Ab initio quantum chemical study of the formation, decomposition and isomerization of the formaldiminoxy radical (CH2NO): comparison of the Gaussian-2 and CASPT2 techniques in the calculation of potential energy surfaces

The reaction between triplet methylene and nitric oxide, producing the formaldiminoxy (CH₂NO) radical, and the subsequent decomposition and isomerization reactions of CH₂NO have been studied using ab␣initio quantum chemical techniques that include the Gaussian-2 (G2), CASSCF and CASPT2 methods. Stationary points on the potential energy surfaces were located at MP2/6-31G(d) and CASSCF/cc-pVDZ levels of theory, while the electronic energies were determined using G2, G2(MP2), QCISD(T)/cc-pVTZ, RCCSD(T)/cc-pVTZ and CASPT2/cc-pVTZ approaches. G2 is believed to be reliable at equilibrium geometries, but the determination of certain transition state geometries and energies requires a MCSCF-based approach. The calculations suggest that CH₂NO (²A^′) forms in a barrierless reaction and could readily decompose to H+HCNO. A subsequent abstraction reaction then results in H₂+CNO. No molecular elimination channel was found. An alternative pathway is the formation of CH₂ON, which readily isomerizes to CH₂NO. Received: 8 May 1998 / Accepted: 11 August / Published online: 9 October 1998     

Cyanovinyl radical: an illustration of the poor performance of unrestricted perturbation theory and density functional theory procedures in calculating radical stabilization energies

Stabilization energies for the 1-cyanovinyl radical (CH₂=CCN) have been calculated using a variety of conventional ab initio (M?ller–Plesset, quadratic configuration interaction and coupled-cluster) and density functional theory (B-LYP, B3-LYP) procedures, as well as with a range of compound methods. Compared with a high-level benchmark value (that predicts a stabilization energy of 17.1 kJ mol⁻¹), UMP2 and UMP4 give the wrong sign and magnitude of the stabilization energy (both methods predicting desta- bilization instead of stabilization), while B-LYP and B3-LYP overestimate the degree of stabilization. The RMP2, RMP4, QCISD(T) and CCSD(T) techniques, and several, but not all, variants of G2 and CBS theories give radical stabilization energies in good agreement with the benchmark value. Received: 15 June 1998 / Accepted: 19 August 1998 /  Published online: 15 February 1999     

Adsorption and dissociation of the methanethiol (CH3SH) molecule on the Fe(100) surface

These contributions explore interaction modes between the methanethoil (CH₃SH) molecule and the Fe(100) surface via implementing accurate density functional theory (DFT) calculations with the inclusion of van der Waals corrections. We consider three adsorption sites over the Fe(100) surface, namely, top(T), bridge (B), and hollow (H) sites as potential catalytic active sites for the molecular and dissociative adsorption of the CH₃SH molecule. The molecular adsorption structures are found to occupy either B or T sites with former sites holding higher stability by 0.17 eV. The inclusion of van der Waals corrections refound to slightly alter adsorption energies. For instance, adsorption energies increased by ~ 0.18 and ~ 0.21 eV for B and T structure, respectively, in reference to values obtained by the plain generalized gradient approximation (GGA) functional. A stability ordering of the dissociation products was found to follow the sequence (CH₄, S) > (CH₃, S, H) > (─SCH_3, H) > (─CH₃, SH). The differential charge density distributions were examined to underpin prominent electronic contributing factors. Direct fission of C─S bond in the CH₃SH molecule attains exothermic values in the range 2.0 to 2.1 eV. The most energetically favorable sites for the surface-mediated fission of the thiol's S─H bond correspond to the structure where the ─SCH₃ and H are both situated on hollow sites with an adsorption energy of −2.43 eV. Overall, we found that inclusion of van der Waals functional to change the binding energies more noticeably in case of dissociative adsorption structures. The results presented herein should be instrumental in efforts that aim to design stand-alone Fe desulfurization catalysts.     

Thermochemistry and kinetics of the 2-butanone-4-yl CH3C(=O)CH2CH2• + O2 reaction system

Thermochemistry and kinetic pathways on the 2-butanone-4-yl (CH₃C(=O)CH₂CH₂•) + O₂ reaction system are determined. Standard enthalpies, entropies, and heat capacities are evaluated using the G3MP2B3, G3, G3MP3, CBS-QB3 ab initio methods, and the B3LYP/6-311g(d,p) density functional calculation method. The CH₃C(=O)CH₂CH₂• radical + O₂ association reaction forms a chemically activated peroxy radical with 35 kcal mol⁻¹ excess of energy. The chemically activated adduct can undergo RO−O bond dissociation, rearrangement via intramolecular hydrogen transfer reactions to form hydroperoxide-alkyl radicals, or eliminate HO₂ and OH. The hydroperoxide-alkyl radical intermediates can undergo further reactions forming ketones, cyclic ethers, OH radicals, ketene, formaldehyde, or oxiranes. A relatively new path showing a low barrier and resulting in reactive product sets involves peroxy radical attack on a carbonyl carbon atom in a cyclic transition state structure. It is shown to be important in ketones when the cyclic transition state has five or more central atoms.     

Ab-inito Calculations in Reductive Bond-breaking Reaction of C-X Bond in CH3X and CH2X2 with X = F and CI

MP4/6-31+G* level calculations are performed to study the reductive bond-breaking reaction of the C-X bond in halomethanes, CH₃X and CH₂X₂ where X is a fluorine atom or chlorine atom. This type of reaction involves a radical anion, after attaching an extra electron to the halomethane molecule, in which a C-X bond-breaking takes place. Products are a radical and a halogen anion. The equilibrium geometry and bond dissociation energy of the C-X bond thus found are in good agreement with previous theoretical and experimental results. The anomeric effect, electrostatic effect, and radical re-stabilization effect, are investigated to find their influences on bond length and bond dissociation energy in CH₃X and CH₂X₂. Potential energy curves are calculated for the reductive bond-cleavage process, and trends in activation energy for various cases are discussed.     

The saddle point of the nucleophilic substitution reaction Cl− + CH3Cl: results of large-scale coupled cluster calculations

On the basis of large-scale coupled cluster calculations including connectedz triple substitutions in a perturbative way, the geometrical parameters of the D _{3 h} saddle point of the Walden inversion reaction Cl⁻ + CH₃Cl′→ ClCH₃ + Cl′⁻ are predicted to be R _s (C—Cl) = 2.301 ? and r _s (C—H) = 1.069 ?. The barrier height with respect to the reactants is recommended to be 11.5 ± 1.0 kJ mol⁻¹. Connected triple substitutions lower the barrier height by almost a factor of 2, but have very little influence on the geometric structure of the saddle point. Received: 26 June 1998 / Accepted: 15 July 1998 / Published online: 28 September 1998     

The glycosyl C1′—N9 bond of deoxyadenosine and deoxyguanosine: response to electrophilic attacks on the purinic nitrogen atoms

Self-consistent-field computations shed light on two relevant conformations of deoxyadenosine (dA) and deoxyguanosine (dG): one with a pseudoequatorial C_1′N₉ glycosyl bond and the other, a slightly more stable one, with its C_1′N₉ bond in a bisectional orientation. In dA, both the N₃ and N₇ nitrogens are plausible sites for electrophilic attack, but only N₇ is a plausible site in dG. The addition of H⁺, CH₃ ⁺, C₂H₅ ⁺ or tert-C₄H₉ ⁺ onto N₇ does not provoke notable structural modifications and leaves the base of dA and dG in an antiperiplanar (or nearly antiperiplanar) position with respect to the sugar C_1′O_4′ bond, but N₃ additions cause the base to adopt a synperiplanar or strongly chiral position. This produces strong interactions between the purine and deoxyribose moieties, whose relief could aid the eventual cleavage of the glycosyl bond of dA. Addition of a radical cation onto N₇ reduces the dissociation energy of the glycosyl bond by an estimated 8 kcal mol⁻¹ in dA and 4 kcal mol⁻¹ in dG – a bond weakening likely to concur to a depurination of DNA induced by radical cations. Received: 13 September 1999 / Accepted: 3 February 2000 / Published online: 21 June 2000     

Gradient optimization of polarization exponents inab initio MO calculations on H2SO → HSOH and CH3SH → CH2SH2

Summary Analytical gradients were used to optimize the polarization function exponents in the 6-31G(d) and 6-31G(d, p) basis sets for the reactants, transition structures and products in the reactions H₂SO HSOH and CH₃SH CH₂SH₂. The optimizedd exponents on the heavy atoms change by ±10% in the course of the reactions and depend on the bonding of the heavy atoms. Thep exponents on the hydrogens change by as much as a factor of 5 and depend on the element to which the hydrogen is bonded and its valency. The effect of exponent optimization on the relative energies is small (±3 kcal/mol). With the 6-31G(d, p) basis set, optimization of the polarization exponents can make some of the bonds significantly more polar, as judged by the Mulliken charges.     

Reaction kinetics and thermochemistry of the chemically activated and stabilized primary ethyl radical of methyl ethyl sulfide,CH3SCH2CH2•, with O2 to CH3SCH2CH2OO•

Oxidation of methyl ethyl sulfide (CH₃SCH₂CH₃, methylthioethane, MES) under atmospheric and combustion conditions is initiated by hydroxyl radicals, MES radicals, generated after loss of a H atom via OH abstraction, will further react with O₂ to form chemically activated and stabilized peroxyl radical adducts. The kinetics of the chemically activated reaction between the CH₃SCH₂CH₂• radical and molecular oxygen are analyzed using quantum Rice-Ramsperger-Kassel theory for k(E) with master equation analysis and a modified strong-collision approach to account for further reactions and collisional deactivation. Thermodynamic properties of reactants, products, and transition states are determined by the B3LYP/6-31+G(2d,p), M062X/6-311+G(2d,p), ωB97XD/6-311+G(2d,p) density functional theory, and CBS-QB3, G3MP2B3, and G4 composite methods. The reaction of CH₃SCH₂CH₂• with O₂ forms an energized peroxy adduct CH₃SCH₂CH₂OO• with a calculated well depth of 34.1 kcal mol⁻¹ at the CBS-QB3 level of theory. Thermochemical properties of reactants, transition states, and products obtained under CBS-QB3 level are used for calculation of kinetic parameters. Reaction enthalpies are compared between the methods. The temperature and pressure-dependent rate coefficients for both the chemically activated reactions of the energized adduct and the thermally activated reactions of the stabilized adducts are presented. Stabilization and isomerization of the CH₃SCH₂CH₂OO• adduct are important under high pressure and low temperature. At higher temperatures and atmospheric pressure, the chemically activated peroxy adduct reacts to new products before stabilization. Addition of the peroxyl oxygen radical to the sulfur atom followed by sulfur-oxygen double bond formation and elimination of the methyl radical to form S(= O)CCO• + CH₃ (branching) is a potentially important new pathway for other alkyl-sulfide peroxy radical systems under thermal or combustion conditions.     

Complete basis set ab initio computational study of ionization potential, electron affinity and the C-F bond dissociation energy for perfluorinated methane derivatives

A computational study of perfluorinated methane derivatives was performed with complete basis set ab initio methods. The total energies for their neutral, cation, and anionic states were computed. From these values, the energy gaps between different electronic states, ionization potentials, electron affinities, and C-F bond dissociation energies were calculated. The computed values are compared with experimental data and the reliability of complete basis set ab initio methods is discussed. New values for C-F bond dissociation energies are suggested. Received: 12 January 1998 / Accepted: 2 April 1998 / Published online: 29 July 1998     

Convergence of the density functional one-centre expansion for the molecular continuum: N2 and (CH3)3N

A large-scale one-centre expansion with a radial B-spline basis set is implemented for bound and continuum states. A Kohn-Sham hamiltonian is employed with Hartree and exchange-correlation potentials calculated from the SCF electron density taken from a previous LCAO calculation. An inverse iteration method is used to obtain the continuum wavefunction, from which the cross section and asymmetry parameter are calculated. The convergence with respect to angular momentum and cut-off radius is analysed for N₂. The relevance of multipolar contributions even at large distances is shown and suggestions for further improvements are given. In order to show that the present method is suitable to treat systems of moderate size, the (CH₃)₃N molecule has also been calculated and the results are compared with experiment. Received: 19 May 1998 / Accepted: 20 August 1998 / Published online: 7 December 1998     

DFT and ab initio study on the reaction mechanism of CH2SH + O2

The mechanism for the CH₂SH + O₂ reaction was investigated by DFT and ab initio chemistry methods. The geometries of all possible stationary points were optimized at the B3LYP/6-311+G(d,p) level, and the single point energy was calculated at the CCSD(T)/cc-pVXZ(X = D and T), G3MP2 and BMC-CCSD levels. The results indicate that the oxidation of CH₂SH by O₂ to form HSCH₂OO is a barrierless process. The most favorable channel is the rearrangement of the initial adduct HSCH₂OO (IM1) to form another intermediate H₂C(S)OOH (IM3) via a five-center transition state, and then the C–O bond fission in IM3 leads to a complex CH₂S. . .HO₂ (MC1), which finally gives out to the major product CH₂S + HO₂. Due to high barriers, other products including cis- and trans-HC(O)SH + HO could be negligible. The direct abstraction channel was also determined to yield CH₂S + HO₂, with the barrier height of 22.3, 18.1 and 15.0 kcal/mol at G3MP2, CCSD(T)/cc-pVTZ and BMC-CCSD levels, respectively, it is not competitive with the addition channel, in which all stationary points are lower than reactant energetically. The other channels to produce cis- and trans-CHSH + HO₂ are also of no importance.     

Ab initio study of the complexes of first-row transition-metal ions with CH, CH2, and CH3

The geometries and bonding characteristics of the complexes of the first-row transition-metal ions with CH, CH₂ and CH₃ were investigated byab initio molecular orbital theory. MCH⁺ and MCH₂ ⁺ are linear and coplanar, respectively. Both of them are with obvious treble or double bond characteristics, but these multiple bonds are mostly “imperfect”. The calculated bond dissociation energies of , and are mostly close to the experimental values, and appear in similar periodic trends from Sc to Zn. Project supported by the National Natural Science Foundation of China (Grant No. 29170070).     

Bond dissociation energies and radical heats of formation in CH3Cl,CH2Cl2, CH3Br,CH2Br2, CH2FCl,and CHFCl2

An analysis of thermochemical and kinetic data on the bromination of the halomethanes CH_4–nX_n (X = F, Cl, Br; n = 1–3), the two chlorofluoromethanes, CH₂FCl and CHFCl₂, and CH₄, shows that the recently reported heats of formation of the radicals CH₂Cl, CHCl₂, CHBr₂, and CFCl₂, and the C? H bond dissociation energies in the matching halomethanes are not compatible with the activation energies for the corresponding reverse reactions. From the observed trends in CH₄ and the other halomethanes, the following revised ΔH°_f,298 (R) values have been derived: ΔH°_f(CH₂Cl) = 29.1 ± 1.0, ΔH°_f(CHCl₂) = 23.5 ± 1.2, ΔH_f(CH₂Br) = 40.4 ± 1.0, ΔH°_f(CHBr₂) = 45.0 ± 2.2, and ΔH°_f(CFCl₂) = ?21.3 ± 2.4 kcal mol^?1. The previously unavailable radical heat of formation, ΔH°_f(CHFCl) = ?14.5 ± 2.4 kcal mol^?1 has also been deduced. These values are used with the heats of formation of the parent compounds from the literature to evaluate C? H and C? X bond dissociation energies in CH₃Cl, CH₂Cl₂, CH₃Br, CH₂Br₂, CH₂FCl, and CHFCl₂.     

Reaction mechanism of HSH and CH3SH with NH2CH2COCH2X (X = F and Cl) molecules

The reaction mechanism of model compounds H₂S and CH₃SH for cysteine proteases with NH₂CH₂COCH₂X (X = F and Cl) molecules has been investigated using DFT methods with B3LYP and B3PW91 hybrid density functionals at 6‐31+G* basis sets. The single point energy has been calculated for the above reactions with B3LYP and B3PW91 functionals using aug‐cc‐PVDZ infinite basis set in both gas and solution phases. The intrinsic reaction coordinates calculations have been performed to confirm that each transition state is linked by the desired reactants and products. The geometries and relative energies for various stationary points have been determined and discussed. The zero point vibrational energy corrections have been made to predict the reliable energy. The negative value of reaction energy indicates that the overall reaction profile is found to be exothermic. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Why betaine crystallizes in high local Cs symmetry. An ab initio MO and DFT study of anhydrous betaine and betaine monohydrate

A theoretical study of the structure, charge distribution, rotational barrier and fundamental vibrations of anhydrous betaine (CH₃)₃NCH₂COO (trimethylglycine) was carried out and compared with available experimental data. Calculations were carried out at HF, MP2 and B3LYP levels using a 6-31+G(d,p) basis set. The calculated rotational barrier of the betaine carboxylic group is 40.5 kJ/mol at the MP4(SDQ)/6-311G(d,p)//HF/6-31+G(d,p) level of theory. The rotation of the carboxylic group changes the molecule from a highly symmetric (C _s ) conformation into a twisted conformation resulting in shortening of the molecule by about 50 pm. Natural population analysis (NPA) indicates intramolecular interaction between the carboxylic oxygen and the nearest methyl hydrogens resulting in internal hydrogen bonding. MP4(SDQ)/6-311G(d,p) single-point NPA calculations on a betaine monohydrate model taken from the X-ray geometry show an expected weakening in the internal hydrogen bond. Calculations explain why betaine preferentially crystallizes in high local C _s symmetry. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 7 December 1998     

Anodic oxidation of 2-aminofluorene in CH2Cl2 + 0.2 M Bu4NBF4: electrochemical behaviour of the derived oxidation products

The physicochemical properties and electrochemical behaviour of products obtained by anodic oxidation of 2-aminofluorene in CH₂Cl₂ + 0.2 M Bu₄NBF₄ are presented together with the oxidation conditions. Received: 8 January 1998 / Accepted: 21 September 1998     

Kinetics and mechanism for the reactions of H atoms with CH3SH and C2H5SH

A kinetic study of the reactions of H atoms with CH₃SH and C₂H₅SH has been carried out at 298 K by the discharge flow technique with EPR and mass spectrometric analysis of the species. The pressure was 1 torr. It was found: k₁ = (2.20 ± 0.20) × 10^?12 for the reaction H + CH₃SH (1) and k₂ = (2.40 ± 0.16) × 10^?12 for the reaction H + C₂H₅SH (2). Units are cm³ molecule^?1 s^?1. A mass spectrometric analysis of the reaction products and a computer simulation of the reacting systems have shown that reaction (1) proceeds through two mechanisms leading to the formation of CH₃S + H₂ (1a) and CH₃ + H₂S (1b).     

Kramers' unrestricted Hartree–Fock and second-order Møller–Plesset perturbation methods using relativistic effective core potentials with spin–orbit operators: Test calculations for HI and CH3I

The Kramers' restricted Hartree–Fock (KRHF) and second-order Møller–Plesset perturbation (KRMP2) methods using relativistic effective core potentials (RECP) with spin–orbit operators and two-component spinors are extended to the unrestricted forms, KUHF and KUMP2. As in the conventional unrestricted methods, the KUHF and KUMP2 methods are capable of qualitatively describing the bond breaking for a single bond. As a result, it is possible to estimate spin–orbit effects along the dissociation curve at the HF and MP2 levels of theory as is demonstrated by the test calculations on the ground states of HI and CH₃I. Since the energy lowering due to spin–orbit interactions is larger for the I atom than for the closed-shell molecules, dissociation energies are reduced and bond lengths are slightly elongated by the inclusion of the spin–orbit interactions. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 91–98, 1998