Intramolecular homolytic substitution of seleninates – a computational study

Ab initio and density functional theory (DFT) calculations predict that intramolecular homolytic substitution by alkyl radicals at the selenium atom in seleninates proceeds through smooth transition states in which the attacking and leaving radicals adopt a near collinear arrangement. When forming a five-membered ring and the leaving radical is methyl, G3(MP2)-RAD calculations predict that this reaction proceeds with an activation energy (ΔE₁³) of 30.4 kJ mol^?1. ROBHandHLYP/6-311++G(d,p) calculations suggest that the formation of five-membered rings through similar intramolecular homolytic substitution by aryl radicals, with expulsion of phenyl radicals, proceeds with the involvement of a hypervalent intermediate. This intermediate further dissociates to the observed products, with overall energy barriers of about 40 kJ mol^?1. Homolytic addition to the phenyl group was found not to be competitive with substitution, with a calculated barrier of 57.6 kJ mol^?1. This computational study provides insight into homolytic substitution chemistry involving seleninates.     

An ab-initio study of some homolytic substitution reactions of acyl radicals at silicon, germanium and tint

Ab initio calculations using the 6-311G**, cc-pVDZ, and (valence) double-zeta pseudopotential (DZP) basis sets, with (MP2, QCISD, CCSD(T)) and without (UHF) the inclusion of electron correlation, and density functional (BHandHLYP, B3LYP) calculations predict that homolytic substitution reactions of acetyl radicals at the silicon atoms in disilane can proceed via both backside and frontside attack mechanisms. At the highest level of theory (CCSD(T)/cc-pVDZ//MP2/cc-pVDZ), energy barriers (deltaE double dagger) of 77.2 and 81.9 kJ mol(-1) are calculated for the backside and frontside reactions respectively. Similar results are obtained for reactions involving germanium and tin with energy barriers (deltaE double dagger) of 53.7-84.2, and 55.0-89.7 kJ mol(-1) for the backside and frontside mechanisms, respectively. These data suggest that both homolytic substitution mechanisms are feasible for homolytic substitution reactions of acetyl radicals at silicon, germanium, and tin. BHandHLYP calculations provide geometries and energy barriers for backside and frontside transition states in good agreement with those obtained by traditional ab initio techniques.     

Intramolecular Homolytic Substitution of Sulfinates and Sulfinamides

A general and efficient method for the synthesis of cyclic sulfinates and sulfinamides based on intramolecular homolytic substitution (S_Hi) at the sulfur atom by aryl or alkyl radicals is described. Both alkyl and benzofused compounds can be accessed directly from easily prepared acyclic precursors. Enantiomerically enriched sulfur‐based heterocycles were formed through an S_Hi process with inversion of configuration at the sulfur atom. Cyclization of prochiral radicals proceeded with varying stereochemical outcomes, depending on the size of the incoming radical. 2‐Pyridyl and 2‐quinolyl radicals led to biaryl compounds, which result from attack onto the ortho position of the arylsulfinate rather than a thiophilic substitution.     

Conformational study of monomeric 2,3-butanediols by matrix-isolation infrared spectroscopy and DFT calculations

The FT-IR spectra of two diastereomers of 2,3-butanediol, (R,S) and (S,S), isolated in low-temperature argon and xenon matrixes were studied, allowing the identification of two different conformers for each compound. These conformers were characterized by a +/-gauche arrangement around the O-C-C-O dihedral angle, thus enabling the establishment of a very weak intramolecular hydrogen bond of the O...H-O type. No other forms of these compounds were identified in matrixes, despite the fact that these four conformers had calculated relative energies from 0 to 5.1 kJ mol(-1) and were expected to be thermally populated from 50 to 6% in the gaseous phase of each compound. The nonobservation of additional conformers was explained in terms of low barriers to intramolecular rotation, resulting in the conformational relaxation of the compounds during deposition of the matrixes. The barriers to internal rotation of the OH groups were computed to be less than 4 kJ mol(-1) and are easily overcome in matrixes within the family of conformers with the same heavy atom backbone. The barriers for intramolecular rearrangement of the O-C-C-O dihedral angle in both diastereomers were calculated to range from 20 to 30 kJ mol(-1). Interconversions between the latter conformers were not observed in matrixes, even after annealing up to 65 K. Energy calculations, barriers, and calculated infrared spectra were carried out at the DFT(B3LYP)/6-311++G theory. Additional MP2/6-311++G calculations of energies and vibrational frequencies were performed on the most relevant conformers. Finally, independent estimations of the hydrogen-bond enthalpy in the studied molecules were also obtained based on theoretical structural data and from vibrational frequencies (using well-established empirical correlations). The obtained values for -DeltaH for both diastereomers of 2,3-butanediol amount to ca. 6-8 kJ mol(-1).     

Does the interconversion of polysulfur compounds proceed via hypervalent intermediates? An ab initio MO study

Ab initio MO calculations at the CCSD(T)/6-311++G(2df,p)//MP2/6-311++G** level have been carried out to determine the reaction energies and Gibbs energies of the homolytic dissociation of the S-S bonds in the chainlike sulfanes H2Sn (n = 2-4). Good agreement with the experimental data is observed. At the same level of theory, the formation of the hypothetical sulfuranes H2S(SH)2, H2S(SSH)2, and S(SH)4 from H2S and the mentioned sulfanes has been studied. Species of this type had been proposed as intermediates in the interconversion reactions of polysulfur compounds (e.g., formation of S7 from S8 and vice versa). The three sulfuranes serve here as model compounds. On the basis of the Gibbs energies and activation energies at 298 K, it is shown that the formation of the three sulfuranes from sulfanes requires too much energy and activation energy to successfully compete with homolytic dissociation reactions. In addition, the formation of the methylsubstituted sulfurane S(SMe)4 from the sulfanes Me2S2 and Me2S3 was studied to elucidate the mechanism of the formal exchange of sulfur atoms between polysulfane molecules. However, both the reaction energy of 199 kJ mol(-1) and the activation energy of 287 kJ mol(-1), calculated at the MP2/6-31G* level, are much higher than the homolytic dissociation energy of the S-S bonds in chain- and ringlike polysulfur compounds, such as Me2S4 (140 kJ mol(-1)) and sulfur homocycles (150 kJ mol(-1)). Therefore, it is concluded that the observed interconversion reactions of sulfur rings and of chainlike polysulfanes do not proceed via sulfurane-type intermediates. Instead, these reactions will take place by a radical chain mechanism at high temperatures, while at temperatures below 100 degrees C they are most probably initiated either by traces of nucleophiles that are present as impurities or by the polar surface groups usually present on the walls of the vessels used.     

Methyl radical also reacts by the frontside mechanism: an ab initio study of some homolytic substitution reactions of methyl radical at silicon,germanium and tin

Ab initio calculations using 6-311G**, cc-pVDZ, aug-cc-pVDZ, and a (valence) double-zeta pseudopotential (DZP) basis sets, with (MP2, QCISD, CCSD(T)) and without (UHF) the inclusion of electron correlation, and density functional (B3LYO) calculations predict that homolytic substitution reactions of the methyl radical at the silicon atom in disilane can proceed via both backside and frontside attack mechanisms. At the highest level of theory (CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ), energy barriers (delta E) of 47.4 and 48.6 kJ mol-1 are calculated for the backside and frontside reactions respectively. Similar results are obtained for reactions involving germanium and tin with energy barriers (delta E) of between 46.5 and 67.3, and 41.0 and 73.3 kJ mol-1 for the backside and frontside mechanisms, respectively. These data suggest that homolytic substitution reactions of methyl radical at silicon, germanium, and tin can proceed via either homolytic substitution mechanism.     

An ab initio and DFT study of some halogen atom transfer reactions from alkyl groups to acyl radical

Ab initio calculations using the 6-311G**, cc-pVDZ, and (valence) double-zeta pseudopotential (DZP) basis sets, with (MP2, QCISD, CCSD(T)) and without (HF) the inclusion of electron correlation, and density functional (BHandHLYP, B3LYP) calculations predict that the transition states for the reaction of acetyl radical with several alkyl halides adopt an almost collinear arrangement of attacking and leaving radicals at the halogen atom. Energy barriers (DeltaE(double dagger)) for these halogen transfer reactions of between 89.2 (chlorine transfer from methyl group) and 25.3 kJ mol(-1) (iodine transfer from tert-butyl group) are calculated at the BHandHLYP/DZP level of theory. While the difference in forward and reverse energy barriers for iodine transfer to acetyl radical is predicted to be 15.1 kJ mol(-1) for primary alkyl iodide, these values are calculated to be 6.7 and -4.2 kJ mol(-1) for secondary and tertiary alkyl iodide respectively. These data are in good agreement with available experimental data in that atom transfer radical carbonylation reactions are sluggish with primary alkyl iodides, but proceed smoothly with secondary and tertiary alkyl iodides. These calculations also predict that bromine transfer reactions involving acyl radical are also feasible at moderately high temperature.     

Understanding (the lack of) homolytic substitution chemistry of sulfones

High level calculations suggest that homolytic substitution (S(H)2) by alkyl radicals at sulfur proceeds through a mechanism that is assisted and dominated by LP → SOMO interactions; in the absence of these interactions, S(H)2 chemistry at sulfur is predicted to be virtually impossible. G3(MP2)-RAD calculations suggest that cyclization of the tert-butylsulfonylbutyl radical 2 (n = 2) proceeds with a rate constant of 1.7 × 10(-24) s(-1) at 80°, some 28 orders of magnitude slower than its sulfide cousin (n = 0).     

Thermochemistry, bond energies, and internal rotor potentials of dimethyl tetraoxide

Thermochemical properties of dimethyl tetraoxide (CH(3)OOOOCH(3)), the dimer of the methylperoxy radical, are studied using ab initio and density functional theory methods. Methylperoxy radicals are known to be important intermediates in the tropospheric ozone cycle, and the self-reaction of methylperoxy radicals, which is thought to proceed via dimethyl tetraoxide, leads to significant chain radical termination in this process. Dimethyl tetraoxide has five internal rotors, three of them unique; the potential energy profiles are calculated for these rotors, as well as for those in the CH(3)OO, CH(3)OOO, and CH(3)OOOO radicals. The dimethyl tetraoxide internal rotor profiles show barriers to rotation of 2-8 kcal mol(-1). Using B3LYP/6-31(d) geometries, frequencies, internal rotor potentials, and moments of inertia, we determine entropy and heat capacity values for dimethyl tetraoxide and its radicals. Isodesmic work reactions with the G3B3 and CBS-APNO methods are used; we calculate this enthalpy as -9.8 kcal mol(-1). Bond dissociation energies (BDEs) are calculated for all C-O and O-O bonds in dimethyl tetraoxide, again with the G3B3 and CBS-APNO theoretical methods, and we suggest the following BDEs: 46.0 kcal mol(-1) for CH(3)-OOOOCH(3), 20.0 kcal mol(-1) for CH(3)O-OOOCH(3), and 13.9 kcal mol(-1) for CH(3)OO-OOCH(3). From the BDE calculations and the isodesmic enthalpy of formation for dimethyl tetraoxide, we suggest enthalpies of 2.1, 5.8, and 1.4 kcal mol(-1) for the CH(3)OO, CH(3)OOO, and CH(3)OOOO radicals, respectively. We evaluate the suitability of 10 different density functional theory (DFT) methods for calculating thermochemical properties of dimethyl tetraoxide and its radicals with the 6-31G(d) and 6-311++G(3df,3pd) basis sets, using a variety of work reaction schemes. Overall, the best-performed DFT methods of those tested were TPSSh, BMK, and B1B95. Significant improvements in accuracy were made by moving from atomization to isodesmic work reactions, with most DFT methods yielding errors of less than 2 kcal mol(-1) with the 6-311++G(3df,3pd) basis set for isodesmic calculations on the dimethyl tetraoxide enthalpy. These isodesmic calculations were basis set consistent, with a considerable reduction in error found by using the 6-311++G(3df,3pd) basis set over the 6-31G(d) basis set. This was not the case, however, for atomization and bond dissociation work reactions, where the two basis sets returned similar results. Improved group additivity terms for the O-O-O moiety (O/O2 central atom group) are also determined.     

DFT-GIAO calculations of 19F NMR chemical shifts for perfluoro compounds

The (19)F NMR shieldings for 53 kinds of perfluoro compounds were calculated by the B3LYP-GIAO method using the 6-31G(d), 6-31+G(d), 6-31G(d,p), 6-31++G(d,p), 6-311G(d,p), 6-311++G(d,p), 6-311G(2d,2p), 6-311++G(2d,2p), 6-311++G(2df,2p), 6-311++G(3d,2p), and 6-311++G(3df,2p) basis sets. The diffuse functions markedly reduce the difference between the calculated and experimental chemical shifts. The calculations using the 6-31++G(d,p) basis set give the chemical shifts within 10 ppm deviations from experimental values except for the fluorine nuclei attached to an oxygen atom, a four- and a six-coordinated sulfur atom, and FC(CF(3))(2) attached to a sulfur atom.     

Molecular structure of the trans and cis isomers of metal-free phthalocyanine studied by gas-phase electron diffraction and high-level quantum chemical calculations: NH tautomerization and calculated vibrational frequencies

The molecular structure of the trans isomer of metal-free phthalocyanine (H2Pc) is determined using the gas electron diffraction (GED) method and high-level quantum chemical calculations. B3LYP calculations employing the basis sets 6-31G**, 6-311++G**, and cc-pVTZ give two tautomeric isomers for the inner H atoms, a trans isomer having D2h symmetry and a cis isomer having C2v symmetry. The trans isomer is calculated to be 41.6 (B3LYP/6-311++G**, zero-point corrected) and 37.3 kJ/mol (B3LYP/cc-pVTZ, not zero-point corrected) more stable than the cis isomer. However, Hartree-Fock (HF) calculations using different basis sets predict that cis is preferred and that trans does not exist as a stable form of the molecule. The equilibrium composition in the gas phase at 471 degrees C (the temperature of the GED experiment) calculated at the B3LYP/6-311++G** level is 99.8% trans and 0.2% cis. This is in very good agreement with the GED data, which indicate that the mole fraction of the cis isomer is close to zero. The transition states for two mechanisms of the NH tautomerization have been characterized. A concerted mechanism where the two H atoms move simultaneously yields a transition state of D2h symmetry and an energy barrier of 95.8 kJ/mol. A two-step mechanism where a trans isomer is converted to a cis isomer, which is converted into another trans isomer, proceeds via two transition states of C(s) symmetry and an energy barrier of 64.2 kJ/mol according to the B3LYP/6-311++G** calculation. The molecular geometry determined from GED is in very good agreement with the geometry obtained from the quantum chemical calculations. Vibrational frequencies, IR, and Raman intensities have been calculated using B3LYP/6-311++G**. These calculations indicate that the molecule is rather flexible with six vibrational frequencies in the range of 20-84 cm(-1) for the trans isomer. The cis isomer might be detected by infrared matrix spectroscopy since the N-H stretching frequencies are very different for the two isomers.     

A quantum chemical study of the protonation of phenylphosphine and its halogenated derivatives

The protonation and methylation of phenylphosphine (C(6)H(5)PH(2)) and its mono-halogenated derivatives have been studied using ab initio quantum chemical calculations. Density functional theory (B3LYP) calculations using the 6-311++G(d,p) basis set consistently confirm that protonation of phenylphosphines takes place at the phosphorus atom; the C(4)-protonated phenylphosphine lying about 66 kJ mol(-1) above the P-protonated isomer. Similarly, methylation of phosphines consistently occurs at phosphorus. The proton and methyl cation affinities are estimated as follows: PA(phenylphosphine) = 863 +/- 10 kJ mol(-1) and MCA(phenylphosphine) = 515 -/+ 12 kJ mol(-1). Mono-halogen substitution appears to reduce the proton affinites by up to 20 kJ mol(-1). In this context, following P-protonation of either ameta- or a para-X-C(6)H(4)-PH(2), an elimination of the halogen X-atom under collisional activation (CA) conditions is expected to lead to a distonic radical cation, a low-energy isomer being 50 kJ mol(-1) above ionized phenylphosphine.     

Intramolecular homolytic translocation chemistry: an ab initio study of 1,n-silyl, germyl, and stannyl group transfer and related ring-closure reactions

Ab initio calculations using 6-311G**, cc-pVDZ, aug-cc-pVDZ, and a (valence) double-zeta pseudopotential (DZP) basis set, with (MP2, QCISD, CCSD(T)) and without (UHF) the inclusion of electron correlation, and density functional methods (B3LYP) predict that 1,n-homolytic transfers (n = 1-5) of silyl, germyl, and stannyl groups from group IV heteroatoms to carbon radicals can proceed via a frontside attack mechanism. At the B3LYP/DZP level of theory, energy barriers (DeltaE++) of 101.2, 98.8, 58.9, and 63.4 kJ/mol are calculated for the 1,2-, 1,3-, 1,4-, and 1,5-translocation reactions, respectively, of SiH3 between silicon atoms. Similar results are obtained for reactions involving germanium and tin with energy barriers (DeltaE++) of 85.9-113.1, 84.4-109.0, 41.7-73.3, and 48.5-78.2 kJ/mol for the 1,2-, 1,3-, 1,4-, and 1,5-translocation reactions, respectively. This study also predicts that four- and five-membered ring-closure reactions can be competitive with the 1,4- and 1,5-translocation reactions. These results suggest that while 1,2- and 1,3-translocation four-membered ring-formation reactions are unlikely to be synthetically viable, 1,4- and 1,5-transfers and five-membered ring-formation have synthetic possibilities.     

Proton affinity of canavanine and canaline, oxyanalogues of arginine and ornithine, from the extended kinetic method

The absolute proton affinities of the nonprotein amino acids canavanine and canaline have been determined using the extended kinetic method in an electrospray ionization quadrupole ion trap instrument. Canavanine results from the substitution of an oxygen atom for the delta-CH2 group in the side chain of the protein amino acid arginine, whereas canaline results from a similar substitution at the delta-CH2 group in the side chain of ornithine. Absolute proton affinities of 1001+/-9 and 950+/-7 kJ/mol are obtained for canavanine and canaline, respectively. For canaline, this proton affinity is in excellent agreement with theoretical predictions obtained using the hybrid density functional theory method B3LYP/6-311++G**//B3LYP/6-31+G*. For canavanine, theory predicts a somewhat larger proton affinity of 1015 kJ/mol. Oxygen atom substitution in these nonprotein amino acids results in a decrease in their proton affinities of 40-50 kJ/mol compared to arginine and ornithine.     

Theoretical conformational analysis for neurotransmitters in the gas phase and in aqueous solution. Norepinephrine

The natural neurotransmitter (R)-norepinephrine takes the monocationic form in 93% abundance at the physiological tissue pH of 7.4. Ab initio and DFT/B3LYP calculations were performed for 12 protonated conformers of (R)-norepinephrine in the gas phase with geometry optimizations up to the MP2/6-311++G level, and with single-point calculations up to the QCISD(T) level at the HF/6-31G-optimized geometries. Four monohydrates were studied at the MP2/6-31G//HF/6-31G level. In the gas phase, the G1 conformer is the most stable with phenyl.NH(3)(+) gauche and HO(alc).NH(3)(+) gauche arrangements. A strained intramolecular hydrogen bond was found for conformers (G1 and T) with close NH(3)(+) and OH groups. Upon rotation of the NH(3)(+) group as a whole unit about the C(beta)-C(alpha) axis, a 3-fold potential was calculated with free energies for barriers of 3-12 kcal/mol at the HF/6-31G level. Only small deviations were found in MP2/6-311++G single-point calculations. A 2-fold potential was calculated for the phenyl rotation with free energies of 11-13 kcal/mol for the barriers at T = 310 K and p = 1 atm. A molecular mechanics docking study of (R)-norepinephrine in a model binding pocket of the beta-adrenergic receptor shows that the ligand takes a conformation close to the T(3) arrangement. The effect of aqueous solvation was considered by the free energy perturbation method implemented in Monte Carlo simulations. There are 4-5 strongly bound water molecules in hydrogen bonds to the conformers. Although hydration stabilizes mostly the G2 form with gauche phenyl.NH(3)(+) arrangement and a water-exposed NH(3)(+) group, the conformer population becomes T > G1 > G2, in agreement with the PMR spectroscopy measurements by Solmajer et al. (Z. Naturforsch. 1983, 38c, 758). Solvent effects reduce the free energies for barriers to 3-6 and 9-12 kcal/mol for rotations about the C(beta)-C(alpha) and the C(1)(ring)-C(beta) axes, respectively.     

Proton affinity of β-oxalylaminoalanine (BOAA): Incorporation of direct entropy correction into the single-reference kinetic method

A new version of the single-reference-extended kinetic method is presented in which direct entropy correction is incorporated. Results of calibration experiments with the monodentate base pyridine and the bidentate base ethylenediamine are presented for which the method provides proton affinities in excellent agreement with published values and reasonable predictions for the protonation entropies. The method is then used to determine the proton affinity and protonation entropy of the non-protein amino acid beta-oxalylaminoalanine (BOAA). The PA of BOAA is found to be 933.1 +/- 7.8 kJ/mol and a prediction for the protonation entropy of -39 J mol(-1) K(-1) is also obtained, indicating a significant degree of intramolecular hydrogen bonding in the protonated form. These results are supported by hybrid density functional theory calculations at the B3LYP/6-311++G**//B3LYP/6-31+G* level. They indicate that the preferred site of protonation is the alpha-nitrogen atom (PA = 935.0 kJ/mol) and that protonated BOAA has a strong hydrogen bond between the hydrogen on the alpha-amino group and one of the carbonyl oxygen atoms on the side chain.     

Homolytic Substitution at the Sulfur Atom as a Tool for Organic Synthesis

The use of intramolecular homolytic substitution at the sulfur atom by aryl and vinyl radicals, as an alternative to the use of alkyl halides, and chalcogenides as radical precursors in organic synthesis is reviewed.     

Structure and vibrational assignment of the enol form of 1,1,1-trifluoro-2,4-pentanedione

Molecular structure of 1,1,1-trifluoro-pentane-2,4-dione, known as trifluoro-acetylacetone (TFAA), has been investigated by means of Density Functional Theory (DFT) calculations and the results were compared with those of acetylacetone (AA) and hexafluoro-acetylacetone (HFAA). The harmonic vibrational frequencies of both stable cis-enol forms were calculated at B3LYP level of theory using 6-31G** and 6-311++G** basis sets. We also calculated the anharmonic frequencies at B3LYP/6-31G** level of theory for both stable cis-enol isomers. The calculated frequencies, Raman and IR intensities, and depolarization ratios were compared with the experimental results. The energy difference between the two stable cis-enol forms, calculated at B3LYP/6-311++G**, is only 5.89 kJ/mol. The observed vibrational frequencies and Raman and IR intensities are in excellent agreement with the corresponding values calculated for the most stable conformation, 2TFAA. According to the theoretical calculations, the hydrogen bond strength for the most stable conformer is 57 kJ/mol, about 9.5kJ/mol less than that of AA and about 14.5 kJ/mol more than that of HFAA. These hydrogen bond strengths are consistent with the frequency shifts for OH/OD stretching and OH/OD out-of-plane bending modes upon substitution of CH(3) groups with CF(3) groups. By comparing the vibrational spectra of both theoretical and experimental data, it was concluded that 2TFAA is the dominant isomer.     

BrSSCl和SSBrCl相对稳定性的理论研究

采用量子化学中的密度泛函理论，在B3LYP／6-311 G(3df)水平上全优化得到了S2BrCl分子线型和分叉型2种异构体的平衡结构，同时对可能发生的分子内原子迁移过程的过渡态进行了考察。计算结果表明，从能量角度看，线型的BrSSCl为稳定构型。采用统计热力学及过渡态理论，研究了Z种平衡结构之间相互转化的热力学和动力学性质。根据计算结果，无论是Cl迁移还是Br迁移，分子内的原子迁移都需要较高的活化能，并且迁移速度较慢。     

2-溴丙酸气相热消除反应的机理

用密度泛函（DFT）方法,在B3LYP/6-31G**水平上对2-溴丙酸气相消除反应机理进行了研究.计算表明,反应主要是通过半极化五元环结构过渡态进行的,羧基上的氢原子协助溴原子离去,羧基氧原子帮助稳定过渡态.在B3LYP/6-311＋＋G(3df,3pd)水平上对B3LYP/6-31G**优化的几何构型进行了单点能计算,计算所得反应的速度控制步骤的活化能为189.461 kJ•mol－1,偏离实验值((180.3±3.4) kJ•mol－1)5.08％.