Concurrent cyclopropanation by carbenes and carbanions? A density functional theory study on the reaction pathways

The mechanisms for the addition reactions of phenylhalocarbenes and phenyldihalomethide carbanions with acrylonitrile (ACN) and trimethylethylene (TME) have been investigated using an ab initio BH and HLYP/6-31G (d, p) level of theory. Solvent effects on these reactions have been explored by calculations that included a polarizable continuum model (PCM) for the solvent (THF). These model calculations show that for the addition of phenylhalocarbenes, a TME species may readily undergo addition reactions with carbenes while ACN has a high-energy barrier to overcome. It was also found that phenyldihalomethide carbanions do not readily add to the electron-rich TME. The cyclopropane yields only appear to occur via addition of PhCBr to TME. However, the cyclopropanation proceeds not only via slow addition of phenylhalocarbenes to ACN but also forms through the stepwise reaction of phenyldihalomethide carbanions with ACN. Our calculation results are in good agreement with experimental observations (Moss, R.A.; Tian, J.-Z. J. Am. Chem. Soc. 2005, 127, 8960) that indicate that the cyclopropanation of phenylhalocarbenes and phenyldihalomethide carbanions with ACN are concurrent in THF.     

Time-dependent density functional theory study on excited-state dihydrogen bonding O-H···H-Ge of the dihydrogen-bonded phenol-triethylgermanium complex

Intermolecular dihydrogen bond O-H···H-Ge in the electronically excited state of the dihydrogen-bonded phenol-triethylgermanium (TEGH) complex was studied theoretically using time-dependent density functional theory. Analysis of the frontier molecular orbitals revealed a locally excited S(1) state in which only the phenol moiety is electronically excited. In the predicted infrared spectrum of the dihydrogen-bonded phenol-TEGH complex, the O-H stretching vibrational mode shifts to a lower frequency in the S(1) state in comparison with that in ground state. The Ge-H stretching vibrational mode demonstrates a relatively smaller redshift than the O-H stretching vibrational mode. Upon electronic excitation to the S(1) state, the O-H and Ge-H bonds involved in the dihydrogen bond both get lengthened, whereas the C-O bond is shortened. With an increased binding energy, the calculated H···H distance significantly decreases in the S(1) state. Thus, the intermolecular dihydrogen bond O-H···H-Ge of the dihydrogen-bonded phenol-TEGH complex becomes stronger in the electronically excited state than that in the ground state.     

A density functional theory study of the ��mythic�� Lindlar hydrogenation catalyst

A Lindlar catalyst is a popular heterogeneous catalyst that consists of 5?wt.% palladium supported on porous calcium carbonate and treated with various forms of lead and quinoline. The additives strategically deactivate palladium sites. The catalyst is widely used for the partial hydrogenation of acetylenic compounds in organic syntheses. Alkyne reduction is stereoselective, occurring via syn addition to give the cis-alkene. Even if it has been employed for about 60?years, there is a lack of molecular level understanding of the Lindlar catalyst. We have applied density functional theory simulations to understand the structure and the nature of the interplay between the multiple chemical modifiers in the Lindlar catalyst. Indeed, the poisons influence different parameters controlling selectivity to the alkene: Pb modifies the thermodynamic factor and hinders the formation of hydrides, while quinoline isolates Pd sites thus minimizing oligomerization.     

Intermolecular potentials of the methane dimer calculated with Møller-Plesset perturbation theory and density functional theory

We have calculated the intermolecular interaction potentials of the methane dimer at the minimum-energy D(3d) conformation using the Hartree-Fock (HF) self-consistent theory, the correlation-corrected second-order M?ller-Plesset (MP2) perturbation theory, and the density functional theory (DFT) with the Perdew-Wang (PW91) functional as the exchange or the correlation part. The HF calculations yield unbound potentials largely due to the exchange-repulsion interaction. In the MP2 calculations, the basis set effects on the repulsion exponent, the equilibrium bond length, the binding energy, and the asymptotic behavior of the calculated intermolecular potentials have been thoroughly studied. We have employed basis sets from the Slater-type orbitals fitted with Gaussian functions (STO-nG) (n=3-6) [Quantum Theory of Molecular and Solids: The Self-Consistent Field for Molecular and Solids (McGraw-Hill, New York, 1974), Vol. 4], Pople's medium size basis sets of Krishnan et al. [J. Chem. Phys. 72, 650 (1980)] [up to 6-311++G(3df,3pd)] to Dunning's correlation consistent basis sets [J. Chem. Phys. 90, 1007 (1989)] (cc-pVXZ and aug-cc-pVXZ) (X=D, T, and Q). With increasing basis size, the repulsion exponent and the equilibrium bond length converge at the 6-31G** basis set and the 6-311++G(2d,2p) basis set, respectively, while a large basis set (aug-cc-pVTZ) is required to converge the binding energy at a chemical accuracy (approximately 0.01 kcal/mol). Up to the largest basis set used, the asymptotic dispersion coefficient has not converged to the destined C6 value from molecular polarizability calculations. The slow convergence could indicate the inefficacy of using the MP2 calculations with Gaussian-type functions to model the asymptotic behavior. Both the basis set superposition error (BSSE) corrected and uncorrected results are presented to emphasize the importance of including such corrections. Only the BSSE corrected results systematically converge to the destined potential curve with increasing basis size. The DFT calculations generate a wide range of interaction patterns, from purely unbound to strongly bound, underestimating or overestimating the binding energy. The binding energy calculated using the PW91PW91 functional and the equilibrium bond length calculated using the PW91VP86 functional are close to the MP2 results at the basis set limit.     

A theoretical study of CO adsorption on gold by Hückel theory and density functional theory calculations

It is crucial to understand the nature of CO adsorption on gold so as to elucidate the mechanism of low-temperature CO oxidation on nanogold catalysts. We performed theoretical analysis of CO adsorption on gold by using Hückel theory and density functional theory (DFT) calculations. Hückel theory indicates that CO adsorption on gold is dominated by the electron distribution at the Au atom, which is greatly affected by neighboring Au atoms, coadsorbed or doping species. The increase of σ-bonding electrons should weaken the CO adsorption, while the increase of π-electrons should strengthen the adsorption. DFT calculations proved this prediction quantitatively for various systems, including CO adsorption on a Au(100)-hex surface with locally varying subsurface configurations and CO coadsorption with acceptor or donor species.     

Are electrophilicity and electrofugality related concepts? A density functional theory study

It is proposed that the electrofugality of a fragment within a molecule is determined by its group nucleophilicity. The variation of electrofugality should be tightly related to the electron releasing ability of the substituent attached to the electrofuge moiety. This contribution closes the set of relationships between philicity and fugality quantities: while nucleofugality appears related to the group electrophilicity of the leaving group, electrofugality is related to the group nucleophilicity of the permanent group.     

Intermolecular potentials of the silane dimer calculated with Hartree-Fock theory, Møller-Plesset perturbation theory, and density functional theory

We have calculated the intermolecular interaction potentials of the silane dimer at the D3d conformation using the Hartree-Fock (HF) self-consistent theory, the correlation-corrected second-order M?ller-Plesset (MP2) perturbation theory, and the density functional theory (DFT) with 108 functionals chosen from the combinations of 9 exchange and 12 correlation functionals. Single-point coupled cluster [CCSD(T)] calculations have also been carried out to calibrate the correlation effect. The HF calculations yield unbound potentials largely because of the exchange-repulsion interaction. In the MP2 calculations, the basis set effects on the repulsion exponent, the equilibrium bond length, the binding energy, and the asymptotic behavior of the calculated intermolecular potentials have been thoroughly studied. We have employed basis sets from the Slater type orbitals fitted with Gaussian functions (STO-nG, n = 3 approximately 6), Pople's medium size basis sets [up to 6-311++G(3df,3pd)], to Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). With increasing basis size, the repulsion exponent and the equilibrium bond length converge at the 6-31G** basis set and the 6-311++G(3d,3p) basis set, respectively, while a large basis set (aug-cc-pVTZ) is required to converge the binding energy at a chemical accuracy ( approximately 0.05 kcal/mol). Up to the largest basis set used, the asymptotic dispersion coefficient has not converged to the expected C6 value from molecular polarizability calculations. We attribute the slow convergence partly to the inefficacy of using the MP2 calculations with Gaussian type functions to model the asymptotic behavior. Both the basis set superposition error (BSSE) corrected and uncorrected results are presented to emphasize the importance of including such corrections. Only the BSSE corrected results systematically converge to the expected potential curve with increasing basis size. The DFT calculations generate a wide range of interaction patterns, from purely unbound to strongly bound, underestimating or overestimating the binding energy. The binding energies calculated using the OPTXHCTH147, PBEVP86, PBEP86, PW91TPSS, PW91PBE, and PW91PW91 functionals and the equilibrium bond lengths calculated using the MPWHCTH93, TPSSHCTH, PBEVP86, PBEP86, PW91TPSS, PW91PBE, and PW91PW91 functionals are close to the MP2 results using the 6-311++G(3df,3pd) basis set. A correlation between the calculated DFT potentials and the exchange and correlation enhancement factors at the low-density region has been elucidated. The asymptotic behaviors of the DFT potentials are also analyzed.     

CH4 dissociation on Co（0001）: A density functional theory study

CH4 dissociation on Co(0001) surfaces is an important step, which has been investigated at the level of density functional theory. It is found that CH4 is unfavorable to adsorb on Co(0001), while CH4 favores to dissociate to CH3, CH2 and CH on Co(0001) surface by sequential dehydrogenation. In the whole process of CH4 dehydrogenation, CH4 dissociate to CH3 and H is the rate-determining step. The calculated results show that CH2 and CH exist mainly on Co(0001) surface, while the dehydrogenation of CH into C and H is difficult.     

Influence of impurity elements on the corrosion of α-uranium surface: a density functional theory study

Journal of Radioanalytical and Nuclear Chemistry - Influence of substitutional Fe, Al and Mg atoms on the corrosion of α-U(110) surface was studied by DFT?+?U method. The...     

How are the ready and unready states of nickel-iron hydrogenase activated by H2? A density functional theory study

We have explored possible mechanisms for the formation of the catalytically active Ni(a)-S state of the enzyme, nickel iron hydrogenase, from the Ni*(r) (ready) or Ni*(u) (unready) state, by reaction with H(2), using density functional theory calculations with the BP86 functional in conjunction with a DZVP basis set. We find that for the reaction of the ready state, which is taken to have an -OH bridge, the rate determining step is the cleavage of H(2) at the Ni(3+) centre with a barrier of approximately 15 kcal mol(-1). We take the unready state to have a -OOH bridge, and find that reaction with H(2) to form the Ni(r)-S state can proceed by two possible routes. One such path has a number of steps involving electron transfer, which is consistent with experiment, as is the calculated barrier of approximately 19 kcal mol(-1). The alternative pathway, with a lower barrier, may not be rate determining. Overall, our predictions give barriers in line with experiment, and allow details of the mechanism to be explored which are inaccessible from experiment.     

A density functional theory study of the Cu+·(CO)n (n = 1–3) complexes

Density functional theory calculations, with an effective core potential for the copper ion, and large polarized basis set functions have been used to construct the potential energy surface of the Cu⁺·(CO)_n (n = 1–3) complexes. A linear configuration is obtained for the global minimum of the Cu⁺·CO and Cu⁺·(CO)₂ complexes with a bond dissociation energy (BDE) of 35.9 and 40.0 kcal mol^-1, respectively. For the Cu⁺·(CO)₃ complex, a trigonal planar geometry is obtained for the global minimum with a BDE of 16.5 kcal mol^?1. C-coordinated copper ion complexes exhibit stronger binding energy than O-coordinated complexes as a result of C_lp → 4s σ-donation. The computed sequential BDEs of Cu⁺·(CO)_n (n = 1–4) complexes agree well with experimental findings, in which the electrostatic energy and σ-donation play an important role in the observed trend.     

Hydrogen fluoride adsorption and reaction on the α-Al2O3(0001) surface: a density functional theory study

The adsorption and reaction behaviors of HF on the α-Al(2)O(3)(0001) surface are systematically investigated using density functional theory method. By increasing the number of HF molecules in a p(2 × 1) α-Al(2)O(3)(0001) slab, we find that HF is chemically dissociated at low coverage; while both physical and dissociative adsorption occurs at a 3/2 monolayer (ML) coverage. At the same coverage (1.0 ML), diverse configurations of the dissociated HF are obtained in the p(2 × 1) model; while only one is observed in the p(1 × 1) slab due to its smaller surface area compared with the former one. Preliminary fluorination reaction study suggests that the total energy of two dissociated HF in the p(2 × 1) slab increases by 1.00 and 0.72 eV for the formation and desorption of water intermediate, respectively. The coadsorption behaviors of HF and H(2)O indicate that the pre-adsorbed water is unfavorable for the fluorination of Al(2)O(3), which is well consistent with the experimental results. The calculated density of states show that the peak of σ(H-F) disappears, while the peaks of σ(H-O) and σ(Al-F) are observed at -8.4 and -5 to -3 eV for the dissociated HF. Charge density difference analysis indicates that the dissociated F atom attracts electrons, while no obvious changes on electrons are observed for the surface Al atoms.     

How accurate is the density functional theory combined with symmetry-adapted perturbation theory approach for CH-pi and pi-pi interactions? A comparison to supermolecular calculations for the acetylene-benzene dimer

Five different orientations of the acetylene-benzene dimer including the T-shaped global minimum structure are used to assess the accuracy of the density functional theory combined with symmetry adapted perturbation theory (DFT-SAPT) approach in its density-fitting implementation (DF-DFT-SAPT) for the study of CH-pi and pi-pi interactions. The results are compared with the outcome of counterpoise corrected supermolecular calculations employing second-order M?ller-Plesset (MP2), spin-component scaled MP2 (SCS-MP2) and single and double excitation coupled cluster theory including perturbative triple excitations (CCSD(T)). For all considered orientations MP2 predicts much deeper potential energy curves with considerably shifted minima compared to CCSD(T) and DFT-SAPT. In spite of being an improvement over the results of MP2, SCS-MP2 tends to underestimate the well depth while DFT-SAPT, employing an asymptotically corrected hybrid exchange-correlation potential in conjunction with the adiabatic local density approximation for the exchange-correlation kernel, is found to be in excellent agreement with CCSD(T). Furthermore, DFT-SAPT provides a detailed understanding of the importance of the electrostatic, induction and dispersion contributions to the total interaction energy and their repulsive exchange corrections.     

Excited-state N-H···S hydrogen bond between indole and dimethyl sulfide: time-dependent density functional theory study

The intermolecular hydrogen bond N-H···S between indole and dimethyl sulfide is theoretically investigated. The formation of N-H···S hydrogen bonds between indole and dimethyl sulfide in ground and excited states is confirmed by the analysis of geometric structure, Mulliken charge, and infrared spectra. The result shows that the S(1) state of hydrogen bonded indole-Me(2)S is mainly a charger transfer state, while the S(2) state is a local excited state and also the state corresponding to the experiment. More importantly, it is demonstrated that the intermolecular hydrogen bond N-H···S of indole-Me(2)S is strengthened in the S(1) and S(2) states compared to that in ground state. Moreover, the strengthening of intermolecular N-H···S hydrogen bond in excited state induces the fluorescence emission peak of indole shifts to the red. These findings may provide insights for further study of N-H···S hydrogen bonds existing in many biomolecular systems.     

A density functional theory study on mechanisms of [4 + 2] annulation of enal with α-methylene cycloalkanone catalyzed by N-heterocyclic carbene

Density functional theory was used to study the reaction mechanisms of the N-heterocyclic carbene (NHC)-catalyzed [4 + 2] annulation reaction between enal and α-methylene cycloalkanone for the formation of tricyclic benzopyran-2-one. The simulations suggest that the energy-favorable catalytic cycle includes five steps: (a) the nucleophilic addition of enal by NHC catalyst; (b) [1, 2]-proton transfer for the formation of Breslow intermediate; (c) [1, 4]-proton transfer for the formation of enolate intermediate; (d) the [4 + 2] cycloaddition process, product formation; and (e) catalyst regeneration. The proton transfer process was particularly designed in two independent ways, the direct proton transfer and the Brønsted acid DBU∙H⁺-mediated proton transfer. Our study reveals that [1, 2]-proton transfer process is the rate-determining step with the accessible energy barrier, which agrees with the experimental observation. Further analysis of the global reaction index confirmed that NHC was primary used as a Lewis base during the reaction processes. The frontier molecular orbital (FMO) analysis indicates that the introduction of the NHC catalyst facilitates the reaction to occur due to the narrower energy gap of FMO.     

Density functional theory study on the –SO3H functionalized acidic ionic liquids

In this work, the structures of the –SO₃H functionalized acidic ionic liquid 1-(3-sulfonic acid) propyl-3-methylimidazolium hydrogen sulfate ([C₃SO₃Hmim]HSO₄), including its precursor compound (zwitterion), cation, and cation–anion ion-pairs, were optimized systematically by the DFT theory at B3LYP/6-311++G** level, and their most stable geometries were obtained. The calculation results indicated that a great tendency to form strong intramolecular hydrogen bonds was present in the zwitterion, and this tendency was weakened in the cation that was the protonation product of zwitterion. The intramolecular hydrogen bonds and intermolecular hydrogen bonds coexisted in the ionic liquid, and they played an important role in the stability of the systems. The strongest interaction in the ionic liquid was found between the anion and the functional group. The transition state research and the intrinsic reaction coordinate analysis of the hydrogen transfer reaction showed that, when the cation and the anion interacted near the functional group by double O–H···O hydrogen bonds, the ionic liquid was inclined to exist in a form of the zwitterion and H₂SO₄.     

The prediction of Fe Mössbauer parameters by the density functional theory: a benchmark study

We report the performance of eight density functionals (B3LYP, BPW91, OLYP, O3LYP, M06, M06-2X, PBE, and SVWN5) in two Gaussian basis sets (Wachters and Partridge-1 on iron atoms; cc-pVDZ on the rest of atoms) for the prediction of the isomer shift (IS) and the quadrupole splitting (QS) parameters of M?ssbauer spectroscopy. Two sources of geometry (density functional theory-optimized and X-ray) are used. Our data set consists of 31 iron-containing compounds (35 signals), the M?ssbauer spectra of which were determined at liquid helium temperature and where the X-ray geometries are known. Our results indicate that the larger and uncontracted Partridge-1 basis set produces slightly more accurate linear correlations of electronic density used for the prediction of IS and noticeably more accurate results for the QS parameter. We confirm and discuss the earlier observation of Noodleman and co-workers that different oxidation states of iron produce different IS calibration lines. The B3LYP and O3LYP functionals have the lowest errors for either IS or QS. BPW91, OLYP, PBE, and M06 have a mixed success whereas SVWN5 and M06-2X demonstrate the worst performance. Finally, our calibrations and conclusions regarding the best functional to compute the M?ssbauer characteristics are applied to candidate structures for the peroxo and Q intermediates of the enzyme methane monooxygenase hydroxylase (MMOH), and compared to experimental data in the literature.