Intrinsic Reaction Coordinate Calculations Research Articles

Ab initio direct dynamics study of cyclopropyl radical ring-opening.

Quasiclassical direct dynamics simulations, at the CASSCF(3,3)/6-31G(d) level of theory, are used to study the stereochemistry of the electrocyclic ring-opening reaction of the cyclopropyl radical. The trajectories are initiated at the reaction's transition state (TS), with their initial conditions sampled from the TS's 174 degrees C Boltzmann distribution. Intrinsic reaction coordinate calculations predict the overall reaction to have disrotatory stereochemistry. Though this is the preferred initial reaction stereochemistry in the trajectories, 43% of the trajectories follow the conrotatory path. Four unique trajectory types are observed during 200 fs dynamics of the product allyl radical. Intramolecular vibrational energy redistribution and internal rotation are incomplete on this time scale, and a statistical distribution of the allyl isomers is not observed.

A Computational Study of Conformers of 2-Thiaoxacyclohexane (1,2-Oxathiane)

Ab initio molecular orbital theory with the 6-31G(d), 6-31G(2d), 6-31+G(d), 6-31G(d,p), 6-31+G(d,p), and 6-311G(d,p) basis sets and the hybrid density functionals B3LYP, B3P86, and B3PW91 have been used to calculate the optimized geometries and relative energies of the chair, half-chair, sofa, twist, and boat structures of 2-thiaoxacyclohexane (1,2-oxathiane). The values of the energy difference (ΔE, kcal/mol) between the chair and 3,6-twist structures of 1,2-oxathiane were 4.92 (HF), 4.73 (MP2), and 4.66 (DFT). The HF chair–twist energy difference (ΔGc–to) for 1,2-oxathane was 5.16 kcal/mol. Intrinsic reaction coordinate (IRC) calculations connected a transition state (TS-A) between the chair conformation and the less stable 2,5-twist form and connected two transition states (TS-B, TS-C) between the chair conformation and the more stable 3,6-twist conformer. The DFT energy differences between the chair and TS-A, TS-B, and TS-C were 11.4, 10.8, and 12.6 kcal/mol, respectively. Hyperconjugative stereoelectronic interactions were observed in the chair (no → \(\sigma _{{\text{C}}6 - {\text{H}}_{{\text{ax}}} }^*\) and \(\sigma _{{\text{C}} - {\text{H}}_{{\text{ax}}} } \) → \(\sigma _{{\text{C}} - {\text{H}}_{{\text{ax}}} }^* \)) and 3,6-twist (nS → \(\sigma _{{\text{C3}} - {\text{His}}_{{\text{oa}}} }^* \) and nO → \(\sigma _{{\text{C6}} - {\text{His}}_{{\text{oa}}} }^* \)) conformers of 1,2-oxathiane. The chair conformation of 1,2-oxthiane is 9.6 and 10.0 kcal/mol, respectively, less stable than the chair conformations of 3-thiaoxacyclohexane (1,3-oxathiane) and 4-thiaoxacyclohexane (1,4-oxathiane, thioxane).

Ab initio calculations of the potential energy surface for the reaction [formula omitted

The extensive potential energy surface for the reaction of N( 2 D) and CH 3F has been studied using the G2MP2 level of theory. The calculations reveal that the reaction will lead to the intermediate trans-CH 3NF firstly, which subsequently decomposes and isomerizes to products. Based on the present ab initio potential energy surface, the production channel, CH 2NF+H is the most feasible. The minimum-energy path is analyzed by an intrinsic reaction coordinate calculation.

Theoretical studies on the structures and isomerization of methylenelithoflurosilylenoid H 2CSiLiF

The main characters of the potential energy surface of the methylenelithoflurosilylenoid (H 2CSiLiF) are studied by ab initio calculations at the G2(MP2) level. Four equilibrium structures, a p-complex, a three-membered ring, a σ-complex and a silene, and three isomerization transition states are located, and isomerization reaction paths are investigated and confirmed by the intrinsic reaction coordinate (IRC) calculations. The calculations have shown that nonplanar p-complex structure has the lowest energy and should be experimentally detectable among four equilibrium structures of the H 2CSiLiF. The silene and σ-complex structures have high energies and are easy to isomerize to the three-membered ring structure with lower energy, but in fact, they will not exist. Also, the structural characteristics and bonding properties of various structures are analyzed in this Letter.

Theoretical studies on the structures and isomerization of silylenoid H2SiNaCl

The structures and isomerization of silylenoid H2SiNaCl were studied by ab initio molecular orbital theory at RHF/6-31G(d) and MP2/6-311G(d,p) levels. Three equilibrium structures and two isomeric transition states were located. Based on the MP2/6-311G(d,p) calculations, harmonic frequencies of various isomers were obtained and further single-point calculations were performed at the QCISD(T)/6-311G(d) and MP2/6-311+G(3df,2p) levels, respectively. G2(MP2) theory was used for calculations on energies. Isomerization paths for isomers were investigated by intrinsic reaction coordinate (IRC) calculations at MP2/6-311G(d,p) level. Changes (ΔH and ΔG) of thermodynamic functions, equilibrium constant K(T), A factor and reaction rate constant k of the isomerization reaction among isomers of H2SiNaCl were calculated and then thermodynamic and kinetic properties were analyzed. The stability, reactivity and existence of various equilibrium structures were also discussed in this paper.

Intrinsic reaction coordinate calculations of the inversion/bending potentials in the [formula omitted] states of ammonia

Mass-weighted intrinsic reaction coordinate calculations were carried out for the inversion/bending motion in the ground and lowest excited singlet states of NH 3 and ND 3. Vibrational eigenstates were obtained from these IRC potentials directly, obviating the need to make assumptions about the coordinate dependence of the reduced mass. The 0 ± inversion splittings for the X ̃ state of NH 3 and ND 3 are found to be 1.17 and 0.89 cm −1 , respectively, at the MP4(SDQ)/aug-cc-pVTZ level of theory. CASPT2-refined IRC scans of both the relaxed and vertical A ̃ -state surfaces were carried out. The A ̃ – X ̃ absorption spectra of NH 3 and ND 3 were modeled using the respective Boltzmann-weighted vibrational electronic transition matrix elements.

Theoretical studies of cyclopropylsilylenes: The structures and stability of cyclopropylsilylene C3H5SiH

AbstractAb initio molecular orbital calculations at the G2(MP2) level have been carried out on cyclopropylsilylene C3H5SiH. Four equilibrium structures were located. Like H2Si, the ground state of C3H5SiH is singlet and the triplet is the low‐lying excited state. The singlet–triplet separation energy is 127.9 kJ/mol. The cis‐trans isomerization path of singlet cyclopropylsilylene was investigated by intrinsic reaction coordinate (IRC) calculations. The calculations show that no gauche conformers exist along the potential energy curve of the cis‐trans isomerization and the isomerization happens with a barrier of 30.1 kJ/mol. Changes (ΔH and ΔG) in thermodynamic functions, equilibrium constant K(T), and A factor and reaction rate constant k(T) in Eyring transition state theory of the cis‐trans isomerization were also calculated. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001

The Electronic Spectroscopy and Photophysics of Piperidine in the Vapor Phase

The ground- and lowest excited-state properties of piperidine vapor are explored with respect to understanding its absorption and fluorescence properties. A ground-state intrinsic reaction coordinate (IRC) calculation was used to model the conformational potential energy surface connecting the equatorial and axial conformers. At the MP2/6-311++G** level of theory, the equatorial conformer is more stable by 310 cm-1 than the axial conformer, and the inversion barrier height is 2033 cm-1. Two transitions in the UV, with origins of 38 707 and 44 070 cm-1 are assigned. The S1 ← S0 transition (fobs ∼ 3.2 × 10-3) is Rydberg in nature, with considerable involvement of all the ring heavy atoms. A vibrational analysis of this transition shows a main progression in 640 cm-1, which is assigned as the N−H out-of-plane bending motion. The CIS-calculated equilibrium geometry of the S1 state indicates considerable distortion of the N atom relative to the Cα atoms. The one-dimensional absorption spectrum is modeled on th...

An ab initio study on the insertion reaction of silylenoid H 2SiLiF with H 2

The insertion reaction of lithofluorosilylenoid H 2SiLiF with H 2, H 2SiLiF+H 2 → SiH 4+LiF, has been studied by ab initio molecular orbital theory at the MP2/6-311G(d, p) level. The structures of reactants, transition state and products were fully optimized. G2(MP2) theory was used for calculations of molecular energies. The reaction path was investigated by intrinsic reaction coordinate (IRC) calculations. Based on the MP2/6-311G(d, p) calculations, harmonic frequencies of various molecules were obtained, and subsequently changes (Δ H and Δ G) in thermodynamic functions, equilibrium constant K( T), and factor A and reaction rate constant k in Eyring transition state theory were calculated.

Metal-assisted coupling of oximes and nitriles: a synthetic, structural and theoretical study

Chlorination of [Ph3PCH2Ph][PtCl3(EtCN)], obtained from the reaction of [PtCl2(EtCN)2] with [Ph3PCH2Ph]Cl, formed the platinum(IV) complex [Ph3PCH2Ph][PtCl5(EtCN)] which, at ambient temperature and both in solution and in the solid phase, hydrolyses to the ammonia compound [Ph3PCH2Ph][PtCl5(NH3)] and undergoes nucleophilic addition by ketoximes or amidoxime HONCR1R2 [R1R2 = Me2, C4H8, C5H10, C9H16, C9H18 or Ph(NH2)] to give the corresponding iminoacylated product [Ph3PCH2Ph][PtCl5{HNC(Et)ONCR1R2}]. All compounds were characterized by elemental analyses, FAB mass spectrometry, IR and 1H, 13C-{1H}, 31P-{1H} and 195Pt NMR spectroscopies. A crystal structure determination of [Ph3PCH2Ph][PtCl5{NHC(Et)ONC(C9H16)}] disclosed amidine one-end rather than the N,N-bidentate co-ordination mode of the N-donor ligand. The iminoacylation by oximes was investigated by ab initio methods (at RHF level using quasi-relativistic pseudopotentials for platinum) for [PtCl5(NCMe)]− which were also applied to the related neutral platinum(IV) [PtCl4(NCMe)2] and platinum(II) [PtCl2(NCMe)2] complexes. The calculations included geometry optimization of the starting and final complexes, location of possible transition states for the reaction discussed and intrinsic reaction coordinate calculations for one reaction. The results obtained provided an interpretation, on the basis of kinetic (activation energies) and thermodynamic (reaction energies) effects, for the order of reactivity observed [neutral PtIV > anionic PtIV > neutral PtII] and indicated that a mechanism based on nucleophilic addition of the protic nucleophile (undeprotonated oxime), to form a transition state with a four-membered NCOH ring, is energetically favoured relative to the alternative one involving prior deprotonation of the oxime, unless base-catalysed conditions are operating.

Disrotatory versus conrotatory electrocyclic ring opening of Dewar benzene: the conrotatory pathway is preferred and does not involve trans-benzene

For the electrocyclic ring opening of Dewar benzene ( 2) into benzene ( 1), both a disrotatory and conrotatory pathway with distinct transition states, TS1 and TS2, respectively, were found at the CASSCF(10,10)/6-311G** level of theory. The importance of the CASSCF(10,10) active space for the proper description of TS1 and TS2 was illustrated by similar calculations using a smaller active space, viz. CASSCF(2,2), CASSCF(4,4) and CASSCF(6,6). Although TS2 represents a true saddle point, TS1 appears to be a higher order saddle point at these levels of theory. Single-point multi-reference SDCI (MRCI) calculations at the CASSCF(10,10)/6-311G** geometries and natural orbitals were performed at all stationary points to obtain more reliable total energies. In contrast to common belief, TS2 lies below TS1 (by 6.62 kcal/mol), i.e. the conrotatory process is favored. Moreover, CASSCF(10,10)/6-311G** Intrinsic Reaction Coordinate (IRC) calculations show that upon conrotatory electrocyclic ring opening 2 does not give the extraordinarily strained trans-benzene ( 3), i.e. cis, cis, trans-cyclohexa-1,3,5-triene. The conversion of 3 into 1 and vice versa is a distinct process on the C 6H 6 potential energy surface.

Structure and [2+2] Cycloreversion of the Cyclobutane Radical Cation

The [2+2] cycloreversion reaction of the cyclobutane radical cation was studied using high-level MO and DFT methods. Three distinct, but energetically very similar, structures are located for the cyclobutane radical cation: a parallelogram that corresponds to the minimum on the Jahn−Teller surface, a rhombus, corresponding to a transition structure connecting two parallelograms, and a rectangle that is a second-order saddle point. Intrinsic reaction coordinate calculations show that the reaction proceeds in a concerted fashion. The calculated reaction mode is not consistent with a putative acyclic intermediate, but rather shifts the two ethylene fragments relative to each other. The transition structure connects the product complex to the parallelogram structure of the cyclobutane radical cation. The overall thermochemistry calculated by the QCISD(T)//QCISD and the B3LYP methods are in good agreement with the available experimental data. It is shown that the experimental hyperfine coupling constants do not imply a puckered structure, as claimed earlier. The electronic structure and magnetic properties of the transition structure are elucidated by NICS calculations.

A new mechanism for the [formula omitted] reaction on the triplet surface

Using second-order Møller–Plesset (MP2) perturbation theory, a new mechanism for the reaction of CH(X 2Π)+NO(X 2Π)→CO(X 1Σ +)+NH(X 3Σ − ) has been revealed on the 3 A″ potential energy surface. The association of CH with NO leads to cis-HCON which decomposes directly to the products CO+NH via a four-membered ring transition state. The minimum-energy path is analyzed by an intrinsic reaction coordinate calculation. G1, G2 and G2MP2 methods are used to obtain the barrier heights and reaction heats.

A theoretical study on reaction mechanism of oxidative coupling reaction of p-phenylenediamine with phenol: a proposal of the route via a [5,5]-sigmatropic rearrangement

We have studied the mechanism for the reaction of p-benzoquinone diimine with phenolate, the model reaction of a key elementary step in oxidative coupling of N,N-dialkyl- p-phenylenediamine with phenolic compounds, using ab initio molecular orbital and density functional theory methods and analyzed the reaction path in detail by the intrinsic reaction coordinate calculation. On the basis of the calculated results, we propose a new reaction mechanism for formation of leuco-indoaniline through the suprafacial [5,5]-sigmatropic rearrangement via an intermediate which has not been so far observed experimentally. After the intermediate is formed regioselectively under charge control with no barrier, the rearrangement proceeds easily under orbital control into leuco-indoaniline via a rotational isomer. The activation energy for this rearrangement was strongly dependent on the electron correlation effects because of the stacking interaction between the two benzene rings in the transition state, and the most reliable activation energy of approximately 7 kcal/mol was obtained by the B3LYP method with the 6-31+G** basis set.

Ab Initio Study on the Keto−Enol Tautomerism of the α-Substituted Acetaldehydes XH2CCHO (X = H, BH2, CH3, NH2, OH, F, CN, NC, and Cl): Comparison with the Tautomerism in α-Substituted Acetaldimines and Acetyl Derivatives

Ab initio molecular orbital calculations have been performed on the α-substituted acetaldehydes XH2CCHO (X=H, BH2, CH3, NH2, OH, F, CN, NC, and Cl) to investigate the substituent effects on the keto−enol tautomerisms. Structures for all stationary point (ketones, enols, and transition states) were optimized and characterized at the MP2(full)/6-31G* and MP2(full)/6-31G** levels of theory. Intrinsic reaction coordinates (IRC) calculations were performed in order to connect transition structures with the appropriate tautomeric pairs. Results from various levels of calculations all show that the keto forms are thermodynamically more stable than the enol forms. At the G2 level, the former tautomers are energetically favored over the latter forms by 2.9, 5.6, 7.8, 9.6, 9.7, 10.2, 10.4, 11.8, and 12.1 kcal/mol for X = BH2, CN, NC, NH2, CH3, OH, Cl, H, and F, respectively. All substituents except F stabilize the enol form relative to its keto counterpart as shown by the reduction of the energy gaps between the fo...

Ab initio molecular orbital and density functional characterization of the potential energy surface of the N2O+Br reaction

The lowest doublet (2A′) potential energy surface for the reaction N2O+Br→N2+OBr was investigated using ab initio and nonlocal density functional theory calculations. Geometries, energies and vibrational frequencies for stationary points were evaluated at HF/6-31G(d), MP2/6-31G(d) and B3LYP/6-31G(d) levels of theory. All levels of calculation give a similar geometry for the transition state, but the MP2 barrier is narrower. Intrinsic reaction coordinate (IRC) calculations starting from the transition state and proceeding toward the two local minima confirmed that IRC trajectories reached the reactant and product regions, respectively. Calculations of kinetic isotope effects were also performed. They are influenced by the theoretical level and the B3LYP method gives results in best agreement with experimental data. The HF method predicts the relative values of both the primary and secondary nitrogen kinetic isotope effects less accurately. At the MP2 level of calculations only the oxygen kinetic isotope effect is reproduced satisfactorily. Finally, the best value for the activation energy is again provided by the B3LYP method.

Modern valence-bond description of chemical reaction mechanisms: the 1,3-dipolar addition of fulminic acid to ethyne

The electronic mechanism for the gas-phase 1,3-dipolar cycloaddition of fulminic acid (HCNO) to ethyne is studied through a combination of modern valence-bond theory in its spin-coupled (SC) form and intrinsic reaction coordinate calculations utilizing a complete-active-space self-consistent field wavefunction. It is shown that the concerted reaction follows a “heterolytic” route, during which three orbital pairs corresponding to three distinct bonds in the reactants (an in-plane π bond in ethyne, and a C-N and an N-O in-plane bond in HCNO) shift simultaneously to create the two new bonds closing the isoxazole ring and a nitrogen lone pair. The analysis of the SC wavefunction strongly suggests that the reacting system remains nonaromatic throughout the most important part of the cycloaddition process. This investigation provides the first demonstration of an alternative SC description of a bond rearrangement, achieved through the movement of singlet orbital pairs through space, during which at least one of the orbitals within a pair becomes completely detached from the atomic centre with which it is associated initially and ends up localized about another centre.

A Kinetic Analysis of the Conformational Flexibility of Steroid Hormones

For a set of 10 androgen steroids and estradiol (E2), the kinetic feasibility of conformation flexibility of the cyclic moieties was studied under the constraint of maintaining the ByC trans and CyD trans ring fusion of the natural and biologically active enantiomer. To this end, the conformational energy surface was quantified using the semiempirical quantum chemical AM1 model. The computational analysis included the location of Conformational transition states with associated barriers, and intrinsic reaction coordinate (IRC) calculations to characterize the trajectories of the rotations and the relationships of the transition states to neighbouring chair and twist conformations. Conformational transformations were observed only for the A and B rings except for E2, which yielded corresponding transformations for the B and C ring, respectively. Interestingly, the rotation barriers starting from the lowest-energy conformations differed substantially, ranging from below 10 kJymol for four compounds to 18 ‐ 20 kJymol for another five compounds. Moreover, chair and twist conformations were found only for steroids with higher saturated rings, while semichairs and semitwists occurred for steroids with aromatic or partly unsaturated rings, and B-ring transformations lead to kinetically unstable conformations with very flat energy minima. Although the rotation barriers for most of the transitions are clearly above the thermal energy (kT) at room temperature when evaluated relative to the lowestenergy conformations, the associated energy demands are well below the gain in energy from ligand-receptor binding. The results suggest that conformer interconversion are feasible from both a thermodynamic and kinetic perspective, and support previous investigations in which conformer distributions rather than lowest energy conformations were considered when assessing hormone receptor topography and the biological activity of ligands.

Is a Transition State Planar or Nonplanar in Oxidative Additions of C−H, Si−H, C−C, and Si−C σ-Bonds to Pt(PH3)2? A Theoretical Study

A theoretical study of oxidative additions of H−CH3, CH3−CH3, H−SiR3, and SiR3−CH3 (RH, Cl, or Me) to Pt(PH3)2 was carried out with ab initio MO/MP2-MP4SDQ, CCD, and CCSD methods. The oxidative addition reactions of C−H and Si−H σ-bonds occur through a planar transition state (TS) structure, in accordance with the expectation from an orbital interaction diagram. However, the oxidative addition reactions of CH3−CH3 and SiH3−CH3 take place through a nonplanar TS structure, unexpectedly; the dihedral angle δ between PtP2 and PtXC planes (X = C or Si) is about 70° for X = Si and about 80° for X = C. Intrinsic reaction coordinate calculation of the SiH3−CH3 oxidative addition clearly indicated that this nonplanar TS is smoothly connected to the planar product on the singlet surface. The dihedral angle δ at the TS is larger in the SiMe3−CH3 and SiCl3−CH3 oxidative additions than that in the SiH3−CH3 oxidative addition. Electron distribution in the TS and effects of bulky substituent on the dihedral angle sugges...

Molecular Orbital Studies of the Intramolecular Reaction of Protonated cis- and trans-3,4-Epoxypentan-1-ol

The transition structures for the intramolecular reaction of protonated cis- and trans-3,4-epoxypentan-1-ol (13) and (16), which result in the formation of protonated cis- and trans-2-methylfuran-3-ols (14) and (18) with inversion and retention, have been determined at the ab initio MP2/6-31G* and hybrid density functional B3LYP/6-31G* levels of theory. Intrinsic reaction coordinate calculations for the lower energy inversion pathways for formation of the 2-methylfuran-3-ols show that intramolecular attack occurs in concert with ring opening. The reaction pathways are far from optimum for best orbital overlap, reflecting the strained bicyclic nature of the transition structures.