yield sulphuric acid, these findings may have significant consequences for current atmospheric chemical models for regions of high sulphur concentrations.

Heavy Atom Secondary Kinetic Isotope Effect on H-Tunneling.

Although frequently employed, heavy atom kinetic isotope effects (KIE) have not been reported for quantum mechanical tunneling reactions. Here we examine the secondary KIE through 13C-substitution of the carbene atom in methylhydroxycarbene (H3C-C̈-OH) in its [1,2]H-tunneling shift reaction to acetaldehyde (H3C-CHO). Our study employs matrix-isolation IR spectroscopy in various inert gases and quantum chemical computations. Depending on the choice of the matrix host gas, the KIE varies within a range of 1.0 in xenon to 1.4 in neon. A KIE of 1.1 was computed using the Wentzel-Kramers-Brillouin (WKB) CVT/SCT, and instanton approaches for the gas phase at the B3LYP/cc-pVTZ level of theory. Computations with explicit consideration of the noble gas environment indicate that the surrounding atoms influence the tunneling reaction barrier height and width. The tunneling half-lives computed with the WKB approach are in good agreement with the experimental results in the different noble gases.

Utilization of generalized energy-based fragmentation method on the study of hydrogen abstraction reactions of large methyl esters

Accurate reaction energies and barrier heights are essential for the construction of reliable combustion kinetics models of various fuels. Nevertheless, the computational cost for electronic energy calculations using high-level ab initio methods increases dramatically with the size of molecules. A solution to this problem is to utilize a generalized energy-based fragmentation (GEBF) approach, as it has been found to be effective in reducing the scaling of the computational cost in calculation of energetics and other molecular properties for many large molecules, clusters, and crystals with various quantum chemistry methods. This work attempts to apply this GEBF approach in the study of one important type of reactions of large methyl esters, i.e., the hydrogen abstraction reactions by hydrogen atoms. The energies of stationary points on the potential energy surfaces were examined using both conventional quantum chemistry methods and the GEBF method at the QCISD(T)/CBS// M06-2X/6-311 + + g(d,p) level for CnH2n+1COOCH3 (n = 4, 5) + H reactions. The results show that the unsigned energy deviation of the GEBF method from the conventional method is less than 0.1 kcal/mol, while the computational time is greatly reduced, e.g. up to 90% at the QCISD(T)/cc-pVTZ level. Based on the quantum chemistry calculations, rate constants of the hydrogen abstraction reactions of CnH2n+1COOCH3 (n = 4, 5, 8) by H atoms were computed.

Barriometry - an enhanced database of accurate barrier heights for gas-phase reactions.

The kinetics of many reactions are critically dependent upon the barrier heights for which accurate determination can be difficult. From the perspective of attaining such quantities using computational quantum chemistry, it is important to appropriately validate routine and efficient methodologies such as density functional theory (DFT) procedures. In the present study, we embark on the journey of establishing diverse databases using a consistent high-level quantum chemistry procedure, against which new and existing methodologies can be assessed. Thus, we have used the composite protocol W3X-L to provide more than 100 refined reference values for existing databases [e.g., Y. Zhao and D. G. Truhlar, J. Phys. Chem. A, 2005, 109, 5656] and additionally establish benchmark data that are of interest to atmospheric and combustion chemists. While our endeavor has just begun, assessment of various DFT methods with our existing results lends support to the use of MN15 as an adequate method for general kinetics applications. We also recommend the use of less-costly W2X and WG composite protocols for obtaining adequately accurate reference thermochemical values for larger molecular systems.

Atmospheric Oxidation of Furan and Methyl-Substituted Furans Initiated by Hydroxyl Radicals.

The atmospheric oxidation mechanism of furan and methylfurans (MFs) initiated by OH radicals is studied using high-level quantum chemistry and kinetic calculations. The reaction starts mainly with OH addition to the C2/C5-position, forming highly chemically activated adduct radical R2*/R5*, which would either be stabilized by collision or promptly isomerize to R2B*/R5B* by breaking the C2-O/C5-O bond and then isomerize to other conformers of R2B/R5B by internal rotations. Under the atmospheric conditions, the ring-retaining radical R2/R5 would recombine with O2 and be converted to a 5-hydroxy-2-furanone compound and a compound containing epoxide, ester, and carbonyl functional groups, while the ring-opening radicals R2B/R5B would react with O2 and form unsaturated 1,4-dicarbonyl compounds. RRKM-ME calculations on the fate of R2*/R5* from the addition of OH and furans predict that the fractions of R2B/R5B formation, i.e., the molar yields of the corresponding dicarbonyl compounds, are 0.73, 0.43, 0.26, 0.07, and 0.28 for furan, 2-MF, 3-MF, 2,3-DMF, and 2,5-DMF, respectively, at 298 K and 760 Torr when using the RHF-UCCSD(T)-F12a/cc-pVDZ-F12 reaction energies and barrier heights. The predicted yields for dicarbonyl compounds agree reasonably with recent experimental measurements. Calculations here also suggest high yields of ring-retaining 5-hydroxy-2-furanone compounds, which might deserve further study.

A Computational Investigation of the Uncatalysed and Water-Catalysed Acyl Rearrangements in Ingenol Esters

Ingenol esters have been identified as potent anticancer and HIV latency reversing agents. Ingenol-3-angelate was recently approved as a topical treatment for precancerous actinic keratosis skin lesions. It was found, however, that ingenol esters can undergo a series of acyl rearrangements, which may affect their biological potency and the shelf-life of drug formulations. We use double-hybrid density functional theory to explore the mechanisms for the uncatalysed and water-catalysed acyl migrations in a model ingenol ester. The uncatalysed reaction may proceed either via a concerted mechanism or via a stepwise mechanism that involves a chiral orthoester intermediate. We find that the stepwise pathway is kinetically preferred by a significant amount of ΔΔH‡298 = 44.5 kJ mol−1. The uncatalysed 3-O-acyl to 5-O-acyl and 5-O-acyl to 20-O-acyl stepwise rearrangements involve cyclisation and ring-opening steps, both concomitant with a proton transfer. We find that the ring-opening step is the rate-determining step for both rearrangements, with reaction barrier heights of ΔH‡298 = 251.6 and 177.1 kJ mol−1 respectively. The proton transfers in the cyclisation and ring-opening steps may be catalysed by a water molecule. The water catalyst reduces the reaction barrier heights of these steps by over 90 kJ mol−1.

DFT study on the alternative NH3 formation path and its functional group effect

This study attempts to better understand through DFT calculations the NH3 formation mechanism associated with the reaction energy and barrier height. The formation of NH3 can be completed by (1) heterogeneous nitrogen migration; (2) NH2 desorption; and (3) homogeneous H-abstraction. Several transition structures have been characterized and we can conclude from energy analysis of these species that the heterogeneous nitrogen migration is the rate determining step and the formation of NH3 is largely dependent on the char-N stability. The NH3 formation is affected not only by the availability of H radicals but also by the vicinity of functional groups. The functional group effect is then investigated and further analyzed by the transferring of valence electrons and NBO charges. The results seem to be clear that NH3 formation is group-dependent. For example, the OH group acting as an electron donor will activate the carbonaceous surface and decrease the barrier height and the endothermicity, while the electron-withdrawing NO2 group plays an opposite role. Our work gives the molecular-level understanding for the previous experimental finding that oxygen-containing functional groups are important for the NH3 formation.

Revised M06-L functional for improved accuracy on chemical reaction barrier heights, noncovalent interactions, and solid-state physics

We present the revM06-L functional, which we designed by optimizing against a larger database than had been used for Minnesota 2006 local functional (M06-L) and by using smoothness restraints. The optimization strategy reduced the number of parameters from 34 to 31 because we removed some large terms that increased the required size of the quadrature grid and the number of self-consistent-field iterations. The mean unsigned error (MUE) of revM06-L on 422 chemical energies is 3.07 kcal/mol, which is improved from 3.57 kcal/mol calculated by M06-L. The MUE of revM06-L for the chemical reaction barrier height database (BH76) is 1.98 kcal/mol, which is improved by more than a factor of 2 with respect to the M06-L functional. The revM06-L functional gives the best result among local functionals tested for the noncovalent interaction database (NC51), with an MUE of only 0.36 kcal/mol, and the MUE of revM06-L for the solid-state lattice constant database (LC17) is half that for M06-L. The revM06-L functional also yields smoother potential curves, and it predicts more-accurate results than M06-L for seven out of eight diversified test sets not used for parameterization. We conclude that the revM06-L functional is well suited for a broad range of applications in chemistry and condensed-matter physics.

The addition reactions of germylenoid H2GeAlCl3 with ethylene: a theoretical investigation.

Theoretical calculations using the M062X and QCISD methods were performed on the addition reactions of the aluminum germylenoid H2GeAlCl3 with ethylene. The most two stable structures of germylenoid H2GeAlCl3, i.e., the p-complex and three-membered ring structures, respectively, were employed as reactants. The calculated results indicate that, for the p-complex, H2GeAlCl3 there are two pathways, I and II, of which path I involves just one transition state, while path II involves two transition states between reactants and products. Comparing the reaction barrier heights of path I (44.6kJmol-1) and II (37.6kJmol-1), the two pathways are competitive, with similar barriers under the same conditions, while for the three-membered ring structure, another two pathways, III and IV, also exist. Path III has one transition state; however, in path IV, two transition states exist. By comparing their barrier heights, path III (barrier height 39.2kJmol-1) could occur more easily than path IV (barrier height 92.8kJmol-1). Considering solvent effects on these addition reactions, the PCM model and CH2Cl2 solvent were used in calculations, and the calculated results demonstrate that CH2Cl2 solvent is unfavorable for the reactions, except for path II. In CH2Cl2 solvent, paths II and III are more favorable than paths I and IV.