Comparison of AM1 and PM3 semiempirical to ab initio methods in the study of Diels-Alder reactions of butadiene and cyclopentadiene with cyanoethylenes

Assuming a concerted synchronous mechanism with one transition state of the Diels-Alder reactions, the structures of the transition states and the activation energies for the reactions of butadiene and cyclopentadiene with cyanoethylenes were calculated by AM1 and PM3 semiempirical methods. The structural parameters were compared with those obtained by high level Gaussian calculations, whereas the activation energies were compared both with the ab initio calculations and those obtained experimentally. The structural properties calculated with PM3 methods are in general in better agreement with the ab initio calculations. The low level ab initio calculations are in many cases worse than the semiempirical methods. All predicted activation energies with both semiempirical methods are up to 300% higher than the experimental values. The predicted reactivity is also opposite to the experimental data. Only the very high level Gaussian calculations are in good correlation with experimental results. The predicted selectivity of the reaction is also opposite to the experimental facts. Two explanations are offered for this discrepancy: AM1 and PM3 methods cannot handle the calculation of the concerted Diels-Alder transition states and are not recommended to be used for that purpose, or this Diels-Alder reaction is not concerted but is stepwise.     

A new mechanism for the Favorskii rearrangement

The title reaction was investigated by the use of ONIOM-RB3LYP calculations. A reaction system composed of alpha-chlorocyclohexanone, a methoxide ion and 8 MeOH solvent molecules was adopted. Two reaction channels, the semibenzilic acid mechanism (A) and cyclopropanone mechanism (B), were compared. B is found to be more favorable than A. The rate-determining step of B is the (MeOH)(3) addition transition state (TS3B) to the cyclopropanone intermediate. While TS3B involves a concerted function of MeO(-) addition and proton relays, it has a large activation energy. A new route was found, where the chloride ion evolved at the cyclopropane formation step (TS2B) works as a nucleophile to the cyclopropanone intermediate. Thus, a cyclopentane-carbonyl chloride intermediate is formed with a small activation energy. A new cyclopropanone mechanism is proposed.     

Origins of stereoselectivity in intramolecular Diels-Alder cycloadditions of dienes and dienophiles linked by ester and amide tethers

B3LYP/6-31+G(d) calculations of structures and relative energies for competing transition states for intramolecular Diels-Alder reactions of substituted 3,5-hexadienyl acrylates and acrylamides show that boatlike conformations are sometimes favored in the forming ring that includes the tether.     

Ab initio study of catalyzed and uncatalyzed amide bond formation as a model for peptide bond formation: Ammonia-Glycine reactions

As a model reaction for peptide and bond formation, the S_N2 reactions between glycine and ammonia have been studied with and without amine catalysis: using ab initio molecular-orbital methods. For each of the catalyzed and uncatalyzed reactions, two reaction mechanisms have been examined: a two-step and a concerted mechanism. The stationary points of each reaction, including intermediate and transition states, have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of the reaction. The calculations demonstrate that a second ammonia molecule catalyzes amide bond formation, and that the two-step mechanism is more favorable than the concerted one for the catalyzed reaction, while for the uncatalyzed reaction both mechanisms are competitive.     

Theoretical investigations on thermal rearrangement reactions of (aminomethyl)silane

Thermal rearrangement reactions of (aminomethyl)silane H(3)SiCH(2)NH(2) were studied by ab initio calculations at the G3 level. The results show that two dyotropic reactions could happen when H(3)SiCH(2)NH(2) is heated. In one reaction, the silyl group migrates from the carbon to the nitrogen atom while a hydrogen atom shifts from the nitrogen to the carbon atom, forming (methylamino)silane CH(3)NHSiH(3) (reaction A). This reaction can proceed via three paths: a path involving two consecutive steps with two transition states and one intermediate metastable carbene species (A-1); and two concerted paths (A-2 and A-3). In the other reaction, the amino group migrates from the carbon to the silicon atom while a hydrogen atom shifts from the silicon to the carbon atom, via a double three-membered ring transition state, forming aminomethylsilane CH(3)SiH(2)NH(2) (reaction B). Reaction rate constants, changes (DeltaS(#), DeltaH, and DeltaG) in thermodynamic functions and equilibrium constants of the reactions were calculated with the MP2(full)/6-311G(d,p) optimized geometries, harmonic vibrational frequencies and G3 energies of reactants, transition states, intermediates and products with statistical mechanical methods and the conventional transition-state theory (TST) with Wigner tunneling approximation over a temperature range 400-1800 K.     

Origin of selectivity of tsuji-trost allylic alkylation of lactones: highly ordered transition States with lithium-containing enolates

We report computational investigations on the mechanism and the selectivity of Pd-catalyzed allylic alkylation of γ-valerolactone. Density functional calculations using the B3LYP functional are performed on the selectivity-determining nucleophilic addition step of this reaction. The B3LYP results of commonly assumed pathways fail to reproduce the observed selectivity of the reaction. Therefore, alternative pathways are considered for the nucleophilic addition step, to explain the experimentally established role of the additives LiCl and lithium diisopropyl amide (LDA) in the Pd-catalyzed reaction. These pathways involve different approaches of the enolate toward the η(3) -allylpalladium complex that are mainly guided by stabilizing Cl(δ-) ???Li(δ+) ???O(enolate) interactions in the transition state. In the calculations, the experimentally observed trans-product selectivity for the prototypical reaction with (S)-BINAP ligands is found only when assuming the addition of a "mixed" Li-enolate/LiCl adduct to the η(3) -allylpalladium complex. This mechanism provides a reasonable explanation for the experimental results and sheds light on the role of LiCl in the reaction. The analysis of the different transition-state models allows us to identify steric and electronic factors that stabilize or destabilize the relevant diastereomeric transition states. Calculations for different combinations of substrates (γ-valerolactone and δ-caprolactone) and catalysts (with (R)- and (S)-BINAP ligands) reproduce the experimentally observed selectivities well and thus provide further support for the proposed mechanism.     

A new insight into using chlorine leaving group and nucleophile carbon kinetic isotope effects to determine substituent effects on the structure of SN2 transition states

Chlorine leaving group k(35)/k(37), nucleophile carbon k(11)/k(14), and secondary alpha-deuterium [(kH/kD)alpha] kinetic isotope effects (KIEs) have been measured for the SN2 reactions between para-substituted benzyl chlorides and tetrabutylammonium cyanide in tetrahydrofuran at 20 degrees C to determine whether these isotope effects can be used to determine the substituent effect on the structure of the transition state. The secondary alpha-deuterium KIEs indicate that the transition states for these reactions are unsymmetric. The theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion; i.e., they suggest that the transition states for these reactions are unsymmetric with a long NC-C(alpha) and reasonably short C(alpha)-Cl bonds. The chlorine isotope effects suggest that these KIEs can be used to determine the substituent effects on transition state structure with the KIE decreasing when a more electron-withdrawing para-substituent is present. This conclusion is supported by theoretical calculations. The nucleophile carbon k(11)/k(14) KIEs for these reactions, however, do not change significantly with substituent and, therefore, do not appear to be useful for determining how the NC-C(alpha) transition-state bond changes with substituent. The theoretical calculations indicate that the NC-C(alpha) bond also shortens as a more electron-withdrawing substituent is placed on the benzene ring of the substrate but that the changes in the NC-C(alpha) transition-state bond with substituent are very small and may not be measurable. The results also show that using leaving group and nucleophile carbon KIEs to determine the substituent effect on transition-state structure is more complicated than previously thought. The implication of using both chlorine leaving group and nucleophile carbon KIEs to determine the substituent effect on transition-state structure is discussed.     

Quantum chemical studies of a model for peptide bond formation. 3. Role of magnesium cation in formation of amide and water from ammonia and glycine

The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.     

Origin of diastereoselectivity in the tandem oxy-Cope/Claisen/ene reaction: experimental and theoretical studies of the ring inversion mechanism

We report herein a detailed investigation into the reaction mechanism of the oxy-Cope/Claisen/ene reaction. A series of chiral substrates was prepared, subjected to the tandem sequence, and the enantiomeric excess of the final products was evaluated. The observed conservation of enantiomeric excess was taken as evidence that the ring inversion of the intermediary enol ether does not occur. DFT calculations were used to map out the potential energy surface for the reaction and evaluate the relative energies of the ring inversions relative to those of the Claisen and ene reactions. Transition state energies thus obtained were found to support the presence of a high-energy transition state for the ring inversion of B to D provided R(1) not equal H. In addition, the calculations lent further support to the hypothesis that the selectivity of the transannular ene reaction is under Curtin-Hammett control.     

A computational study of the effect of bending on secondary kinetic isotope effects in SN2 transition states

Using conventional transition state theory, the secondary deuterium kinetic isotope effect (KIE) in the inversion SN2 reaction of CH3F and F- is calculated to be small, 0.98 (T = 298 K). This is shown to be the result of a balance among opposing entropy and enthalpy terms. By contrast, KIE in the retention SN2 mechanism is calculated to be large (1.5). Accordingly, KIE is a potential observable for discriminating between the two mechanisms. Large KIE's are also found for the inversion and retention mechanisms of the ion pair reactions between CH3F and LiF. All of the transition structures leading to large KIE's have a bent FCF angle and an imaginary frequency that is sensitive to deuterium labeling.     

Decomposition reactions of azo compounds,as studied by quantum chemistry methods and the parabolic model

Decomposition reactions of azoalkanes of different structure were studied by quantum chemistry methods (MP2/6-311++G** calculations) and by the method of three intersecting parabolas (M3IP). The MP2 method was used to obtain the transition-state geometries, the bond lengths in the molecules under study, and the activation energies. Possible mechanisms of decomposition are discussed. Concerted decomposition of branched azoalkanes was shown to be the most probable mechanism of the process. The M3IP method was used to calculate the kinetic and thermodynamic parameters of concerted decomposition of azoalkanes and to determine and evaluate the main factors affecting the activation energy (E). The stabilization energy of the radical being formed in the decomposition reaction is one of the key factors determining the concerted mechanism. The kinetic parameters calculated by the two independent methods are in good agreement.

     

Glycine Peptide Bond Formation Catalyzed by Faujasite

The catalysis of peptide bond formation between two glycine molecules on H‐FAU zeolite was computationally studied by the M08‐HX density functional. Two reaction pathways, the concerted and the stepwise mechanism, starting from three differently adsorbed reactants, amino‐bound, carboxyl‐bound, and hydroxyl‐bound, are studied. Adsorption energies, activation energies, and reaction energies, as well as the corresponding intrinsic rate constants were calculated. A comparison of the computed energetics of the various reaction paths for glycine indicates that the catalyzed reaction proceeds preferentially via the concerted reaction mechanism of the hydroxyl‐bound configuration. This involves an eight‐membered ring of the transition structure instead of the four‐membered ring of the others. The step from the amino‐bound configuration to glycylglycine is the rate‐determining step of the concerted mechanism. It has an estimated activation energy of 51.2 kcal mol^?1. Although the catalytic reaction can also occur via the stepwise reaction mechanism, this path is not favored.     

Dynamic and static conformational analysis of acylated tetrahydrobenzazepines

A detailed high-field NMR analysis of several acylated tetrahydrobenzazepines, supported by molecular mechanics calculations, indicates that the heterocyclic ring in these compounds exists in a chair conformation, with the carbonyl oriented anti to the aryl moiety in the dominant rotamer. Surprisingly, ring methylenes are typically diastereotopic at room temperature, as the barriers for the process of enantiomerization of the seven-membered ring are much higher than expected. It is shown that ring inversion is correlated (but not concerted) with rotation of the amide moiety, as the carbonyl is forced out of conjugation with the nitrogen in the transition state.     

Theoretical investigation of lone pair inversions, ring openings, and hydride shifts in O-methylated epoxides

Mechanisms associated with the isomerization of the O-methylethylene oxonium ion and its tetramethyl-substituted analogue have been explored using correlated electronic structure calculations. The minima and transition states associated with inversion at the oxygen atom, as well as those associated with opening of the epoxide ring, have been characterized. The calculated barrier to inversion at the oxygen atom for the O-methylethylene oxonium ion, 15.7 kcal/mol, agrees well with the experimentally determined value, 10+/-2 kcal/mol. Our calculations indicate that a significantly higher barrier exists for the ring-opening mechanism that leads to more thermodynamically stable structures. This work includes the first known calculations on the O-methyl-2,3-dimethyl-2-butene oxonium ion along with transition states and intermediates associated with ring opening and inversion at the oxygen atom. Results show that there is a significantly lower barrier to ring opening as compared to the O-methylethylene oxonium ion species, leading to a lower probability of isolating this species. The effects of basis sets and correlation techniques on these ions were also analyzed in this work. Our results indicate that the B3LYP/6-31G* level is reliable for obtaining molecular geometries for both minima and transition states on the C3H7O+ and C7H15O+ potential energy surfaces.     

Internal dynamics of flexible molecules: Cyclohexane

Summary The international motions of a single cyclohexane molecule are studied by molecular dynamics calculations. Classical trajectories are calculated by integrating Newton's equation of motion. The potential functions used are essentially the same as in Allinger's MM2 program which is widely applied for calculations on conformational energies of organic molecules.Geometries and relative energies are reported for all stable low energy conformers and some transition states of cyclohexane. Vibrational frequencies of classical oscillations of individual bonds — computed for ethane as reference system — are close to the experimental values.Two trajectories of the molecular dynamics of cyclohexane were simulated. In the first we were able to follow the process of ring inversion: chair twisted forms inverted chair. The reaction path is analysed in detail and compared with static approaches. The second trajectory shows the correlated reorientation of the possible twisted forms alone. This process is known as pseudorotation.Dedicated to Prof. Dr. Karl Schlögl     

Secondary fluorescences of 4'-(1-pyrenyl)acetophenone and p-dimethylaminoacetophenone

4'-(1-Pyrenyl)acetophenone (PYRA) and p-dimethylaminoacetophenone (DMAA) were investigated in nonpolar and polar protic and aprotic solvents over a wide temperature range. Quantum chemical (INDO/S) calculations of the energies of electronic transitions, oscillator strengths and dipole moments were performed for planar and twisted conformations of both compounds. For DMAA, the experimental results are well explained in terms of the TICT state. In the case of PYRA in polar aprotic solvents, two alternative models are discussed: TICT state formation or inversion of the two low lying singlet states.     

Theoretical study of the highly diastereoselective 1,3-dipolar cycloaddition of 1,4-dihydropyridine-containing azomethine ylides to [60]fullerene (Prato's reaction)

The 1,3-dipolar cycloaddition of azomethine ylides bearing the biologically active 1,4-dihydropiridine ring to C(60) was investigated by means of quantum mechanical calculations at the semiempirical AM1 and DFT (B3LYP/6-31G) methods. The presence of two chiral centers and one chiral axis in the resulting fulleropyrrolidines leads to four possible [6,6] cycloaddition products. Formation of atropoisomers has also been considered. The transition-state structures were computed for the four different cycloaddition pathways to find out the lowest activation energy stereoisomer. In all cases, a frequency analysis and an IRC calculation were carried out to fully characterize the located transition-state structures. AM1 results and single-point energy calculations at the B3LYP/6-31G//AM1 level for the four transition-state structures yield activation energies values below 5 kcal/mol.     

An ab initio investigation into the SN2 reaction: Frontside attack versus backside attack in the reaction of F− with CH3F

The energy hypersurface for the attack of fluoride ion on methyl fluoride has been explored with ab initio LCAO-SCF calculations at a split-valence basis set level. Transition states for frontside and backside attack have been located. In addition to transition states, two possible F^–-CH₃F clusters have been identified. The transition state for the substitution of fluoride with retention of configuration is found to be 56 kcal/mol higher than the transition state for inversion of configuration. The transition state for hydride displacement with inversion is 62 kcal/mol above the transition state for fluoride substitution with inversion.