The diradical mechanism for 1,3-dipolar cycloadditions and related thermal pericyclic reactions

A critical comparison is given of the diradical and concerted mechanisms for 1,3-dipolar cycloadditions, with references also to the Diels-Alder reaction and Cope rearrangement. The experimental facts for the field as a whole favor the diradical mechanism. Among the topics considered are stereospecificity, solvent effects, energetics, penselectivity, substituent effects, acetylenic dipolarophiles, U-shaped Hammett plots, orientation, steric effects, partial charges, conformation and scission of diradicals, hydrogen transfer in extended diradicals and cycloadditions of fluorinated olefins.     

Computational methods to calculate accurate activation and reaction energies of 1,3-dipolar cycloadditions of 24 1,3-dipoles

Theoretical calculations were performed on the 1,3-dipolar cycloaddition reactions of 24 1,3-dipoles with ethylene and acetylene. The 24 1,3-dipoles are of the formula X≡Y(+)-Z(-) (where X is HC or N, Y is N, and Z is CH(2), NH, or O) or X═Y(+)-Z(-) (where X and Z are CH(2), NH, or O and Y is NH, O, or S). The high-accuracy G3B3 method was employed as the reference. CBS-QB3, CCSD(T)//B3LYP, SCS-MP2//B3LYP, B3LYP, M06-2X, and B97-D methods were benchmarked to assess their accuracies and to determine an accurate method that is practical for large systems. Several basis sets were also evaluated. Compared to the G3B3 method, CBS-QB3 and CCSD(T)/maug-cc-pV(T+d)Z//B3LYP methods give similar results for both activation and reaction enthalpies (mean average deviation, MAD, < 1.5 kcal/mol). SCS-MP2//B3LYP and M06-2X give small errors for the activation enthalpies (MAD < 1.5 kcal/mol), while B3LYP has MAD = 2.3 kcal/mol. SCS-MP2//B3LYP and B3LYP give the reasonable reaction enthalpies (MAD < 5.0 kcal/mol). The B3LYP functional also gives good results for most 1,3-dipoles (MAD = 1.9 kcal/mol for 17 common 1,3-dipoles), but the activation and reaction enthalpies for ozone and sulfur dioxide are difficult to calculate by any of the density functional methods.     

Investigations on intramolecular 1,3-dipolar cycloadditions for the synthesis of isoxazolo-annulated pyrrolidines,piperidines and azepanes

Pyrrolidines, piperidines, and azepanes with annulated isoxazole, isoxazoline or isoxazolidine rings were prepared by intramolecular 1,3-dipolar cycloadditions of nitrones or nitrile oxides. The corresponding 1,3-dipoles were obtained from N-Boc-protected and N-allyl-, N-propargyl- or N-(3-butenyl)-substituted 2-aminoethanal or 3-aminopropanal.     

Regio- and stereoselectivity of captodative olefins in 1,3-dipolar cycloadditions. A DFT/HSAB theory rationale for the observed regiochemistry of nitrones

Captodative olefins 1-acetylvinyl carboxylates proved to be highly regioselective dipolarophiles in 1,3-dipolar cycloadditon to propionitrile oxide, arylphenylnitrile imines, diazoalkanes, and nitrones to yield the corresponding 5-substituted heterocycles. The addition of the latter was also stereoselective, being slightly susceptible to steric demand of the carboxylate substituent in the olefin. All atempts to cleave the isoxazolidine N-O bond under reductive conditions failed, providing diverse products with side-group reduction. FMO theory was unsuccessful to explain the regioselectivity observed with nitrones, since the opposite orientation was predicted. The recently formulated DFT/HSAB theoretical model was able to rationalize this regioselectivity, identifying the nucleophilic and electrophilic atoms involved in the process via calculation of interaction energies, suggesting the specific direction of the electronic process at each of the reaction sites.     

Transition states for the dimerization of 1,3-cyclohexadiene: a DFT, CASPT2, and CBS-QB3 quantum mechanical investigation

Quantum mechanical calculations using restricted and unrestricted B3LYP density functional theory, CASPT2, and CBS-QB3 methods for the dimerization of 1,3-cyclohexadiene (1) reveal several highly competitive concerted and stepwise reaction pathways leading to [4 + 2] and [2 + 2] cycloadducts, as well as a novel [6 + 4] ene product. The transition state for endo-[4 + 2] cycloaddition (endo-2TS, DeltaH(double dagger)(B3LYP(0K)) = 28.7 kcal/mol and DeltaH(double dagger)(CBS-QB3(0K)) = 19.0 kcal/mol) is not bis-pericyclic, leading to nondegenerate primary and secondary orbital interactions. However, the C(s) symmetric second-order saddle point on the B3LYP energy surface is only 0.3 kcal/mol above endo-2TS. The activation enthalpy for the concerted exo-[4 + 2] cycloaddition (exo-2TS, DeltaH(double dagger)(B3LYP(0K)) = 30.1 kcal/mol and DeltaH(double dagger)(CBS-QB3(0K)) = 21.1 kcal/mol) is 1.4 kcal/mol higher than that of the endo transition state. Stepwise pathways involving diallyl radicals are formed via two different C-C forming transition states (rac-5TS and meso-5TS) and are predicted to be competitive with the concerted cycloaddition. Transition states were located for cyclization from intermediate rac-5 leading to the endo-[4 + 2] (endo-2) and exo-[2 + 2] (anti-3) cycloadducts. Only the endo-[2 + 2] (syn-3) transition state was located for cyclization of intermediate meso-5. The novel [6 + 4] "concerted" ene transition state (threo-4TS, DeltaH(double dagger)(UB3LYP(0K)) = 28.3 kcal/mol) is found to be unstable with respect to an unrestricted calculation. This diradicaloid transition state closely resembles the cyclohexadiallyl radical rather than the linked cyclohexadienyl radical. Several [3,3] sigmatropic rearrangement transition states were also located and have activation enthalpies between 27 and 31 kcal/mol.     

Vibrational analysis,conformational stability,force constants,internal rotation barriers,MP2=full and DFT calculations of 1,3-dimethyluracil tautomers

The molecular structure of 1,3-dimethyluracil (C₆H₈N₂O₂; 1,3-DMU) is studied theoretically and experimentally using Gaussian 98 calculations and different spectroscopic techniques. The vibrational spectrum for 1,3-DMU in the solid phase is recorded in the IR range 4000-400 cm^–1. Initially, in order to get the most stable structure, twelve structures were proposed for the titled compound as a result of the internal rotation of CH₃ around C–N bonds and keto-enol tautomerism. The single point energy and frequency calculations are obtained by MP2 (Full) and DFT/B3LYP methods with the 6-31G(d) basis set using the Gaussian 98 computation package. After the complete relaxation of twelve isolated isomers, the (diketo) tautomer was the only favored structure owing to its low energy relative to the other isomers and the prediction of real frequencies. This interpretation is supported by the recorded infrared spectrum that shows the presence of only the diketo tautomer. Aided by the normal coordinate analysis and potential energy distributions, a confident vibrational assignment of the fundamental frequencies is calculated. The results are discussed herein and compared with similar molecules whenever possible.     

Ab initio base-pairing energies of an oxidized thymine product, 5-formyluracil, with standard DNA bases at the BSSE-free DFT and MP2 theory levels

Oxidation of the thymine methyl group produces two stable products, non-mutagenic 5-hydroxymethyluracil and highly mutagenic 5-formyluracil. We have calculated the interaction energy of base-pair formation involving 5-formyluracil bound to the natural DNA bases adenine (A), cytosine (C), guanine (G), and thymine (T), and discuss the effects of the 5-formyl group with respect to similar base-pairs containing uracil, 5-hydroxyuracil, thymine (5-methyluracil), and 5-hydroxycytosine. The interaction geometries and energies were calculated four ways: (a) using density functional theory (DFT) without basis set super-position error (BSSE) corrections, (b) using DFT with BSSE correction of geometries and energies, (c) using M?ller-Plesset second order perturbation theory (MP2) without BSSE correction, and (d) using MP2 with BSSE geometry and energy correction. All calculations used the 6-311G(d,p) basis set. Notably, we find that the A:5-formyluracil base-pair is more stable than the precursor A:T base-pair. The relative order of base-pair stabilities is A:5-Fo-U > G:5-Fo-U > C:5-Fo-U > T:5-Fo-U.     

A simple,self-consistent electrostatic model for quantitative prediction of the activation energies of four-center reactions. II.*

A simple electrostatic model of point dipoles is used which permits direct calculation of the activation energies for the addition of the molecules H₂O, H₂S, H₃N, and H₃P to olefins. These calculated values agree with the known experimental data to within ±2 kcal/mole on the average. It was found that the best fit could be obtained with a polar transition state that corresponded to a reduction in bond order from 1 to ½ for the bond-breaking coordinates and an increase in bond order from 0 to 0.18 for the bond-forming coordinates. The replacement of a hydrogen atom of the species H₂O, H₂S, H₃N, or H₃P by a polarizable methyl group is expected to stabilize the charge on the central atoms. The following stabilization energies for the pairs H₂O? CH₃OH, H₂S? CH₃SH, H₃N? CH₃NH₂, H₃P? CH₃PH₂ were calculated: ?4.8 kcal/mole, ?0.7 kcal/mole, ?1.9 kcal/mole, ?0.8 kcal/mole, respectively.     

Synthesis of oximes,conversion to nitrile oxides and their subsequent 1,3-dipolar cycloaddition reactions under microwave irradiation and solvent-free reaction conditions

Aldoximes and ketoximes were readily synthesized from aldehydes and hydroxylamine hydrochloride on Al₂O₃ without solvent under microwave irradiation. At higher irradiation power, aldoximes dehydrated to nitriles and ketoximes rearranged to amides. Aldoximes reacted in a one-pot reaction with N-chlorosuccinimide and alkenes or alkynes over alumina under microwave irradiation to give isoxazolines or isoxazoles. © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:351–354, 1998     

An expedient approach for the synthesis of dispiropyrrolidine bisoxindoles, spiropyrrolidine oxindoles and spiroindane-1,3-diones through 1,3-dipolar cycloaddition reactions

A series of dispiropyrrolidine bisoxindoles were synthesized via a multicomponent 1,3-dipolar cycloaddition reaction of isatin, sarcosine and isatylidene malononitrile in refluxing methanol. Also a series of spiropyrrolidine oxindoles and spiroindane-1,3-diones were synthesized using 2-(1H-Indole-3-carbonyl)-3-phenyl-acrylonitrile and 2-(1,3-dioxo-indan-2-ylidene)-malononitrile as dipolarophiles, respectively.     

Extension of the bebo method for the calculation of activation energies of intraradical 1,3-, 1,4- and 1,5-hydrogen shift reactions

The bond-energy—bond-order (BEBO) method has been extended for the calculation of activation energies of the radical isomerization reactions occurring via 1,3-, 1,4- and 1,5-hydrogen atom shifts. The energy of the cyclic activated complexes comprises four contributions, i.e. the energy change in formation of the transition state due to the occurrence of fractional and strained bonds, the triplet repulsion, the deformation energy and the non-bonding interaction. The method has been applied to a set of 11 reactions. The agreement between the calculated and the experimental activation energies is satisfactory.     

On the accuracy of DFT-SAPT, MP2, SCS-MP2, MP2C, and DFT+Disp methods for the interaction energies of endohedral complexes of the C(60) fullerene with a rare gas atom

Selected points on the potential energy surface for the complexes Rg@C(60) (Rg = He, Ne, Ar, Kr) are calculated with various theoretical methods, like symmetry-adapted perturbation theory with monomers described by density functional theory (DFT-SAPT), supermolecular M?ller-Plesset theory truncated on the second order (MP2), spin-component-scaled MP2 (SCS-MP2), supermolecular density functional theory with empirical dispersion correction (DFT+Disp), and the recently developed MP2C method that improves the MP2 method for long-range electron correlation effects. A stabilization of the endohedral complex is predicted by all methods, but the depth of the potential energy well is overestimated by the DFT+Disp and MP2 approaches. On the other hand, the MP2C model agrees well with DFT-SAPT, which serves as the reference. The performance of SCS-MP2 is mixed: it produces too low interaction energies for the two heavier guests, while its accuracy for He@C(60) and Ne@C(60) is similar to that of MP2C. Fitting formulas for the main interaction energy components, i.e. the dispersion and first-order repulsion energies are proposed, which are applicable for both endo- and exohedral cases. For all examined methods density fitting is used to evaluate two-electron repulsion integrals, which is indispensable to allow studies of noncovalent complexes of this size. It has been found that density-fitting auxiliary basis sets cannot be used in a black-box fashion for the calculation of the first-order SAPT electrostatic energy, and that the quality of these basis sets should be always carefully examined in order to avoid an unphysical long-range behavior.     

Accurate reaction barrier heights of pericyclic reactions: Surprisingly large deviations for the CBS‐QB3 composite method and their consequences in DFT benchmark studies

Accurate barrier heights are obtained for the 26 pericyclic reactions in the BHPERI dataset by means of the high‐level Wn‐F12 thermochemical protocols. Very often, the complete basis set (CBS)‐type composite methods are used in similar situations, but herein it is shown that they in fact result in surprisingly large errors with root mean square deviations (RMSDs) of about 2.5 kcal mol^?1. In comparison, other composite methods, particularly G4‐type and estimated coupled cluster with singles, doubles, and quasiperturbative triple excitations [CCSD(T)/CBS] approaches, show deviations well below the chemical‐accuracy threshold of 1 kcal mol^?1. With the exception of SCS‐MP2 and the herein newly introduced MP3.5 approach, all other tested Møller‐Plesset perturbative procedures give poor performance with RMSDs of up to 8.0 kcal mol^?1. The finding that CBS‐type methods fail for barrier heights of these reactions is unexpected and it is particularly troublesome given that they are often used to obtain reference values for benchmark studies. Significant differences are identified in the interpretation and final ranking of density functional theory (DFT) methods when using the original CBS‐QB3 rather than the new Wn‐F12 reference values for BHPERI. In particular, it is observed that the more accurate Wn‐F12 benchmark results in lower statistical errors for those methods that are generally considered to be robust and accurate. Two examples are the PW6B95‐D3(BJ) hybrid‐meta‐general‐gradient approximation and the PWPB95‐D3(BJ) double‐hybrid functionals, which result in the lowest RMSDs of the entire DFT study (1.3 and 1.0 kcal mol^?1, respectively). These results indicate that CBS‐QB3 should be applied with caution in computational modeling and benchmark studies involving related systems. © 2015 Wiley Periodicals, Inc.     

Multi-component, 1,3-dipolar cycloaddition reactions for the chemo-, regio- and stereoselective synthesis of novel hybrid spiroheterocycles in ionic liquid

A library of novel 1-methyl-4-arylpyrrolo-(spiro[2.2′]indan-1′,3′-dione)-spiro[3.3″]-1″-methyl/benzyl-5″-(arylmethylidene)piperidin-4″-ones and 1-methyl-4-arylpyrrolo-(spiro[2.11′]-11H-indeno[1,2-b]quinoxaline)-spiro[3.3″]-1″-methyl/benzyl-5″-(arylmethylidene)piperidin-4″-ones have been synthesized via 1,3-dipolar azomethine ylide cycloaddition in the ionic liquid, 1-butyl-3-methylimidazolium bromide ([BMIm]Br), in excellent yields.     

Benchmarking of DFT methods using experimental free energies and volumes of activation for the cycloaddition of alkynes to cuboidal Mo3S4 clusters

Here, the kinetics of the concerted [3 + 2] cycloaddition reaction between the [Mo₃(μ₃-S)(μ-S)₃Cl₃(dmen)₃]⁺ (dmen = N,N′-dimethyl-ethylenediamine) ([ 1 ]⁺) cluster and various alkynes to form dithiolene derivatives is thoroughly studied, with measurements at different temperatures and pressures allowing the determination of the free energies and volumes of activation. These parameters, together with the available single-crystal X-ray diffraction structures, are used to test a number of commonly used density functional theory (DFT) methods from Jacob's ladder, as well as the effects associated with the size of the basis sets, the way in which solvent effects are taken into account, or the inclusion of dispersion effects. Overall, a protocol that leads to average deviations between experimental and computed ΔV^‡ and ΔG^‡ values similar to the uncertainty of the experimental measurements is obtained.     

Energetics, transition states, and intrinsic reaction coordinates for reactions associated with O(3P) processing of hydrocarbon materials

Electronic structure calculations based on multiconfiguration wave functions are used to investigate a set of archetypal reactions relevant to O(3P) processing of hydrocarbon molecules and surfaces. These include O(3P) reactions with methane and ethane to give OH plus methyl or ethyl radicals, O(3P) + ethane to give CH3O + CH3, and secondary reactions of the OH product radical with ethane and the ethyl radical. Geometry optimization is carried out with CASSCF/cc-pVTZ for all reactions, and with CASPT2/cc-pVTZ for O(3P) + methane/ethane. Single-point energy corrections are applied with CASPT2, CASPT3, and MRCI + Q with the cc-pVTZ and cc-pVQZ basis sets, and the energies extrapolated to the complete basis set limit (CBL). Where comparison of computed barriers and energies of reaction with experiment is possible, the agreement is good to excellent. The best agreement (within experimental error) is found for MRCI + Q/CBL applied to O(3P) + methane. For the other reactions, CASPT2/CBL and MRCI + Q/CBL predictions differ from experiment by 1-5 kcal/mol for 0 K enthalpies of reaction, and are within 1 kcal/mol of the best-estimate experimental range of 0 K barriers for O(3P) + ethane and OH + ethane. The accuracy of MRCI + Q/CBL is limited mainly by the quality of the active space. CASPT2/CBL barriers are consistently lower than MRCI + Q/CBL barriers with identical reference spaces.     

Silicate glass and mineral dissolution: calculated reaction paths and activation energies for hydrolysis of a q3 si by H3O+ using ab initio methods

Molecular orbital energy minimizations were performed with the B3LYP/6-31G(d) method on a [((OH)3SiO)3SiOH-(H3O+).4(H2O)] cluster to follow the reaction path for hydrolysis of an Si-O-Si linkage via proton catalysis in a partially solvated system. The Q3 molecule was chosen (rather than Q2 or Q1) to estimate the maximum activation energy for a fully relaxed cluster representing the surface of an Al-depleted acid-etched alkali feldspar. Water molecules were included in the cluster to investigate the influence of explicit solvation on proton-transfer reactions and on the energy associated with hydroxylating the bridging oxygen atom (Obr). Single-point energy calculations were performed with the B3LYP/6-311+G(d,p) method. Proton transfer from the hydronium cation to an Obr requires sufficient energy to suggest that the Si-(OH)-Si species will occur only in trace quantities on a silica surface. Protonation of the Obr lengthens the Si-Obr bond and allows for the formation of a pentacoordinate Si intermediate ([5]Si). The energy required to form this species is the dominant component of the activation energy barrier to hydrolysis. After formation of the pentacoordinate intermediate, hydrolysis occurs via breaking the [5]Si-(OH)-Si linkage with a minimal activation energy barrier. A concerted mechanism involving stretching of the [5]Si-(OH) bond, proton transfer from the Si-(OH2)+ back to form H3O+, and a reversion of [5]Si to tetrahedral coordination was predicted. The activation energy for Q3Si hydrolysis calculated here was found to be less than that reported for Q3Si using a constrained cluster in the literature but significantly greater than the measured activation energies for the hydrolysis of Si-Obr bonds in silicate minerals. These results suggest that the rate-limiting step in silicate dissolution is not the hydrolysis of Q3Si-Obr bonds but rather the breakage of Q2 or Q1Si-Obr bonds.     

DCMB that combines divide‐and‐conquer and mixed‐basis set methods for accurate geometry optimizations,total energies,and vibrational frequencies of large molecules

We present a method, named DCMB, for the calculations of large molecules. It is a combination of a parallel divide‐and‐conquer (DC) method and a mixed‐basis (MB) set scheme. In this approach, atomic forces, total energy and vibrational frequencies are obtained from a series of MB calculations, which are derived from the target system utilizing the DC concept. Unlike the fragmentation based methods, all DCMB calculations are performed over the whole target system and no artificial caps are introduced so that it is particularly useful for charged and/or delocalized systems. By comparing the DCMB results with those from the conventional method, we demonstrate that DCMB is capable of providing accurate prediction of molecular geometries, total energies, and vibrational frequencies of molecules of general interest. We also demonstrate that the high efficiency of the parallel DCMB code holds the promise for a routine geometry optimization of large complex systems. © 2012 Wiley Periodicals, Inc.