Protonation of group 14 oxides: the proton affinity of SnO

Molecular orbital calculations are reported for the monoxides, XO, of group 14 elements (X = C, Si, Ge and Sn) and for both isomers, XOH⁺ and HXO⁺, of the protonated monoxides. Structure optimisation has been carried out using the Density Functional Theory employing the B3LYP procedure and at both Hartree-Fock and MP2 (full) levels, all with a variety of medium-sized Gaussian basis sets. In all XO molecules the oxygen atom is the preferred site for protonation, except when X = C where HCO⁺ is the lower energy isomer. Barriers to interconversion between the two isomers XOH⁺ and HXO⁺ are over-estimated by the Hartree-Fock calculations, but with wave functions that include electron correlations they generally fall into the range 27-44 kcal mol⁻¹. Proton affinities increase as the atomic number of X increases, and values calculated by averaging over all wave functions that include electron correlation, give the following proton affinities: for CO, 141.5; for SiO, 189.3; for GeO, 196.1; and for SnO, 215.6 (all in kcal mol⁻¹).     

Electronic structures and electronic spectra of the linkage isomers NSO and SNO

The relative stabilities and electronic structures of the linkage isomers NSO⁻ and SNO⁻ have been determined by the MNDO and ab initio Hartree—Fock—Slater methods. Both approaches predict a higher stability for SNO⁻ by ca. 100 kcal mol⁻¹, but an overlap population analysis indicates substantially higher bond orders for NSO⁻ compared to SNO⁻. The calculations also reveal a low energy pathway with a barrier of ca. 6 kcal mol⁻¹ for the isomerization process NSO⁻ → SNO⁻. Good agreement was found between the observed UV-visible absorption bands for NSO⁻ (λ_max 379 nm) and SNO⁻ (λ_max 340 nm) and calculated values of the electronic transition energies.     

Thermochemistry of organosilicon compounds VII. Permethylcyclosilazanes and 1,1,3,3-tetramethyldisilazane

The enthalpy of formation (ΔH_f⁰), enthalpy of evaporation (ΔH_v⁰) and enthalpy of atomization (ΔH_a) of permethylcyclosilazanes (Me₂SiNH)_n (n = 3, 4) and 1,1,3,3-tetramethyldisilazane (Me₂SiH)₂NH have been determined. The enthalpies of formation of these compounds were compared with those calculated by the Benson-Buss-Franklin and Tatevskii additive schemes. In higher permethylcyclosilazanes the energy of the endocyclic Si---N bond is 306 ± 2 kJ mol⁻¹ (73 kcal mol⁻¹), that is 12 ± 2 kJ mol⁻¹ (3 kcal mol⁻¹) lower than the energy of the acyclic Si---N bond. The strain energy of the cyclotrisilazane ring is estimated to be 10.5 kJ mol⁻¹ (2.5 kcal mol⁻¹), whereas the energy of the ring Si---N bond is 295 kJ mol⁻¹ (70.5 kcal mol⁻¹).

The thermochemical data for permethylcyclosilazanes were compared with the corresponding values for permethylcyclosiloxanes calculated from the results of previously reported studies.     

Pentacoordinate silicon compounds: Stereochemical non-rigidity of chelates formed by intramolecular ring-closure. Crystal structure of 8-dimethylamino-1-trifluorosilylnaphthalene

The application of dynamic NMR spectroscopy to the study of stereochemical non-rigidity in pentacoordinate chelated organosilicon compounds is described. It is shown that in the compounds Me₂ iXYZ, non-dissociative ligand permutation at silicon can be distinguished unambiguously from processes associated with rupture of the chelate ring and nitrogen inversion. The crystal and molecular structure of 8-Me₂NC₁₀H₆SiF₃ has been determined. Pentacoordination of the silicon atom is confirmed, with the donor nitrogen atom and a fluorine atom occupying axial sites in an overall trigonal bipyramidal geometry. The N → Si separation is 2.3 Å (average of two distinct but closely related molecular conformations), which is less than the C¹---C⁸ distance in the naphthalene nucleus, indicating a substantial bonding interaction. NMR studies of the dynamic behaviour of the Me₂N group, and where possible (¹⁹F, ¹H) of the monodentate ligands in 8-dimethylamino-1-silylnaphthalene compounds, together with the results for the chelated benzylaminosilicon compounds, confirm that inversion of the absolute configuration at the silicon atom is not achieved by this process. The free energies of activation for non-dissociative ligand permutation at a silicon range from less than 7 kcal mol⁻¹ [SiH₃, Si(OR)₃], which is below the limit of direct measurement, to 13 kcal mol⁻¹ for Me₂NCH(Me)C₆H₄SiF₃; difunctional silicon chelate compounds (Cl, F, OR) display values from 9–12 kcal mol⁻¹. These are comparable with those determined for fluxional processes in acyclic pentacoordinate silicon compounds.     

Negative hyperconjugation in methyl and silyl anions and its effect on the acidities of CH(4-n)Fn CH(4-n)C1n SiH(4-n)Fn and SiH(4-n)Cln

Group separation reactions calculated using an ab intio molecular orbital calculation at the MP4/6-31 + + G(d,p) level of theory, show the negative hyperconjugation between fluorine atoms to be larger in methanes than in silanes. Stabilisation due to negative hyperconjugation is larger in anions than in identically substituted neutral molecules, e.g. 43.1 kcal mol⁻¹ in CF₃⁻ compared with 26.7 kcal mol⁻¹ in CHF₃. By contrast, in chloro-substituted methanes, silanes, methyl anions and silyl anions, group separation energies are approximately zero, indicating no appreciable negative hyperconjugation. An -chloro substituent is more effective than an -fluoro one at delocalising the negative charge of an anion and, as a consequence, the chloromethanes and chlorosilanes are all more acidic than the identically substitued fluoromethanes and fluorosilanes. For chloro-substituted molecules the acidity is linearly dependent on the number of chlorine atoms; for fluoro-substituted molecules stabilisation by negative hyperconjugation results in each additional fluorine atom increasing the acidity by larger increments.     

Ab initio MO study on the global minimum structure of C3H3 anion: propynl-1-yl versus allenyl anions

The geometrical structures of the C₃H⁻₃ anion are surveyed at the coupled-cluster doubles (CCD) level of theory with the aug-cc-pVDZ basis set. To clarify the CCD geometries, the stable two isomers -- propynl-l-yl 1 and allenyl 2 anions -- are further optimized at the coupled-cluster singles, doubles (triples) (CCSD(T)) level of theory both with the aug-cc-pVDZ and aug-cc-pVTZ basis sets. The final energies are calculated at the CCSD(T) and the complete active space self-consistent field (CASSCF) multi-reference internally contracted CI (MRCI) levels of theory with the aug-cc-pVTZ basis set. At the MRCI level of theory including both the corrections due to the cluster energies (MRCI+Q) and the zero-point vibrational energies, the allenyl anion 2 is about 1.3 kcal mol⁻¹ lower in energy than the propynl-l-yl anion 1. These results contrast with the previous theoretical estimates, where the propynl-l-yl anion 1 is 2-3 kcal mol⁻¹ lower in energy than the allenyl anion 2. The activation energies of the intramolecular hydrogen transfer in the 1 → 2 conversion reactions are 63.5 kcal mol⁻¹ at the MRCI+Q level of theory with the aug-cc-pVTZ basis set including the zero-point energy corrections. The adiabatic electron affinity of the planer propargyl (H₂CCCH) radical, which is the global minimum of the C₃H₃ radical, is calculated to be 0.976 eV (after correction for the zero-point energy changes) at the CCSD(T) level of theory with the aug-cc-pVTZ basis set. The present electron affinity is in fairly good agreement with the experimental one (0.893 eV) observed by Oakes and Ellison.     

Theoretical study of the N---H tautomerism in free base porphyrin

The N---H tautomerism of free base porphyrin is investigated at the semiempirical spin-unrestricted AM1 (UAM1) and ab initio RHF/3-21G levels. The UAM1 method provides delocalized geometries for all stationary structures without imposing any symmetry constraint. RHF/3-21G geometry optimizations have to be performed under symmetry restrictions to ensure that realistic delocalized structures are obtained. Both the semiempirical and the ab initio calculations predict that the interconversion between trans tautomers proceeds in an asynchronous two-step process via intermediate cis tautomers. The cis tautomers are characterized as minima in the potential energy surface and are 8–10 kcal mol⁻¹ higher in energy. The activation energy for the trans → cis interconversion is calculated to be approximately 23 kcal mol⁻¹ at the 3-21G level. The activation energy for the synchronous trans → trans interconversion is higher and has a value of 30.5 kcal mol⁻¹. The activation energies obtained at the semiempirical UAM1 level are twice as large as the ab initio values.     

Kinetic study of thermal decomposition of CoOOH

The kinetics of the thermal decomposition of CoOOH powder has been studied isothermally in a temperature range of 260—310°C in air. The reaction was found to proceed by the advance of a two-dimensional reaction interface. The kinetics results indicate that there are two phases in the decomposition in this temperature range: up to 280°C with an activation energy E₁ = 34.75 kcal mol⁻¹ and above 280°C with E₂ = 18.91 kcal mol⁻¹. A reaction mechanism is proposed to account for these observations.     

Kinetic study of trifluoromethylation with s-(trifluoromethyl) dibenzothiophenium salts

The kinetic parameters were determined for C-trifluoromethylation of aniline with S-(trifluoromethyl)dibenzothiophenium triflate (1), its 3,7-dinitro derivative (2) and S-(trifluoromethyl)diphenylsulfonium triflate (3) in DMF-d₇. The higher reactivity of heterocyclic 1 compared with non-heterocyclic 3 could be explained on the basis of its greatly enhanced activation entropy (ΔS^≠: −11.2 cal mol ⁻¹ K⁻¹ for 1; −47.1 for 3), but not its enhanced activation enthalpy (ΔH^≠: 21.2 kcal mol⁻¹ for 1; 12.1 for 3). The aromatic delocalization of the heterocyclic ring may thus be only slightly disturbed by the S-trifluoromethyl substituent. The high reactivity of 2 was attributed to the great electron deficiency caused by two nitro groups in addition to the heterocyclic salt system (ΔH^≠ 17.0 kcal mol⁻¹, ΔS^≠ −9.1 cal mol⁻¹ K⁻¹ for 2). The reaction mechanism is discussed; the conventional S_N2 attack mechanism was ruled out and a mechanism for a side-on attack to the CF₃-S bond may possibly be applicable.     

An ab initio molecular orbital study on the gas-phase rapid reaction of the silicon cation Si with ammonia

The gas-phase rapid ion-molecule reaction Si⁺ (²P) + NH₃→ SiNH₂⁺ + H is theoretically investigated by the ab initio molecular orbital methods. Several possible pathways (A, B, C) on its potential energy surface have been examined, discussed and compared. Theoretical calculations indicate that pathway A is favourable in energy and that the reaction begins by forming a collision complex of the ion-dipole molecule Si-NH⁺₃, which forms with no barrier into the first energy well of the reaction coordinate. Migration of an H atom from an N atom to a Si atom forms the intermediate HSi-NH⁺₂, which corresponds to the second energy well and can fragment to the observed product SiNH⁺₂ by losing an H atom from the Si atom. The barriers for migration and fragmentation are 52.5 and 38.6 kcal mol⁻¹ respectively. Pathway A has a negative activation energy of −42.1 kcal mol⁻¹.     

Ab initio calculations of the vibrational spectra of the ammonia and fluoramide complexes with HF

The structures, energetics, vibrational frequencies and IR intensities of the H₃N HF, H₃N F₂ and NH₂FHF (three isomers) complexes were examined using the self-consistent field method within the 6-311G^** basis set. The interaction energies were calculated using the MP2 approach. The results are compared with monomer calculations and experimental data. The complex NH₂FHF was found to exist in three forms: one with the HF molecule hydrogen bonded to the nitrogen lone pair of NH₂F (D₀ =7.403 kcal mol⁻¹), another a complex formed through the F atom lone pair (D₀=4.698 kcal mol⁻¹) and third a cyclic structure (D₀=5.644 kcal mol⁻¹).     

Discussion of the catalytic pathway of cysteine proteases based on AM1 calculations

The deacylation reaction of the cysteine protease papain was examined by AM1 reaction-coordinate calculations. The transition-state (TS) structure was extracted from the reaction pathway as corresponding to the maximum point along this minimum-energy pathway. Consistent with experimental kinetic data revealing that deacylation is about 60 times faster for thioester (---C(O)---S---) than dithioester (---C(S)---S---) intermediates, calculated E_a values are about 10 kcal mol⁻¹ lower for the former than the latter. The calculated partial atomic charges indicate that the C=O carbon in the thioester is a good site for nucleophilic attack whereas the corresponding C=S carbon in the dithioester is a poor site. The present calculations reveal that the enzyme's oxyanion hole contributes about 9 kcal mol⁻¹ toward reducing E_a for the anionic tetrahedral intermediate and TS structure. On the other hand, the presence of Asn in the putative Asn-His-Cys catalytic triad contributes only about l kcal mol⁻¹ toward reducing their E_a value. The presence of this Asn, however, did appear to stabilize His in its protonated form (ImH⁺) over its unprotonated form (Im). Two novel mechanisms are introduced to explain the unusual effect of a remote X substituent on the deacylation kinetics of the substrate family under consideration. The first mechanism invokes a “field effect” while the second mechanism embodies the concepts of induction and homoconjugation. The unique feature of these two mechanisms is that, unlike other proposed models, they circumvent the requirement for a close N…S interaction which has stimulated controversy.     

Semiempirical and ab initio calculations on the alkaline hydrolysis of the β-lactam ring Influence of the solvent

We used semiempirical and ab initio calculations to investigate the nucleophilic attack of the hydroxyl ion on the β-lactam carbonyl group. Both allowed us to detect reaction intermediates pertaining to proton-transfer reactions. We also used ab initio calculations and the PM3 semiempirical method to investigate the influence of the solvent on the process. The AMSOL method predicts the occurrence of a potential energy barrier of 20.7 kcal mol⁻¹ due to the desolvation of the hydroxyl ion in approaching the β-lactam carbonyl group. Using the supermolecular approach and a water solvation sphere of 20 molecules around the solute, the potential energy barrier is lowered to 17.5 kcal mol⁻¹. Ab initio calculations using the SCRF method predict a potential energy barrier of 13.6 kcal mol⁻¹. These three values, especially the last two, are very close to the experimental value of 16.7 kcal mol⁻¹.     

Can chlorine anion catalyze the reaction of HOCl with HCl?

The reaction of HOCl + HCl → Cl₂ + H₂O in the presence of chlorine anion Cl⁻ has been studied using ab initio methods. The overall exothermicity is 15.5 kcal mol⁻¹ and this reaction has been shown to have a high activation barrier of 46.5 kcal mol⁻¹. Cl⁻ is found to catalyze the reaction via the formation of HOCl·Cl⁻, ClH·HOCl·Cl⁻ and Cl⁻·H₂) intermediate ion-molecule complexes or by interacting with a concerted four-center transition state of the reaction of HOCl + HCl.     

Adsorption of oligooxypropylenated amines at the aqueous solution—air interface: Homologous series of piperidine and morpholine derivatives

The surface tension isotherms for pure oligooxypropylenated piperidine and morpholine at the aqueous solution—air interface were determined and interpreted. The surface excess concentration, Γ, the surface area per molecule, A, and the standard free energy of adsorption, ΔG°, were calculated according to a new empirical adsorption equation. The standard free energy contribution for the oxypropylene group (PO) in morpholine derivatives,ΔG° (PO) = −3.34 kJ mol⁻¹, is substantially lower than that for the PO group located in the piperidine derivatives, i.e. ΔG° (PO)= −3.12 kJ mol⁻¹.     

Pyramidane 2. Further computational studies: potential energy surface, basicity and acidity, electron-withdrawing and electron-donating power, ionization energy and electron affinity, heat of formation and strain energy, and NMR chemical shifts

The novel cycloalkane pyramidane (tetracyclo[2.1.0.0^1,30^2,5]pentane, [3.3.3.3]fenestrane), C₅H₄, with a pyramidal carbon atom, was investigated further. Calculations at the B3LYP/6-31G^* and G2(MP2) levels supported earlier conclusions from QCISD(T)/6-31G^*//MP2(FC)/6-31G^* energies that pyramidane lies in a deep well (ca. 100 kJ mol⁻¹) on the potential energy surface. The pyramidal carbon is predicted to have a lone electron pair, and calculations (CBS-4) indicate that pyramidane is remarkably basic for a saturated hydrocarbon (proton affinity 976, cf. 922 and 915 kJ mol⁻¹ for pyridine and aniline, respectively). The calculated (CBS-4) acidity is similar to that of tetrahedrane and toluene; the pyramidyl group (C₅H₃) attached to an atom bearing a lone electron pair appears to be much more strongly electron-withdrawing than the phenyl group. The infrared CO stretching frequency and C–CHO rotational barriers of pyramCHO, PhCHO and cyclopropylCHO indicate that the pyramidyl group is comparable to phenyl and cyclopropyl in its ability to donate electrons to an electron-deficient carbon. The adiabatic ionization energy of pyramidane is ca. 9.0 eV (MP2/6-31G^*, energy differences and Koopmans’ theorem), similar to that of typical cycloalkanes. The heat of formation of pyramidane was calculated by the G2(MP2) method and isodesmic reactions to be to be 585 kJ mol⁻¹ and the strain energy was estimated to be 622 kJ mol⁻¹; pyramidane is 122 kJ mol⁻¹ more strained than its isomer spiropentadiene. Application of the NMR NICS method, varying the position of the probe nucleus, gave no evidence for benzenoid-type aromaticity in the potentially cyclobutadiene cation-like base of pyramidane.     

Structures and energetics of C3H6S isomers: a Gaussian-3 ab initio study

Twenty-two isomers/conformers of C₃H₆S^+√ radical cations have been identified and their heats of formation (ΔH_f) at 0 and 298 K have been calculated using the Gaussian-3 (G3) method. Seven of these isomers are known and their ΔH_f data are available in the literature for comparison. The least energy isomer is found to be the thioacetone radical cation (4⁺) with C_2v symmetry. In contrast, the least energy C₃H₆O^+√ isomer is the 1-propen-2-ol radical cation. The G3 ΔH_f298 of 4⁺ is calculated to be 859.4 kJ mol⁻¹, ca. 38 kJ mol⁻¹ higher than the literature value, ≤821 kJ mol⁻¹. For allyl mercaptan radical cation (7⁺), the G3 ΔH_f298 is calculated to be 927.8 kJ mol⁻¹, also not in good agreement with the experimental estimate, 956 kJ mol⁻¹. Upon examining the experimental data and carrying out further calculations, it is shown that the G3 ΔH_f298 values for 4⁺ and 7⁺ should be more reliable than the compiled values. For the five remaining cations with available experimental thermal data, the agreement between the experimental and G3 results ranges from fair to excellent.

Cation CH₃CHSCH₂^+√ (10⁺) has the least energy among the eleven distonic radical cations identified. Their ΔH_f298 values range from 918 to 1151 kJ mol⁻¹. Nevertheless, only one of them, CH₂=SCH₂CH₂^+√ (12⁺), has been observed. Its G3 ΔH_f298 value is 980.9 kJ mol⁻¹, in fair agreement with the experimental result, 990 kJ mol⁻¹.

A couple of reactions involving C₃H₆S^+√ isomers CH₂=SCH₂CH₂^+√ (12⁺) and trimethylene sulfide radical cation (13⁺) have also been studied with the G3 method and the results are consistent with experimental findings.     

Ab initio calculations of the rotational barriers in formamide and acetamide: The effects of polarization functions and correlation

Ab initio calculations have been used to determine the gas-phase rotational barrier about the CN bond in formamide and acetamide. The results indicate that the inclusion of polarization functions in the basis set leads to a substantial decrease (ca. 5 kcal mol⁻¹) in the calculated barrier height at the SCF level. Electron correlation effects decrease the barrier by less than 1 kcal mol⁻¹, while the addition of zero point energy corrections changes the barrier height only slightly. Based upon the current calculations, the 0 K rotational barriers for isolated formamide and acetamide are predicted to be 14.2 and 12.5 kcal mol⁻¹, respectively.     

Ab initio study of the two competitive channels HO2 + H → H2 + O2 and HO2 + H → H2O + O

Saddle point geometries and barrier heights have been calculated for the H abstraction reaction HO₂(²A″)+H(²S) → H₂(¹Σ⁺_g)+O₂(³Σ⁻_g) and the concerted H approach-O removing reaction HO₂ (²A″)+H(²S) → H₂O(¹A₁)+O(³P) by using SDCI wavefunctions with a valence double-zeta plus polarization basis set. The saddle points are found to be of C_s symmetry and the barrier heights are respectively 5.3 and 19.8 kcal by including size consistent correction. Moreoever kinetic parameters have been evaluated within the framework of the TST theory. So activation energies and the rate constants are estimated to be respectively 2.3 kcal and 0.4×10⁹ ℓ mol⁻¹ s⁻¹ for the first reaction, 20.0 kcal and 5.4.10⁻⁵ ℓ mol⁻¹ s⁻¹ for the second. Comparison of these results with experimental determinations shows that hydrogen abstraction on HO₂ is an efficient mechanism for the formation of H₂ + O₂, while the concerted mechanism envisaged for the formation of H₂O + O is highly unlikely.     

Theoretical investigations of structure and enzymatic mechanisms of aspartyl proteinases : Part I. Ab-initio calculations on an active site model: hydrogen diformiate with H2O and H3O

The active site of aspartyl proteinases (Asp) was modelled as two formiates connected with a proton and set in geometry corresponding to Asp 32 and Asp 215 side chain carboxylate groups of endothiapepsin. The shared solvent molecule was alternatively H₂O and H₃O⁺. Their positions and those of hydrogen-bonded protons were optimized using the STO-3G basis set. Full geometry optimizations were made of the hydrogen diformiate complexes with H₂O and H₃O⁺. Asymmetric hydrogen-bonded structures resulted from these calculations, except for the fully optimized complex with H₂O. In the complexes with H₃O⁺, one proton moved consistently to the proximate carboxylic oxygen yielding a neutral, hydrated formic acid dimer. Interaction energies and proton potential energy curves were calculated using the 4-31G basis set. The interaction energy with H₂O was found to be 20.49 kcal mol⁻¹ and 202.75 kcal mol⁻¹ with H₃O⁺.