A quantum-chemical study of the LiH + LiH⋅− ⇄ LiH2− + Li⋅ reaction

Parts of the potential energy surface of the title process and related processes have been investigated at the SCF /6-31G **, SCF /6-31++G **, and MP 2/6-31++G ** levels. The investigated reaction is exothermic (?6.23 kcal/mol, MP 4/6-31++G **//MP 2/6–31++G** level, ZPE included): A linear intermediate radical anion, Li? H? Li? H??, is significantly stabilized with respect to LiH + LiH?? (?38.74 kcal/mol, the same level as above). The BSSE at MP 2/6–31++G **//MP 2/6–31++G ** amounts to 1.8 kcal/mol. The title process seems to be suitable for experimental study in molecular beams.     

Theoretical study on the nitration of methane by acyl nitrate catalyzed by H-ZSM5 zeolite

A theoretical study on the nitration of methane by acyl nitrate catalyzed by HZSM-5 zeolite is reported. The zeolite was represented by a "double ring" 20T cluster. The calculations were performed at the DFT/X3LYP/6-31G** and MP2/6-31G** levels. The first step of the mechanism involves the protonation of the acyl nitrate by the zeolite and the formation of a nitronium-like ion. The reaction proceeds through a concerted step with the attack of the methane molecule by the nitronium-like ion and the simultaneous transfer of a proton from the methane molecule to the zeolite, thus reconstructing the acidic site. The activation energies for the first and second steps of this reaction are, respectively, 14.09 and 10.14 kcal/mol at X3LYP/6-31G** level and 16.68 and 13.85 kcal/mol at the MP2/6-31G**.     

Ab initio and density function theory computational studies of the CH4 + H → CH3 + H2 reaction

The activation barrier for the CH₄ + H → CH₃ + H₂ reaction was evaluated with traditional ab initio and Density Functional Theory (DFT) methods. None of the applied ab initio and DFT methods was able to reproduce the experimental activation barrier of 11.0-12.0 kcal/mol. All ab initio methods (HF, MP2, MP3, MP4, QCISD, QCISD(T), G1, G2, and G2MP2) overestimated the activation energy. The best results were obtained with the G2 and G2MP2 ab initio computational approaches. The zero-point corrected energy was 14.4 kcal mol⁻¹. Some of the exchange DFT methods (HFB) computed energies which were similar to the highly accurate ab initio methods, while the B3LYP hybrid DFT methods underestimated the activation barrier by 3 kcal mol⁻¹. Gradient-corrected DFT methods underestimated the barrier even more. The gradient-corrected DFT method that incorporated the PW91 correlational functional even generated a negative reaction barrier. The suitability of some computational methods for accurately predicting the potential energy surface for this hydrogen radical abstraction reaction was discussed.     

Quantum Chemical Model of a Lysozyme+Substrate Complex and a Cooperative Process in It

This paper presents an ab initio (RHF/6-31G** and MP2(full)6-31G**) and density functional (DFT) study of the structure and energetics of formation of an intermolecular complex which is the simplest model of an active center lysozyme with a substrate. The calculated energy of complex formation is 41.4 (RHF), 53.4 (MP2), and 52.7 kcal/mole (DFT). The proton transfer reaction is a concerted reaction having an energy barrier of 41.1 (RHF), 31.6 (MP2), and 25.3 (DFT) kcal/mole.     

Theoretical studies of proton-transfer reactions of 2-hydroxypyridine--(H2O)n (n = 0-2) in the ground and excited states

The potential energy profiles for proton-transfer reactions of 2-hydroxypyridine and its complexes with water were determined by MP2, CASSCF and MR-CI calculations with the 6-31G** basis set. The tautomerization reaction between 2-hydroxypyridine (2HP) and 2-pyridone (2PY) does not take place at room temperature because of a barrier of approximately 35 kcal/mol for the ground-state pathway. The water-catalyzed enol-keto tautomerization reactions in the ground state proceed easily through the concerted proton transfer, especially for the two-water complex. The S1 tautomerization between the 2HP and 2PY monomers has a barrier of 18.4 kcal/mol, which is reduced to 5.6 kcal/mol for the one-water complex and 6.4 kcal/mol for the two-water complex. The results reported here predict that the photoinduced tautomerization reaction between the enol and keto forms involves a cyclic transition state having one or two water molecules as a bridge.     

Aromatic dienophiles. 1. A theoretical study of an inverse-electron demand Diels-Alder reaction between 2-aminopyrrole and 1,3,5-triazine

This study is devoted to a detailed theoretical study of an inverse-electron demand Diels-Alder reaction (IDA) with 1,3,5-triazine as the diene and 2-aminopyrrole 1A(alpha) as the dienophile, which is a key step in a cascade reaction for the one-pot synthesis of purine analogues. Geometries were optimized with the B3LYP/6-31G* method and energies were evaluated with the MP2/6-311++G** method. This IDA reaction occurs through a stepwise mechanism, where the first step corresponds to the nucleophilic attack of 2-aminopyrrole to triazine to form a zwitterionic intermediate, which is in equilibrium with a neutral intermediate through a hydrogen transfer process, followed by a rate-determining ring-closure step. It is shown that the B3LYP method significantly overestimates the activation energy, whereas the MP2 method offers a reasonable activation barrier of 27.9 kcal/mol in the gas phase. The solvation effect has been studied by the PCM model. In DMSO, the calculated activation energy of the IDA reaction is decreased to 24.0 kcal/mol with a strong endothermicity of 17.4 kcal/mol due to the energy penalty of transforming two aromatic reactants into a nonaromatic IDA adduct. The possible stepwise [2+2] pathway is ruled out based on its higher activation and reaction energies than those of the [4+2] pathway. By comparing the IDA reactions of triazine to 2-aminopyrrole and pyrrole, we address two crucial roles of the alpha-amino substituent in lowering activation and reaction energies and controlling the reaction regiochemistry.     

Ab initio studies on the mechanism of the size-dependent hydrogen-loss reaction in Mg+(H2O)n

The mechanism of size-dependent intracluster hydrogen loss in the cluster ions Mg(+)(H(2)O)(n), which is switched on around n=6, and off around n=14, was studied by ab initio calculations at the MP2/6-31G* and MP2/6-31G** levels for n=1-6. The reaction proceeds by Mg(+)-assisted breaking of an H-O bond in one of the H(2)O molecules. The reaction barrier is dependent on both the cluster size and the solvation structure. As n increases from 1 to 6, there is a dramatic drop in the reaction barrier, from greater than 70 kcal mol(-1) for n=1 to less than 10 kcal mol(-1) for n=6. In the transition structures, the Mg atom is close to the oxidation state of +2, and H(2)O molecules in the first solvation shell are much more effective in stabilizing the transition structures and lowering the reaction barriers than H(2)O molecules in the other solvation shells. While the reaction barrier for trimer core structures with only three H(2)O molecules in the first shell is greater than 24 kcal mol(-1), even for Mg(+)(H(2)O)(6), it drops considerably for clusters with four-six H(2)O molecules in the first shell. The more highly coordinated complexes have comparable or slightly higher energy than the trimer core structures, and the presence of such high coordination number complexes is the underlying kinetic factor for the switching on of the hydrogen-loss reaction around n=6. For clusters with trimer core structures, the hydrogen loss reaction is much easier when it is preceded by an isomerization step that increases the coordination number around Mg(+). Delocalization of the electron on the singly occupied molecular orbital (SOMO) away from the Mg(+) ion is observed for the hexamer core structure, while at the same time this isomer is the most reactive for the hydrogen-loss reaction, with an energy barrier of only 2.7 kcal mol(-1) at the MP2/6-31G** level.     

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     

Fixation of heterocumulenes. 1. A theoretical study on the irreversible reaction of CO(2) with a 2-lithio-1,3-dithiane

The mechanism of electrophilic addition of CO(2) to 2-lithio-2-phenyl-1, 3-dithiane-tetrahydrofuran-tetramethylethylendiamine, a Corey-Seebach "umpolungs" reagent for nucleophilic acylation, was investigated at the B3YLP/6-311+G//HF/6-31+G level of theory with specific solvation effects being included in the study. The overall reaction is exothermic by 18.8 kcal/mol and proceeds via precomplexation of the CO(2) (necessary for activation). The reaction barrier is calculated to be 11.9 kcal/mol (relative to the precomplex 2a) and represents a lower boundary for the activation energy. The reaction barrier is shown to originate from specific solvent effects. A detailed survey of the electronic effects governing the reaction is given. The ab initio results were then compared with semiempirical PM3 calculations, which were extended to include the heterocumulenes COS and CS(2). As expected, the reduced electrophilicity of these molecules leads to a higher activation barrier by retention of the same reaction mechanism.     

The mechanisms of the reactions of W and W+ with COx (x=1, 2): a computational study

The mechanisms of the reactions of W and W+ with COx (x=1, 2) were studied at the CCSD(T)/[SDD+6-311G(d)]//B3LYP/[SDD+6-31G(d)] level of theory. It was shown that the gas-phase reaction of W with CO2 proceeds with a negligible barrier via an insertion pathway, W(7S)+CO2(1A1)-->W(eta2-OCO)(6A')-->OW(eta1-CO)(1A)-->WO (3Sigma+)+CO(1Sigma). This oxidation process is calculated to be exothermic by 32.4 kcal/mol. Possible intermediates of this reaction are the W(eta2-OCO) and OWCO complexes, among which the latter is 37.4 kcal/mol more stable and lies 39.7 and 7.3 kcal/mol lower than the reactants, W(7S)+CO2(1A1), and the products, WO (3Sigma+)+CO(1Sigma), respectively. The barrier separating W(eta2-OCO) from OWCO is 8.0 kcal/mol (relative to the W(eta2-OCO) complex), which may be characterized as a W+delta-(CO2)-delta charge-transfer complex. Ionization of W does not change the character of the reaction of W with CO2: the reaction of W+ with CO2, like its neutral analog, proceeds via an insertion pathway and leads to oxidation of the W-center. The overall reaction W+(6D) + CO2(1A1)-->W(eta1-OCO)+(6A)-->OW(eta1-CO)+(4A)-->WO+(4Sigma+)+CO(1Sigma) is calculated to be exothermic by 25.4 kcal/mol. The cationic reaction proceeds with a somewhat large (9.9 kcal/mol) barrier and produces two intermediates, W(eta1-OCO)+(6A) and OW(eta1-CO)+(4A). Intermediate W(eta1-OCO)+(6A) is 20.0 kcal/mol less stable than OW(eta1-CO)+(4A), and separated from the latter by a 35.2 kcal/mol barrier. Complex W(eta1-OCO)+(6A) is characterized as an ion-molecular complex type of W+-(CO2). Gas-phase reactions of M=W/W+ with CO lead to the formation of a W-carbonyl complex M(eta1-CO) for both M=W and W+. The C-O insertion product, OMC, lies by 5.2 and 69.3 kcal/mol higher than the corresponding M(eta1-CO) isomer, for M=W and W+, respectively, and is separated from the latter by a large energy barrier.     

2-hydroxypyridine <--> 2-pyridone tautomerization: catalytic influence of formic acid

A 1:1 hydrogen-bonded complex between 2-pyridone and formic acid has been characterized using laser-induced-fluorescence excitation and dispersed fluorescence spectroscopy in a supersonic jet expansion. Under the same expansion condition, the fluorescence signal of the tautomeric form of the complex (2-hydroxypyridine...formic acid) is absent, although both the bare tautomeric molecules exhibit well-resolved laser-induced-fluorescence spectra. Quantum chemistry calculation at the DFT/B3LYP/6-311++G** level predicts that in the ground electronic state the activation barrier for tautomerization from hydroxy to keto form in bare molecules is very large (approximately 34 kcal/mol). However, the process turns out to be nearly barrierless when assisted by formic acid, and double proton transfer occurs via a concerted mechanism.     

Br2+2HI=2HBr＋I2应机理的密度泛函理论

用密度泛函理论(DFT)B3LYP方法，取3-21G**基组研究了气相反应Br2＋2HI=2HBr＋I2的机理，求得一系列四中心和三中心的过渡态.双分子基元反应Br2＋HI→HBr＋IBr和IBr＋HI→I2＋HBr的活化能(81.02和121.08 kJ•mol－1)小于Br2、HI和IBr的解离能(249.21、320.16和232.42 kJ•mol－1)，故从理论上证明了标题反应将优先以分子与分子作用形式分两步完成.同时发现I原子与Br2分子反应生成较稳定的IBr2是一个无能垒过程，IBr2分解为IBr和Br原子的能垒为70.88 kJ•mol－1.     

Ab initio studies on Al(+)(H(2)O)(n), HAlOH(+)(H(2)O)(n-1), and the size-dependent H(2) elimination reaction

We report computational studies on Al(+)(H(2)O)(n), and HAlOH(+)(H(2)O)(n-1), n = 6-14, by the density functional theory based ab initio molecular dynamics method, employing a planewave basis set with pseudopotentials, and also by conventional methods with Gaussian basis sets. The mechanism for the intracluster H(2) elimination reaction is explored. First, a new size-dependent insertion reaction for the transformation of Al(+)(H(2)O)(n), into HAlOH(+)(H(2)O)(n-1) is discovered for n > or = 8. This is because of the presence of a fairly stable six-water-ring structure in Al(+)(H(2)O)(n) with 12 members, including the Al(+). This structure promotes acidic dissociation and, for n > or = 8, leads to the insertion reaction. Gaussian based BPW91 and MP2 calculations with 6-31G* and 6-31G** basis sets confirmed the existence of such structures and located the transition structures for the insertion reaction. The calculated transition barrier is 10.0 kcal/mol for n = 9 and 7.1 kcal/mol for n = 8 at the MP2/6-31G** level, with zero-point energy corrections. Second, the experimentally observed size-dependent H(2) elimination reaction is related to the conformation of HAlOH(+)(H(2)O)(n-1), instead of Al(+)(H(2)O)(n). As n increases from 6 to 14, the structure of the HAlOH(+)(H(2)O)(n-1) cluster changes into a caged structure, with the Al-H bond buried inside, and protons produced in acidic dissociation could then travel through the H(2)O network to the vicinity of the Al-H bond and react with the hydride H to produce H(2). The structural transformation is completed at n = 13, coincident approximately with the onset of the H(2) elimination reaction. From constrained ab initio MD simulations, we estimated the free energy barrier for the H(2) elimination reaction to be 0.7 eV (16 kcal/mol) at n = 13, 1.5 eV (35 kcal/mol) at n = 12, and 4.5 eV (100 kcal/mol) at n = 8. The existence of transition structures for the H(2) elimination has also been verified by ab initio calculations at the MP2/6-31G** level. Finally, the switch-off of the H(2) elimination for n > 24 is explored and attributed to the diffusion of protons through enlarged hydrogen bonded H(2)O networks, which reduces the probability of finding a proton near the Al-H bond.     

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.     

Quantum mechanical study of the potential energy surface of the ClO + NO2 reaction

In the study of the reaction pathways of the ClO + NO2 reaction including reliable structures of the reactants, products, intermediates, and transition states as well as energies the MP2/6-311G(d), B3LYP/6-311G(d), and G2(MP2) methods have been employed. Chlorine nitrate, ClONO2, is formed by N-O association without an entrance barrier and is stabilized by 29.8 kcal mol(-1). It can undergo either a direct 1,3 migration of Cl or OCl rotation to yield an indistinguishable isomer. The corresponding barriers are 45.8 and 7.1 kcal mol(-1), respectively. ClONO2 can further decompose into NO3 + Cl with an endothermicity of 46.4 kcal mol(-1). The overall endothermicity of the NO2 + ClO --> NO3 + Cl reaction is calculated to be 16.6 kcal mol(-1). The formation of cis-perp and trans-perp conformer of chlorine preoxynitrite, ClOONO(cp) and ClOONO(tp), are exothermic by 5.4 and 3.8 kcal mol(-1), respectively. Calculations on the possible reaction pathways for the isomerization of ClOONO to ClONO2 showed that the activation barriers are too high to account for appreciable nitrate formation from peroxynitrite isomerization. All quoted relative energies are related to G2(MP2) calculations.     

Computational modeling of a stereoselective epoxidation: reaction of carene with peroxyformic acid

Electronic structure theory was used to model the epoxidation of 3-carene by peroxyformic acid. Reactants, products, and transition states were optimized at the B3LYP/6-31G* level of theory, followed by B3LYP/6-311+G** and MP2/6-311+G** single point calculations. The reaction pathway yielding the trans-epoxide product was found to have a significantly lower reaction barrier (7.8 kcal/mol) than that leading to the cis-epoxide product (9.4 kcal/mol), in agreement with expectations. Magnetic shieldings of the two isomeric carene epoxides were also calculated, using the GIAO method, and compared to experimental (1)H and (13)C NMR spectra. Although the calculated carbon spectra proved inconclusive, the proton shieldings calculated for the trans-epoxide correlated much more closely to the experimental values for the major epoxidation product than did the shieldings calculated for the cis-epoxide, serving to verify the identity of the major product.     

Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structures

Histone lysine methylation is emerging as an important mechanism to regulate chromatin structure and gene activity. To provide theoretical understanding of its reaction mechanism and product specificity, ab initio quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations and molecular dynamics simulations have been carried out to investigate the histone lysine methyltransferase SET7/9. It is found that the methyl-transfer reaction catalyzed by SET7/9 is a typical in-line S(N)2 nucleophilic substitution reaction with a transition state of 70% dissociative character. The calculated average free energy barrier at the MP2(6-31+G) QM/MM level is 20.4 +/- 1.1 kcal/mol, consistent with the activation barrier of 20.9 kcal/mol estimated from the experimental reaction rate. The barrier fluctuation has a strong correlation with the nucleophilic attack distance and angle in the reactant complex. The calculation results show that the product specificity of SET7/9 as a monomethyltransferase is achieved by disrupting the formation of near-attack conformations for the dimethylation reaction.     

Radical-molecule reactions HCO/HOC + C2H2: mechanistic study

A detailed computational study is performed on the unknown radical-molecule reactions between HCO/HOC and acetylene (C2H2) at the CCSD(T)/6-311G(2d,p)//B3LYP/6-311G(d,p)+ZPVE, Gaussian-3//B3LYP/6-31G(d), and Gaussian-3//MP2(full)/6-31G(d) levels. For the HCO + C2H2 reaction, the most favorable pathway is direct C-addition forming the intermediate HC=CHCH=O followed by a 1,3-H-shift leading to H2C=CHC=O, which finally dissociates to the product C2H3 + CO. The overall reaction barrier is 13.8, 10.5, and 11.3 kcal/mol, respectively, at the three levels. The quasi-direct H-donation process to produce C2H3 + CO with barriers of 14.0, 14.1, and 14.1 kcal/mol is less competitive. Thus only at higher temperatures could the HCO + C2H2 reaction play a role. In contrast, the HOC + C2H2 reaction can barrierlessly generate C2H3 + CO via the quasi-direct H-donation mechanism proceeding via a prereactive complex with OH...C2 hydrogen bonding. This is suggestive of the potential importance of the HOC + C2H2 reaction in both combustion and interstellar processes. However, the direct C-addition channel is much less competitive. For both reactions, the possible formation of the intriguing interstellar molecules propadiene and propynal is also discussed. The present theoretical study represents the first attempt to probe the reaction mechanism between HOC and pi-systems. Future laboratory investigations on both reactions (particularly HOC + C2H2) are recommended.