Theoretical study of the internal rotational barriers in nitrobenzene, 2‐nitrotoluene, 2‐nitrophenol,and 2‐nitroaniline

The molecular geometries and internal rotational barriers of the nitro group of nitrobenzene (NB), 2‐nitrotoluene (2‐NT), 2‐nitroaniline (2‐NA), and 2‐nitrophenol (2‐NP) were calculated by five different types of density functional theory (DFT) methods with three different levels of basis sets. Analysis of the torsional angles of the nitro, methyl, amino, and hydroxyl groups indicate that NB, 2‐NA, and 2‐NP are planar molecules, but 2‐NT is not a planar molecule. Internal rotational barriers of the nitro group were calculated as V₂ barriers, and the NO₂ torsional potentials for each molecule were given. The values of the V₂ barriers depend on the DFT methods and basis sets. The average values of the V₂ barriers for NB, 2‐NT, 2‐NA, and 2‐NP are 6.47 kcal/mol, 3.00 kcal/mol, 10.20 kcal/mol, and 13.26 kcal/mol, respectively. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 332–337, 2001     

The computation of the potential energy surface for H2 + OH → H2O + H using ab initio and density functional theory methods

The reaction energy profile for H₂ + OH → H + H₂O was computed using HF, MP2, MP4, QCISD, G1, G2, and G2MP2 ab initio methods. In addition, the B3LYP, B3P86, B3PW91, BLYP, BP291, and SVWN density functional theory (DFT) methods were also used. All the ab initio methods, with the exception of the G series, produced much higher activation barriers and heats of reaction than the experimental values. On the other hand, the DFT methods produced negative forward and reverse barriers which were too low, with the exception of the hybrid DFT methods. The G2 ab initio method generated energies which deviated from the experimental values by ∼ 1 kcal/mol and therefore should be considered a very accurate computational method. The hybrid DFT methods produced positive forward reaction barriers with energies that were 2–4 kcal/mol lower than the experimental values. The geometries of the transition state and energies computed by the ab initio and DFT methods were compared. These results suggest that, in the hybrid exchange functional, the portion of the Slater exchange term should be increased. This may be the reason why the computed energies were too low. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 62: 639–644, 1997     

The influence of the counter-ion MeB(C6F5)3− and solvent effects on ethylene polymerization catalyzed by [(CpSiMe2NR)TiMe]+: a combined density functional theory and molecular mechanism study

A combined density functional theory and molecular mechanism (QM/MM) method has been used to study the first (R = Me) and the second (R = propyl) insertion of the ethylene monomer into the Ti-R bond of (CpSiMe₂N^t Bu)(R)Ti-m-MeB(C₆F₅)₃. The computational results, in agreement with experimental findings, show the influence of the counter-ion and the solvent not only changes the reaction barriers, but also alters the rate-determining step for the second ethylene propagation, from insertion to uptake. The total reaction barrier for the first ethylene propagation has been calculated to be slightly higher than that for the second ethylene propagation, in general agreement with experimental results. The total barriers in solution are 11.7 kcal/mol and 10.5 kcal/mol for the first and second ethylene insertions, respectively. These insertion barriers are comparable to the activation energy (13.3 kcal/mol) found experimentally for the same catalyst (CGC).     

An ONIOM and DFT study of water and ammonia adsorption on anatase TiO2 (001) cluster

Density functional theory (DFT) calculations at ONIOM DFT B3LYP/ 6‐31G**‐MD/UFF level are employed to study molecular and dissociative water and ammonia adsorption on anatase TiO₂ (001) surface represented by partially relaxed Ti₂₀O₃₅ ONIOM cluster. DFT calculations indicate that water molecule is dissociated on anatase TiO₂ (001) surface by a nonactivated process with an exothermic relative energy difference of 58.12 kcal/mol. Dissociation of ammonia molecule on the same surface is energetically more favorable than molecular adsorption of ammonia (?37.17 kcal/mol vs. ?23.28 kcal/mol). The vibration frequency values also are computed for the optimized geometries of adsorbed water and ammonia molecules on anatase TiO₂ (001) surface. The computed adsorption energy and vibration frequency values are comparable with the values reported in the literature. Finally, several thermodynamical properties (ΔH°, ΔS°, and ΔG°) are calculated for temperatures corresponding to the experimental studies. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Modeling the catalysis of anti-cocaine catalytic antibody: competing reaction pathways and free energy barriers

The competing reaction pathways and the corresponding free energy barriers for cocaine hydrolysis catalyzed by an anti-cocaine catalytic antibody, mAb15A10, were studied by using a novel computational strategy based on the binding free energy calculations on the antibody binding with cocaine and transition states. The calculated binding free energies were used to evaluate the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis for each reaction pathway. The free energy barriers for the antibody-catalyzed cocaine hydrolysis were predicted to be the corresponding free energy barriers for the cocaine hydrolysis in water plus the calculated free energy barrier shifts. The calculated free energy barrier shift of -6.87 kcal/mol from the dominant reaction pathway of the cocaine benzoyl ester hydrolysis in water to the dominant reaction pathway of the antibody-catalyzed cocaine hydrolysis is in good agreement with the experimentally derived free energy barrier shift of -5.93 kcal/mol. The calculated mutation-caused shifts of the free energy barrier are also reasonably close to the available experimental activity data. The good agreement suggests that the protocol for calculating the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis may be used in future rational design of possible high-activity mutants of the antibody as anti-cocaine therapeutics. The general strategy of the free energy barrier shift calculation may also be valuable in studying a variety of chemical reactions catalyzed by other antibodies or proteins through noncovalent bonding interactions with the substrates.     

Mechanistic pathways of the hydroxyl radical reactions of quinoline. 2. Computational analysis of hydroxyl radical attack at C atoms

Density functional theory (DFT) calculations are employed to compare the mechanism of the *OH attacks at all carbon atoms in quinoline. The computational analysis of the energy surface for the reaction of *OH with quinoline reveals that the formation of OH adducts proceeds through exothermic formation of pi-complexes/H-bonded complexes. The gas-phase reactions have activation energies ranging from <1.3 kcal/mol for the attack at positions C3 through C8 to 8.6 kcal/mol for the attack at the C2 position. Solvation, as described by the CPCM cavity model, lowers these activation barriers so that the attack at all carbon atoms except C2 is effectively barrierless. The *OH attack at C2 in solution is significantly different than at all other quinoline positions because it involves the only transition structure with energy higher than that of the starting materials and with an energetic barrier of 5.1 kcal/mol. The specific solvation approach also corroborates this finding because the attack at C2 was shown to have an energy barrier of 2.3 kcal/mol compared to the barrierless attack at C5. These results are in agreement with our recent experimental studies but differ from literature reports on the degradation of quinoline using the photo-Fenton reaction.     

Force field parameters for sulfates and sulfamates based on ab initio calculations: Extensions of AMBER and CHARMm fields

Ab initio self-consistent field (SCF) Hartree-Fock calculations of sulfates R? O? SO₃(?1) (R = Me, Et, i-Pr) and sulfamates R? NHSO₃(?1) (R = H, Me, Et, i-Pr) were performed at the 4-31G(*S*N) //3-21G(*S*N) basis set levels, where asterisks indicate d functions on sulfur and nitrogen atoms. These standard levels were determined by comparing calculation results with several basis sets up to MP2/6-31G*//6-31G*. Several conformations per compound were studied to obtain molecular geometries, rotational barriers, and potential derived point charges. In methyl sulfate, the rotational barrier around the C? O bond is 1.6 kcal/mol at the MP2 level and 1.4 kcal/mol at the standard level. Its ground state has one of three HCOS torsion angles trans and one of three COSO torsion angles trans. Rotation over 60° around the single O? S bond in the sulfate group costs 2.5 kcal/mol at the MP2 and 2.1 kcal/mol at the standard level. For ethyl sulfate, the calculated rotational barrier in going from the ground state, which has its CCOS torsion angle trans, to the syn-periplanar conformation (CCOS torsion angle cis) is 4.8 kcal/mol. However, a much lower barrier of 0.7 kcal/mol leads to a secondary gauchelike conformation about 0.4 kcal/mol above the ground state, with the CCOS torsion angle at 87.6°. Again, one of the COSO torsion angles is trans in the ground state, and the rotational barrier for a 60° rotation of the sulfate group amounts to 1.8 kcal/mol. For methyl sulfamate, the rotational barriers are 2.5 kcal/mol around the C? N bond and 3.3 kcal/mol around the N? S bond. This is noteworthy because sulfamate itself has a calculated rotational barrier around the N? S bond of only 1.7 kcal/mol. These and other data were used to parameterize the well-known empirical force fields AMBER and CHARMm. When the new fields were tested by means of vibrational frequency calculations at the 6-31G*//6-31G* level for methyl sulfate, sulfamate, and methyl sulfamate ground states, the frequencies compared favorably with the AMBER and CHARMm calculated frequencies. The transferability of the force parameters to β-D -glucose-6-sulfate and isopropyl sulfate appears to be better than to isopropyl sulfamate. © 1995 by John Wiley & Sons, Inc.     

Methylene transfer or carbometalation? A theoretical study to determine the mechanism of lithium carbenoid-promoted cyclopropanation reactions in aggregation and solvation States

Density functional theory calculations for the lithium carbenoid-promoted cyclopropanations in aggregation and solvation states are presented in order to investigate the controversy of the mechanistic dichotomy, that is, the methylene-transfer mechanism and the carbometalation mechanism. The methylene-transfer mechanism represents the reaction reality, whereas the carbometalation pathway does not appear to compete significantly with the methylene-transfer pathway and should be ruled out as a major factor. A simple model calculation for monomeric lithium carbenoid-promoted cyclopropanations with ethylene in the gas phase is not sufficient to reflect the reaction conditions accurately or to determine the reaction mechanism since its result is inconsistent with the experimental facts. The aggregated lithium carbenoids are the most probable reactive species in the reaction system. The calculated reaction barriers of the methylene-transfer pathways are 10.1 and 8.0 kcal/mol for the dimeric (LiCH2F)2 and tetrameric (LiCH2F)4 species, respectively, compared with the reaction barrier of 16.0 kcal/mol for the monomeric LiCH2F species. In contrast, the reaction barriers of the carbometalation pathways are 26.8 kcal/mol for the dimeric (LiCH2F)2 and 33.9 kcal/mol for the tetrameric (LiCH2F)4 species, compared with the reaction barrier of 12.5 kcal/mol for the monomeric LiCH2F species. The effects of solvation were investigated by explicit coordination of the solvent molecules to the lithium centers. This solvation effect is found to enhance the methylene-transfer pathway, while it is found to impede the carbometalation pathway instead. The combined effects of the aggregation and solvation lead to barriers to reaction in the range of 7.2-9.0 kcal/mol for lithium carbenoid-promoted cyclopropanation reactions along the methylene-transfer pathway. Our computational results are in good agreement with the experimental observations.     

An Ab initio determination of the rate constant for H2 + CN → H + HCN

The reactants, products, and saddle point for the reaction H₂ + CN → H + HCN have been studied by ab initio calculations. The computed structures, frequencies, and energetics are compared directly to available measurements and, indirectly, to experimental rateconstants. The theoretical rate constants used in the comparison are calculated with conventional transition state theory. By reduction of the computed reaction barrier to 4.1 kcal mol,^?1 good agreement with experimental rate constants is obtained over a 3250-K temperature range. This computed rate constant is well represented by the form 4.9 × 10_?18 T^2.45 e^{?1, 126/T} over the temperature range of 250 K–3500 K. Substantial reaction rate curvature is found due to low-frequency bending modes at the saddle point. The results for this reaction are compared to other abstraction reactions involving H atom transfer to identify correlations between reaction exothermicity and both abstraction barriers and reaction rate curvature.     

A multilayered representation,quantum mechanical and molecular mechanics study of the CH3F + OH− reaction in water

The bimolecular nucleophilic substitution (S_N2) reaction of CH₃F + OH^? in aqueous solution was investigated using a combined quantum mechanical and molecular mechanics approach. Reactant complex, transition state, and product complex along the reaction pathway were analyzed in water. The potentials of mean force were calculated using a multilayered representation with the DFT and CCSD(T) level of theory for the reactive region. The obtained free energy activation barrier for this reaction at the CCSD(T)/MM representation is 18.3 kcal/mol which agrees well with the experimental value at ～21.6 kcal/mol. Both the solvation effect and solute polarization effect play key roles on raising the activation barrier height in aqueous solution, with the former raising the barrier height by 3.1 kcal/mol, the latter 1.5 kcal/mol. © 2013 Wiley Periodicals, Inc.     

Theoretical study for the HNSi–HSiN isomerization: ab initio and DFT calculations

Ab initio and density functional theory (DFT) calculations using the GAUSSIAN 94 program have been performed to investigate the molecular structures of HNSi and HSiN in the ground state as well as the transition state for the HNSi–HSiN isomerization reaction at the 6-311G(d,p), 6-311+G(2d,p) and 6-311+G(2df,p) basis sets. The results show that DFT calculations at higher levels of theory reproduce experimental vibrational frequencies of both HNSi and HSiN better than ab initio methods including electron correlation effects. Those calculated geometries are accurate enough to predict the rotational constant of HNSi. The barrier height for the isomerization reaction is found to be about 10 kcal/mol.     

Activation energies of pericyclic reactions: performance of DFT, MP2, and CBS-QB3 methods for the prediction of activation barriers and reaction energetics of 1,3-dipolar cycloadditions, and revised activation enthalpies for a standard set of hydrocarbon pericyclic reactions

Activation barriers and reaction energetics for the three main classes of 1,3-dipolar cycloadditions, including nine different reactions, were evaluated with the MPW1K and B3LYP density functional methods, MP2, and the multicomponent CBS-QB3 method. The CBS-QB3 values were used as standards for 1,3-dipolar cycloaddition activation barriers and reaction energetics, and the density functional theory (DFT) and MP2 methods were benchmarked against these values. The MPW1K/6-31G* method and basis set performs best for activation barriers, with a mean absolute deviation (MAD) value of 1.1 kcal/mol. The B3LYP/6-31G* method and basis set performs best for reaction enthalpies, with a MAD value of 2.4 kcal/mol, while the MPW1K method shows large errors for reaction energetics. The MP2 method gives the expected systematic underestimation of barriers. Concerted and nearly synchronous transition structures are predicted by all DFT and MP2 methods. Also reported are revised estimated 0 K experimental activation enthalpies for a standard set of hydrocarbon pericyclic reactions and updated comparisons to experiment for DFT, ab initio, and multicomponent methods. B3LYP and MPW1K methods with MAD values of 1.5 and 2.1 kcal/mol, respectively, fortuitously outperform the multicomponent CBS-QB3 method, which has a MAD value of 2.3. The MAD value of the O3LYP functional improves to 2.4 kcal/mol from the previously reported 3.0 kcal/mol.     

The Curtius rearrangement of cyclopropyl and cyclopropenoyl azides. A combined theoretical and experimental mechanistic study

A combined experimental and theoretical study addresses the concertedness of the thermal Curtius rearrangement. The kinetics of the Curtius rearrangements of methyl 1-azidocarbonyl cycloprop-2-ene-1-carboxylate and methyl 1-azidocarbonyl cyclopropane-1-carboxylate were studied by (1)H NMR spectroscopy, and there is close agreement between calculated and experimental enthalpies and entropies of activation. Density functional theory (DFT) calculations (B3LYP/6-311+G(d,p)) on these same acyl azides suggest gas phase barriers of 27.8 and 25.1 kcal/mol. By comparison, gas phase activation barriers for the rearrangement of acetyl, pivaloyl, and phenyl azides are 27.6, 27.4, and 30.0 kcal/mol, respectively. The barrier for the concerted Curtius reaction of acetyl azide at the CCSD(T)/6-311+G(d,p) level exhibited a comparable activation energy of 26.3 kcal/mol. Intrinsic reaction coordinate (IRC) analyses suggest that all of the rearrangements occur by a concerted pathway with the concomitant loss of N2. The lower activation energy for the rearrangement of methyl 1-azidocarbonyl cycloprop-2-ene-1-carboxylate relative to methyl 1-azidocarbonyl cyclopropane-1-carboxylate was attributed to a weaker bond between the carbonyl carbon and the three-membered ring in the former compound. Calculations on the rearrangement of cycloprop-2-ene-1-oyl azides do not support pi-stabilization of the transition state by the cyclopropene double bond. A comparison of reaction pathways at the CBS-QB3 level for the Curtius rearrangement versus the loss of N2 to form a nitrene intermediate provides strong evidence that the concerted Curtius rearrangement is the dominant process.     

MnZSM-5催化剂上NH3-SCR反应机理的研究

通过密度泛函理论（DFT）对Mn/ZSM-5催化剂上NH3-SCR反应机理进行了理论研究。一种为气态NO直接参与反应的E-R机理,NO分子与[NH2]反应生成中间体[NH2NO],该反应路径的能垒为43.35 kcal/mol;另一种为吸附态NO参与反应的L-H机理,[NO]与[NH3]反应生成[NH2NO],该反应路径的能垒为44.73 kcal/mol。因两种机理的反应能垒相差不大,因此在一定温度下遵循两种机理的反应皆能进行。     

N‐arylamides and N‐arylcarbamates N?CO internal rotation barrier study by molecular modeling

Amides and carbamates present an energetic barrier associated to N? C(O) bond rotation, which determines two different equilibrium geometries. In this work, the conformational equilibrium of formanilide, acetanilide, methyl and t‐butyl phenylcarbamates, and their N‐methylderivatives was studied by AM1 and B3LYP/6‐31G(d,p) calculations. The effect of aryl p‐substituents (MeO, Me, Cl, Br, CN, and NO₂) was also studied. Amide barriers were found by DFT calculation between 12 and 21 kcal/mol. Carbamates, on the other hand, showed barriers between 11 and 15 kcal/mol. AM1 underestimates the energetic barriers and provides values around half those obtained by B3LYP/6‐31G(d,p) calculations. Electron withdrawing substituents on aryl group decrease the barrier. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

An ONIOM and DFT study of water adsorption on rutile TiO2 (110) cluster

Density functional theory (DFT) calculations performed at ONIOM DFT B3LYP/6‐31G**‐MD/UFF level are employed to study molecular and dissociative water adsorption on rutile TiO₂ (110) surface represented by partially relaxed Ti₂₅O₃₇ ONIOM cluster. DFT calculations indicate that dissociative water adsorption is not favorable because of high activation barrier (23.2 kcal/mol). The adsorption energy and vibration frequency of both molecularly and dissociatively adsorbed water molecule on rutile TiO₂ (110) surface compare well with the values reported in the literature. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Principle and mechanism of direct porphyrin metalation: joint experimental and theoretical investigation

The direct metalation of tetraphenylporphyrin with bare metal atoms (Co and Zn) was studied with X-ray photoelectron spectroscopy, scanning tunneling microscopy, and temperature-programmed reaction measurements on ordered monolayer films of the molecules adsorbed on a Ag(111) surface. The mechanism of this novel type of surface reaction was investigated using density functional theory (DFT) calculations for the related gas-phase reactions of the unsubstituted porphyrin with the metals Fe, Co, Ni, Cu, and Zn. The reaction starts with the formation of an initial complex, in which the metal atom is coordinated by the intact unreduced porphyrin. This complex resembles the sitting-atop complex proposed for porphyrin metalation with metal ions in solution. In two subsequent steps, the pyrrolic hydrogen atoms are transferred to the metal atom, forming H2, which is eventually released. The activation barriers of the H-transfer steps vary for the different metal atoms. DFT calculations suggest that metalations with Fe, Co, and Ni show two-state reactivity, while those with Cu and Zn proceed on a single potential energy surface. For metalation with Zn, we calculated a barrier of the first hydrogen transfer step of 32.6 kcal mol(-1), in good agreement with the overall experimental activation energy of 31 kcal mol(-1).     

Reactions of hydrogen atom with hydrogen peroxide

Rate coefficients are calculated using canonical variational transition state theory with multidimensional tunneling (CVT/SCT) for the reactions H + H2O2 --> H2O + OH (1a) and H + H2O2 --> HO2 + H2 (1b). Reaction barrier heights are determined using two theoretical approaches: (i) comparison of parametrized rate coefficient calculations employing CVT/SCT to experiment and (ii) high-level ab initio methods. The evaluated experimental data reveal considerable variations of the barrier height for the first reaction: although the zero-point-exclusive barrier for (1a) derived from the data by Klemm et al. (First Int. Chem. Kinet. Symposium 1975, 61) is 4.6 kcal/mol, other available measurements result in a higher barrier of 6.2 kcal/mol. The empirically derived zero-point-exclusive barrier for (1b) is 10.4 kcal/mol. The electronic structure of the system at transition state geometries in both reactions was found to have "multireference" character; therefore special care was taken when analyzing electronic structure calculations. Transition state geometries are optimized by multireference perturbation theory (MRMP2) with a variety of one-electron basis sets, and by a multireference coupled cluster (MR-AQCCSD) method. A variety of single-reference benchmark-level calculations have also been carried out; included among them are BMC-CCSD, G3SX(MP3), G3SX, G3, G2, MCG3, CBS-APNO, CBS-Q, CBS-QB3, and CCSD(T). Our data obtained at the MRMP2 level are the most complete; the barrier height for (1a) using MRMP2 at the infinite basis set limit is 4.8 kcal/mol. Results are also obtained with midlevel single-reference multicoefficient correlation methods, such as MC3BB, MC3MPW, MC-QCISD/3, and MC-QCISD-MPWB, and with a variety of hybrid density functional methods, which are compared with high-level theory. On the basis of the evaluated experimental values and the benchmark calculations, two possible recommended values are given for the rate coefficients.     

DFT and CASPT2 study of two thermal reactions of nitromethane: C–N bond cleavage and nitro-to-nitrite isomerization. An example of the inverse symmetry breaking deficiency in density functional calculations of an homolytic dissociation

The reaction paths of nitromethane leading to the dissociation products or isomerization to methyl nitrite have been computationally investigated at the CAS-SCF and DFT levels of theory. Additionally, the CAS-SCF wave functions were used as reference in a second-order perturbation treatment, CASPT2, in order to obtain a good estimate for the activation energy of each reaction path. Both methods predict the isomerization as a concerted reaction. However, the behavior of the two approximations with respect to dissociation is rather different; while CASPT2 predicts a barrier height of (≈59 kcal/mol) in good accordance with the experimental activation energy (59.0 kcal/mol), B3-LYP/6-31G^* calculations overestimate the barrier for more than 30 kcal/mol. The DFT prediction of the dissociation channel exhibits inverse symmetry breaking, dissociating to the unphysical absurd CH₃^δ+ plus NO₂^δ−.