Ab initio studies of three-membered ring formation through intramolecular nucleophilic substitution

Three-membered ring (3MR) forming processes of ⁻X(SINGLE BOND)CH₂(SINGLE BOND)CH₂(SINGLE BOND)F and ⁻CH₂(SINGLE BOND)C((SINGLE BOND)Y)(SINGLE BOND)CH₂(SINGLE BOND)F (X(DOUBLE BOND)CH₂, O, or S and Y(DOUBLE BOND)0 or S) through a gas phase neighboring group mechanism (S_Ni) are studied theoretically using the ab initio molecular orbital method with the 6–31+G* basis set. When electron correlation effects are considered, the activation (ΔG^≠) and reaction energies (ΔG⁰) are lowered by ca. 10 kcal mol⁻¹, indicating the importance of the electron correlation effect in these reactions. The contribution of entropy of activation (−TΔS^≠) at 298 K to ΔG^≠ is very small, and the reactions are enthalpy controlled. The ΔG^≠ and ΔG⁰ values for these ring closure processes largely depend on the stabilities of the reactants and the heteroatom acting as a nucleophilic center. The Bell–Evans–Polanyi principle applies well to all these reaction series. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1773–1784, 1997     

Definitive ab initio studies of model SN2 reactions CH(3)X+F- (X=F,Cl, CN,OH, SH,NH(2), PH(2))

The energetics of the stationary points of the gas-phase reactions CH(3)X+F(-)-->CH(3)F+X(-) (X=F, Cl, CN, OH, SH, NH(2) and PH(2)) have been definitively computed using focal point analyses. These analyses entailed extrapolation to the one-particle limit for the Hartree-Fock and MP2 energies using basis sets of up to aug-cc-pV5Z quality, inclusion of higher-order electron correlation [CCSD and CCSD(T)] with basis sets of aug-cc-pVTZ quality, and addition of auxiliary terms for core correlation and scalar relativistic effects. The final net activation barriers for the forward reactions are: E (b/F,F)=-0.8, E (b/F, Cl)=-12.2, E (b/F,OH)=+13.6, E b/F,OH=+16.1, E b/F,SH=+2.8, Eb/F, NH=+32.8, and E b/F,PH =+19.7 kcal x mol(-1). For the reverse reactions E b/F,F= -0.8, Eb/Cl,F =+18.3, E b/CN,F=+12.2, E b/OH,F =-1.8, E b/SH,F =+13.2, E b/NH(2),=-1.5, and E b/PH(2) =+9.6 kcal x mol(-1). The change in energetics between the CCSD(T)/aug-cc-pVTZ reference prediction and the final extrapolated focal point value is generally 0.5-1.0 kcal mol(-1). The inclusion of a tight d function in the basis sets for second-row atoms, that is, utilizing the aug-cc-pV(X+d)Z series, appears to change the relative energies by only 0.2 kcal x mol(-1). Additionally, several decomposition schemes have been utilized to partition the ion-molecule complexation energies, namely the Morokuma-Kitaura (MK), reduced variational space (RVS), and symmetry adapted perturbation theory (SAPT) techniques. The reactant complexes fall into two groups, mostly electrostatic complexes (FCH(3).F(-) and ClCH(3).F(-)), and those with substantial covalent character (NCCH(3).F(-), CH(3)OH.F(-), CH(3)SH.F(-), CH(3)NH(2).F(-) and CH(3)PH(2).F(-)). All of the product complexes are of the form FCH(3).X(-) and are primarily electrostatic.     

Complete basis set ab initio and hybrid density functional theory exploration of the potential energy surface in the reaction between an amino radical and nitrogen oxide

The potential energy surface for the reaction involving NH₂ plus NO was explored with a quadratic complete basis set ab initio approach and three hybrid density functional theory methods, the target being to accurately estimate activation barriers and the relative stability of the nitrogen–oxygen isomers. The computational results were compared with previously performed ab initio calculations and new, more accredited values for the NH₂NO rearrangement to HNNOH and for the HNNOH decomposition reaction were suggested. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 409–414, 1998     

Intramolecular nucleophilicS N 2 substitution at the tetrahedral carbon atom: Anab initio study

Pentacoordination of carbon atom in bicyclic organic compounds of the pentalene type was studied by theab initio RHF/6-31G^** and MP2(full)/6-31G^** methods. It was shown that intramolecularS _N 2 reactions with energy barriers within the energy scale of NMR spectroscopy can occur in systems in which a linear orientation of the attacking and leaving groups is realized. The barrier to the intramolecular nucleophilic substitution reaction in 2,3-dihydro-3-formylmethylenefuran is 36.9 (RHF) and 27.7 kcal mol⁻¹ (MP2) and decreases to 16.4 and 19.4 kcal mol⁻¹, respectively, in the case of diprotonation at the O atoms in this system. For model pentalene type compounds containing electron-deficient B atoms in the ring, theab initio calculations predict a further decrease in the barrier height (down to less than 10 kcal mol⁻¹). Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 7, pp. 1246–1256, July, 1999.     

Ab initio quantum chemical studies of reaction mechanism for CN with CH2CO

Six product channels have been found in the association reaction of CN + CH₂CO, and a variety of possible complexes and saddle points along the minimum energy reaction paths have been characterized at the UMP2(full)/6‐31G(d) level. The dominant reaction channels are the production of CH₂CN + CO and CH₂NC + CO. The isomerization and dissociation reactions of the major products of CH₂CN and CH₂NC have been investigated using the G2MP2 level. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Intramolecular nucleophilic substitution at an sp carbon: synthesis of substituted thiazoles and imidazole-2-thiones

The nucleophilic substitution reactions of vinylic bromides with intramolecular thioamide or thiourea moieties proceed to give a series of substituted thiazoles and imidazole-2-thiones.     

An Ab initio Theoretical Study on the Nonadiabatic Coupling for Na＋I2 Collision System

The ionic and neutral state potential energy surfaces (PESs) of Na I2 collision system have been calculated on QCISD(T) level by using ab initio method.The location and depth of the potential well,the collision radius and their fine structures have been analyzed at the equilibrium geometry of I2 molecule.The electronic transfer probabilities are also calculated in terms of Landau-Zener model.The lifetime of scattering resonance state is evaluated by the uncertainty principle.All the results have been compared with those obtained according to the Aten-Lanting-Los PES and Feng‘s PES.     

Ab initio calculation of dynamic polarizability and dielectric constant of carbon and silicon cubic crystals

Valence and conduction bands of carbon silicon cubic systems are first obtained by a process called linear combination of atomic orbitals self-consistent field (LCAO-SCF), both at the Hartree-Fock (HF) and local density approximation (LDA) levels. Then, the crystalline orbitals are used in a sum-over-states (SOS) method to calculate the corresponding dielectric constants related to electronic polarizabilities. This method allows parallel computations with large granularity of the optical properties and leads to uncoupled HF and LDA results. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1253–1263, 1997     

Theoretical study on the mechanisms of the nucleophilic substitution reactions of hydrosulfide ion and halomethanes

Three species involved in the nucleophilic substitution reaction of hydrosulfide ion and halomethanes are investigated by ab initio calculations. Geometries for stationary structures along the reaction paths are fully performed with the second‐order Møller–Plesset perturbation approximation with the cc‐pVDZ basis set. The monomer geometries determined by the MP2 method match the experimental results very well. Single point energy calculations are carried out at the coupled cluster with perturbative triple excitations CCSD (T) theory with aug‐cc‐pVDZ basis set. Halomethanes have three conformers here, which lead to the three product channels, HSCH₃ + F^?1, HSCH₃ + Cl^?1, and HSCH₃ + Br^?1. The investigation encompasses the six complexes formed among three channels, respectively. By selecting the six complexes as the model, we investigate the binding energy, topological property of the electron charge density and their Laplacian in detail theoretically. Electrostatic density potential maps of halomethanes are generated for the determination of attractive interaction sites. It is proved that the similar misshaped electron clouds of the three halogen atoms result in the similar properties of the carbon‐halogen bonds, and reveals that the product ion‐dipole complexes interactions are predominantly electrostatic in nature. The calculated results predict the binding energy of the most stable complex in six complexes is ?47.06 kcal/mol at the MP2 level of theory. The second channel has the lowest energy barrier, which is ?3.63 kcal/mol at the CCSD (T) levels of theory, is expected to be the most important pathway. It occurs via C? Cl cleavage accompanied by C? S bond formation. The other two channels have higher energy barriers and are expected to have smaller rates. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Nucleophilic Substitution at Phosphorus Centers (SN2@P)

We have studied the characteristics of archetypal model systems for bimolecular nucleophilic substitution at phosphorus (S_N2@P) and, for comparison, at carbon (S_N2@C) and silicon (S_N2@Si) centers. In our studies, we applied the generalized gradient approximation (GGA) of density functional theory (DFT) at the OLYP/TZ2P level. Our model systems cover nucleophilic substitution at carbon in X^?+CH₃Y (S_N2@C), at silicon in X^?+SiH₃Y (S_N2@Si), at tricoordinate phosphorus in X^?+PH₂Y (S_N2@P3), and at tetracoordinate phosphorus in X^?+POH₂Y (S_N2@P4). The main feature of going from S_N2@C to S_N2@P is the loss of the characteristic double‐well potential energy surface (PES) involving a transition state [X? CH₃? Y]^? and the occurrence of a single‐well PES with a stable transition complex, namely, [X? PH₂? Y]^? or [X? POH₂? Y]^?. The differences between S_N2@P3 and S_N2@P4 are relatively small. We explored both the symmetric and asymmetric (i.e. X, Y=Cl, OH) S_N2 reactions in our model systems, the competition between backside and frontside pathways, and the dependence of the reactions on the conformation of the reactants. Furthermore, we studied the effect, on the symmetric and asymmetric S_N2@P3 and S_N2@P4 reactions, of replacing hydrogen substituents at the phosphorus centers by chlorine and fluorine in the model systems X^?+PR₂Y and X^?+POR₂Y, with R=Cl, F. An interesting phenomenon is the occurrence of a triple‐well PES not only in the symmetric, but also in the asymmetric S_N2@P4 reactions of X^?+POCl₂? Y.     

Ab initio potential energy surface and vibration‐rotation energy levels of silicon dicarbide,SiC2

The accurate ground‐state potential energy surface of silicon dicarbide, SiC₂, has been determined from ab initio calculations using the coupled‐cluster approach. Results obtained with the conventional and explicitly correlated coupled‐cluster methods were compared. The core‐electron correlation, higher‐order valence‐electron correlation, and scalar relativistic effects were taken into account. The potential energy barrier to the linear SiCC configuration was predicted to be 1782 cm^?1. The vibration‐rotation energy levels of the SiC₂, ²⁹SiC₂, ³⁰SiC₂, and SiC¹³C isotopologues were calculated using a variational method. The experimental vibration‐rotation energy levels of the main isotopologue were reproduced to high accuracy. In particular, the experimental energy levels of the highly anharmonic vibrational ν₃ mode of SiC₂ were reproduced to within 6.7 cm^?1, up to as high as the v₃ = 16 state.     

Oxidative addition of the ethane C-C bond to Pd. An ab initio benchmark and DFT validation study

We have computed a state-of-the-art benchmark potential energy surface (PES) for the archetypal oxidative addition of the ethane C-C bond to the palladium atom and have used this to evaluate the performance of 24 popular density functionals, covering LDA, GGA, meta-GGA, and hybrid density functionals, for describing this reaction. The ab initio benchmark is obtained by exploring the PES using a hierarchical series of ab initio methods [HF, MP2, CCSD, CCSD(T)] in combination with a hierarchical series of five Gaussian-type basis sets, up to g polarization. Relativistic effects are taken into account either through a relativistic effective core potential for palladium or through a full four-component all-electron approach. Our best estimate of kinetic and thermodynamic parameters is -10.8 (-11.3) kcal/mol for the formation of the reactant complex, 19.4 (17.1) kcal/mol for the activation energy relative to the separate reactants, and -4.5 (-6.8) kcal/mol for the reaction energy (zero-point vibrational energy-corrected values in parentheses). Our work highlights the importance of sufficient higher angular momentum polarization functions for correctly describing metal-d-electron correlation. Best overall agreement with our ab initio benchmark is obtained by functionals from all three categories, GGA, meta-GGA, and hybrid DFT, with mean absolute errors of 1.5 to 2.5 kcal/mol and errors in activation energies ranging from -0.2 to -3.2 kcal/mol. Interestingly, the well-known BLYP functional compares very reasonably with a slight underestimation of the overall barrier by -0.9 kcal/mol. For comparison, with B3LYP we arrive at an overestimation of the overall barrier by 5.8 kcal/mol. On the other hand, B3LYP performs excellently for the central barrier (i.e., relative to the reactant complex) which it underestimates by only -0.1 kcal/mol.     

Ab initio study of the topology of the charge distribution of H3SiO(H)AlH3 conformers

The topologic properties of the electronic charge distribution of conformers of H₃SiO(H)AlH₃ molecule hydroxyl groups of zeolites are reported. The studied properties—total density, Laplacian density, and bond ellipticity—were evaluated at the position of the critical points of the O Si, O Al, and O H bonds, by using Hartree–Fock and second‐order Møller–Plesset levels of theory, and the STO/6‐31+G(d,p) standard basis set. For the H₃SiO(H)AlH₃ molecule, four conformers are identified. It is demonstrated that for these conformers, the total density and Laplacian density remain almost constant by effect of the rotations of the T H bonds, T=(Si, Al), around the corresponding O T bonds, respectively. However, these rotations induce sensible variations in the ellipticity at the position of the critical point of the O Al bonds, which are reflected in the OH bond distance, OH vibrational mode, and the stabilization energy of conformers. These results lead to a linear relationship between the magnitude of the bond ellipticity at the critical point of the O Al bonds and the frequency values of the OH bonds, with a correlation coefficient of r²=0.98. In addition, a good linear relationship between the ellipticity of the O Al bond and the pattern of the stabilization energy of conformers was also found. © 1999 John Wiley & Sons, Inc. Int J Quant Chem 76: 1–9, 2000     

Rotational barriers of disilane,hexafluorodisilane, and hexamethyldisilane: Ab initio,density functional,and molecular mechanics (MM3) studies

We investigated structures, vibrational frequencies, and rotational barriers of disilane (Si₂H₆), hexafluorodisilane (Si₂F₆), and hexamethyldisilane (Si₂Me₆) by using ab initio molecular orbital and density functional theories. We employed four different levels of theories (i.e., HF/6–31G*, MP2/6–31G*, BLYP/6–31G*, and B3LYP/6–31G*) to optimize the structures and to calculate the vibrational frequencies (except for Si₂Me₆ at MP2/6–31G*). MP2/6–31G* calculations reproduce experimental bond lengths well, while BLYP/6–31G* calculations largely overestimate some bond lengths. Vibrational frequencies from density functional theories (BLYP/6–31G* and B3LYP/6–31G*) were in reasonably good agreement with experimental values without employing additional correction factors. We calculated the ΔG^‡(298 K) values of the internal rotation by correcting zero-point vibration energies, thermal vibration energies, and entropies. We performed CISD/6–31G*//MP2/6–31G* calculations and found the ΔG^‡(298 K) values for the internal rotation of Si₂H₆, Si₂F₆, and Si₂Me₆ to be 1.36, 2.06, and 2.69 kcal/mol, respectively. The performance of this level was verified by using G2 and G2(MP2) methods in Si₂H₆. According to our theoretical results, the ΔG^‡(298 K) values were marginally greater than the ΔE^‡(0 K) values in Si₂F₆ and Si₂Me₆ due to the contribution of the entropy. In Si₂H₆ the ΔE^‡(0 K) and ΔG^‡(298 K) values were coincidently similar due to a cancellation of two opposing contributions between zero-point and thermal vibrational energies, and entropies. Our calculated ΔG^‡(298 K) values were in good agreement with experimental values published recently. In addition, we also performed MM3 calculations on Si₂H₆ and Si₂Me₆. MM3 calculated rotational barriers and thermodynamic properties were compared with high level ab initio results. Based on this comparison, MM3 calculations reproduced high level ab initio results in rotational barriers and thermodynamic properties of Si₂H₆ derivatives including vibrational energies and entropies, although large errors exist in some vibrational frequencies. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1523–1533, 1997     

Pentacoordination of boron, carbon, aluminum, and silicon atoms in organic compounds: Anab initio study

Pentacoordination of boron, carbon, aluminum, and silicon atoms in bicyclic organic compounds of the pentalene type was studied using theab initio RHF/6-31G^** and MP2(full)/6-31G^** methods. It was shown that the ability of the atom to form pentacoordinate structures increases on going from B to Al and from C to Si atom,i.e. as the number of the element of Groups IIIA and IVA of the periodic system increases. At the same time, the reverse tendencies are observed in the 2nd and 3rd periods of the periodic system,viz., the ability of the atom to form pentacoordinate structures increases on going from C to B and from Al to Si atom. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1238–1245, July, 1999.     

An ab initio MO study on the direct and migratory reaction mechanism for the formation of HF in H+ClF system

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Ab initio and DFT studies on van der Waals trimers: the OCS.(CO2)2 complexes

Ab initio calculations [MP2, MP4SDTQ, and QCISD(T)] using different basis sets [6-31G(d,p), cc-pVXZ (X = D, T, Q), and aug-cc-pVDZ] and density functional theory [B3LYP/6-31G(d,p)] calculations were carried out to study the OCS.(CO2)2 van der Waals trimer. The DFT has proved inappropriate to the study of this type of systems where the dispersion forces are expected to play a relevant role. Three minima isomers (two noncyclic and one cyclic) were located and characterized. The most stable isomer exhibits a noncyclic barrel-like structure whose bond lengths, angles, rotational constants, and dipole moment agree quite well with the corresponding experimental values of the only structure observed in recent microwave spectroscopic studies. The energetic proximity of the three isomers, with stabilization energies of 1442, 1371, and 1307 cm-1, respectively, at the CBS-MP2/cc-pVXZ (X = D, T, Q) level, strongly suggests that the two unobserved structures should also be detected as in the case of the (CO2)3 trimer where both noncyclic and cyclic isomers have been reported to exist. The many-body symmetry-adapted perturbation theory is employed to analyze the nature of the interactions leading to the formation of the different structures. The three-body contributions are small and stabilizing for the two most stable structures and almost negligible for the cyclic isomer.     

A fully ab initio potential energy surface for ClH2 reactive system

An ab initio analytical potential energy surface called BW3 for the ClH2 reactive system is presented. The fit of this surface is based on about 1 200 ab initio energy points, computed with multi-reference configuration interaction(MRCI) and scaling external correlation (SEC) method and a very large basis set. The precision in the fit is very high. The BW3 surface could reproduce correctly the dissociation energy of H2 and HCl, and the endothermicity of the Cl + H2 abstraction reaction. For the Cl + H2 abstraction reaction, the saddle point of BW3 lies in collinear geometries, and the barrier height is 32.84 kJ/mol; for the H + ClH exchange reaction, the barrier of BW3 is also linear, with a height of 77.40 kJ/mol.