Mechanism of the aminolysis of methyl benzoate: a computational study

Density functional and ab initio methods were applied in examining the possible mechanistic pathways for the reaction of methyl benzoate with ammonia. Transition state structures and energies were determined for concerted and neutral stepwise mechanisms. The theoretical results show that the two possible pathways have similar activation energies. The general base catalysis of the process was also examined. The predictions reveal that the catalytic process results in considerable energy savings and the most favorable pathway of the reaction is through a general-base-catalyzed neutral stepwise mechanism. The structure and transition vectors of the transition states indicate that the catalytic role of ammonia is realized by facilitating the proton-transfer processes. Comparison of the energetics of the aminolysis for methyl benzoate and methyl formate shows the more favorable process to be that for the aliphatic ester. The differing reactivity of the two esters is explained in terms of the electrostatic potential values at the atoms of the ester functionality.     

CH stretching vibration of N-methylformamide as a sensitive probe of its complexation: infrared matrix isolation and computational study

The complexes between trans-N-methylformamide (t-NMF) and Ar, N(2), CO, H(2)O have been studied by infrared matrix isolation spectroscopy and/or ab initio calculations. The infrared spectra of NMF/Ne, NMF/Ar and NMF/N(2)(CO,H(2)O)/Ar matrices have been measured and the effect of the complexation on the perturbation of t-NMF frequencies was analyzed. The geometries of the complexes formed between t-NMF and Ar, N(2), CO and H(2)O were optimized in two steps at the MP2/6-311++G(2d,2p) level of theory. The four structures, found for every system at this level, were reoptimized on the CP-corrected potential energy surface; both normal and CP corrected harmonic frequencies and intensities were calculated. For every optimized structure the interaction energy was partitioned according to the SAPT scheme and the topological distribution of the charge density (AIM theory) was performed. The analysis of the experimental and theoretical results indicates that the t-NMF-N(2) and CO complexes present in the matrices are stabilized by very weak N-H···N and N-H···C hydrogen bonds in which the N-H group of t-NMF serves as a proton donor. In turn, the t-NMF-H(2)O complex present in the matrix is stabilized by O-H···O(C) hydrogen bonding in which the carbonyl group of t-NMF acts as a proton acceptor. Both, the theoretical and experimental results indicate that involvement of the NH group of t-NMF in formation of very weak hydrogen bonds with the N(2) or CO molecules leads to a clearly noticeable red shift of the CH stretching wavenumber whereas engagement of the CO group as a proton acceptor triggers a blue shift of this wavenumber.     

Degradation mechanism of methyl mercury selenoamino acid complexes: a computational study

Density functional theory (DFT) calculations have been carried out on the possible degradation/demethylation mechanism of methyl mercury (CH(3)Hg(+)) complexes with free cysteine and seleonocysteine. The binding of CH(3)Hg(+) ions with one (seleno)amino acid is thermodynamically favorable. However, the binding with another acid molecule is a highly unfavorable process. The CH(3)Hg-(seleno)cysteinate then degrades to bis(methylmercuric)sulphide (selenide for the Se-containing complex) which in turn forms dimethyl mercury and HgS/HgSe, the latter being precipitated out as nanoparticles. The dimethyl mercury interacts with water molecules and regenerates the CH(3)HgOH precursor. The calculated free energies of formation confirm the thermodynamic feasibility of every intermediate step of the degradation cycle and fully support earlier experimental results. In completing the cycle, one unit of mercury precipitates out from two units of sources, and thereby Se antagonizes the Hg toxicity. The degradation of CH(3)Hg-L-cysteinate is thermodynamically more favorable than the formation of CH(3)Hg-L-cysteinate. The preferred degradation of the CH(3)Hg-L-cysteinate suggests that another mechanism for CH(3)Hg to cross the blood-brain barrier should exist.     

Molecular structure of the octatetranyl anion, C8H-: a computational study

The equilibrium molecular structure of the octatetranyl anion, C8H(-), which has been recently detected in two astronomical environments, is investigated with the aid of both ab initio post-Hartree-Fock and density functional theory (DFT) calculations. The model chemistry adopted in this study was selected after a series of benchmark calculations performed on molecular acetylene for which accurate gas-phase structural data are available. Geometry optimizations performed at the CCSD/6-311+G(2d,p), QCISD/6-311+G(2d,p), and MP4(SDQ)/6-311+G(2d,p) levels of theory yield for C8H(-) an interesting polyyne-type structure that defies the chemical formula displaying a simple alternation of triple and single carbon-carbon bonds, [:C[triple bond]C-C[triple bond]C-C[triple bond]C-C[triple bond]CH](1-). In the optimized geometry of C8H(-), as one proceeds from the naked carbon atom on one side of the chain to the CH unit on the opposite side of the chain, the short (formally triple) carbon-carbon bonds decrease in length from 1.255 to 1.213 A whereas the long (formally single) carbon-carbon bonds increase (albeit only slightly) in length from 1.362 to 1.378 A (CCSD results). In striking contrast, both MP2 and DFT (B3LYP and PBE0) calculations fail in reproducing the pattern of the carbon-carbon bond lengths obtained with the CCSD, QCISD, and MP4 methods. The structures of three shorter n-even chains, C(n)H(-) (n = 2, 4, and 6), along with those of four n-odd compounds (n = 3, 5, 7, and 9) are also investigated at the CCSD/6-311+G(2d,p) level of theory.     

Dissociation of carbanions from acyl iridium compounds: an experimental and computational investigation

Instead of reductive elimination of aldehyde, or decarbonylation to give a trifluoroalkyl hydride, heating Cp(PMe(3))Ir(H)[C(O)CF(3)] (1) leads to the quantitative formation of Cp(PMe(3))Ir(CO) (2) and CF(3)H. Kinetic experiments, isotope labeling studies, solvent effect studies, and solvent-inclusive DFT calculations support a mechanism that involves initial dissociation of trifluoromethyl anion to give the transient ion-pair intermediate [Cp(PMe(3))Ir(H)(CO)](+)[CF(3)](-). Further evidence for the ability of CF(3)(-) to act as a leaving group came from the investigation of the analogous methyl and chloride derivatives Cp(PMe(3))Ir(Me)[C(O)CF(3)] and Cp(PMe(3))Ir(Cl)[C(O)CF(3)]. Both of these compounds undergo a similar loss of trifluoromethyl anion, generating an iridium carbonyl cation and CF(3)D in CD(3)OD. Three additional acyl hydrides, Cp(PMe(3))Ir(H)[C(O)R(F)] (where R(F) = CF(2)CF(3), CF(2)CF(2)CF(3), or CF(2)(CF(2))(6)CF(3)) undergo R(F)-H elimination to give 2 at a faster rate than CF(3)H elimination from 1. Stereochemical studies using a chiral acyl hydride with a stereocenter at the beta-position reveal that ionization of the carbanion occurs to form a tight ion-pair with high retention of configuration and enantiomeric purity upon proton transfer from iridium.     

Nucleophilic reactivities of carbanions in water: the unique behavior of the malodinitrile anion

The kinetics of the reactions of nine carbanions 1a-i, each stabilized by two acyl, ester, or cyano groups, with benzhydrylium ions in water were investigated photometrically at 20 degrees C. Because the competing reactions of the benzhydrylium ions with water and hydroxide ions are generally slower, the second-order rate constants of the reactions of the benzhydrylium ions with the carbanions can be determined with high precision. The rate constants thus obtained can be described by the Ritchie equation, log(k/k(0)) = N(+) (eq 1), which allows us to calculate Ritchie N(+) parameters for a series of stabilized carbanions, for example, malonate, acetoacetate, malodinitrile, etc., and compare them with those of other n-nucleophiles in water (hydroxide, amines, azide, thiolates, etc.). Because the Ritchie relationship (eq 1) is a special case of the more general relationship log k = s(N + E) (eq 4), the reactivity parameters N and s for the carbanions 1a-i can also be calculated and compared with the nucleophilic reactivities of a large variety of n-, pi-, and sigma-nucleophiles, including reactivities of carbanions in dimethyl sulfoxide. While the acyl and ester substituted carbanions are approximately 3 orders of magnitude less reactive in water than in dimethyl sulfoxide, the malodinitrile anion (1i) shows almost the same reactivity in both solvents. Correlations between the nucleophilic reactivities of carbanions with the pK(a) values of the corresponding CH acids reveal that the malodinitrile anion (1i) is considerably more nucleophilic than was expected on the basis of its pK(a) value. This deviation is assigned to the exceptionally low Marcus intrinsic barriers of the reactions of the malodinitrile anion (1i).     

Vanadium oxide anion cluster reactions with methyl isobutyrate and methyl methacrylate monomer and dimer: a study by FT/ICR mass spectrometry

Laser ablation of vanadium pentoxide (V₂O₅) powder produces VO₃⁻, V₂O₅⁻, V₃O₇⁻, V₃O₈⁻, and V₄O₁₀⁻ cluster ions which have subsequently been reacted with methyl isobutyrate, methyl methacrylate monomer and its dimer in the ion cell region of a Fourier transform ion cyclotron resonance mass spectrometer. Gas phase ion/molecule chemistry has revealed that reactivity decreases with increased mass of the vanadium oxide cluster anions. VO₃⁻, V₂O₅⁻, and V₃O₇⁻ ions react with the three reagents, methyl isobutyrate, methyl methacrylate and its dimer, respectively, either by addition of a whole reagent molecule or an associated fragment. All products formed are a result of parallel processes. V₄O₁₀⁻ undergoes no reaction for reaction times of up to 500 s, while V₃O₈⁻ adds a water molecule. Although the ions possess a net negative charge, the reactive site toward electron rich reagents such as methyl isobutyrate, methyl methacrylate and its dimer is the under-coordinated vanadium atom. This observation is supported by the lack of reactivity toward the studied reagents by those anions (V₃O₈⁻ and V₄O₁₀⁻) whose most likely stable structures contain fully coordinated vanadium atoms.     

Infrared spectra and structure of carbanions: XVIII. A semiempirical study of carbanions of cyanoacetic acid derivatives

The IR spectra of cyanoacetic acid, ethyl cyanoacetate and cyanoacetamide as well as those of related mono- and, whenever possible, dianions have been studied in dimethyl-sulphoxide (DMSO) and DMSO-d₆.The observed nitrile and carbonyl absorption frequencies correlate linearly with the corresponding Wiberg bond indices given by CNDO/2 calculations with full geometry optimization. These calculations predict carbanionic structures throughout except in the case of the dinegative ion of cyanoacetamide, which could be considered as originating from the aminoacetylenic tautomer of NCCH₂CONH₂. Parallel MINDO/3 calculations, however, predict that the latter dianion is again a carbanion. This result is in reasonable agreement with normal coordinate calculations and the experimental isotopic shifts of vibrational frequencies of the dianion ¹⁵NCCH^?CONH^?.     

A computational study of the reaction of methane with methyl radical

The activation energy and optimized transition-state geometry for the abstraction of a hydrogen atom from methane by methyl radical have been calculated by the semiempirical methods MINDO /3 and MNDO . These results are compared with other semiempirical and ab initio results. The MINDO /3 method, based upon accuracy of the computed energy of activation, appears to be the computational method of greatest reliability. A method of locating the transition state on semiempirical surfaces is demonstrated.     

Monosilicon-substituted cyanoacetylene: a computational study

A detailed theoretical investigation of the [H,Si,C(2),N] potential energy surfaces including 28 minimum isomers and 65 interconversion transition states is reported at the Gaussian-3//B3LYP/6-31G(d) level. Generally, the triplet species lie energetically higher than the singlet ones. The former three low-lying isomers are linear HCCNSi 1 (0.00 kcal/mol), branched SiC(H)CN 12 (7.09 kcal/mol), and bent HNCCSi 7 (14.22 kcal/mol), which are separated by rather high barriers from each other and are kinetically very stable with the least conversion barriers of 32.6-70.5 kcal/mol. Two energetically high-lying isomers HCNCSi 3 (42.99 kcal/mol) and SiC(H)NC 13 (36.05 kcal/mol) are also kinetically stable with a barrier of 49.19 and 21.42 kcal/mol, respectively. Additionally, five high-lying isomers, that is, three chainlike isomers, HCCSiN 2 (55.17), HCSiNC 6 (47.80), HSiNCC 11 (78.83), and one three-membered ring isomer HN-cSiCC 19 (51.21), and one four-membered ring isomer cSiCN(H)C 27 (50.6 kcal/mol), are predicted to each have lower conversion barriers of 12-18 kcal/mol and can be considered as meta-stable species. All of the predicted 10 isomers could exist as stable or meta-stable intermediates under suitable conditions. Finally, the structural and bonding analysis indicate that the [H,Si,C(2),N] molecule contains various properties that are of chemical interest (e.g., silylene, SiC triple bonding, and conjugate SiN triple bonding and CC triple bonding, charge-transfer specie, planar aromatic specie, cumulate double bonding). This is the first detailed theoretical study on the potential energy surfaces of the series of hydrogenated Si,C,C,N-containing molecules. The knowledge of the present monohydrogenated SiC(2)N isomerism could provide useful information for more highly hydrogenated or larger Si,C(2),N-containing species.     

Maya blue: a computational and spectroscopic study

Maya Blue pigment, used in pre-Colombian America by the ancient Mayas, is a complex between the clay palygorskite and the indigo dye. The pigment can be manufactured by mixing palygorskite and indigo and heating to T > 120 degrees C. The most quoted hypothesis states that the dye molecules enter the microchannels which permeate the clay structure, thus creating a stable complex. Maya Blue shows a remarkable chemical stability, presumably caused by interactions formed between indigo and clay surfaces. This work aims at studying the nature of these interactions by means of computational and spectroscopic techniques. The encapsulation of indigo inside the clay framework was tested by means of molecular modeling techniques. The calculation of the reaction energies confirmed that the formation of the clay-organic complex can occur only if palygorskite is heated at temperatures well above the water desorption step, when the release of water is entropically favored. H-bonds between the clay framework and the indigo were detected by means of spectroscopic methods. FTIR spectroscopy on outgassed palygorskite and freshly synthesized Maya Blue samples showed that the presence of indigo modifies the spectroscopic features of both structural and zeolitic water, although no clear bands of the dye groups could be observed, presumably due to its very low concentration. The positions and intensities of delta(H2O) and nu(H2O) modes showed that part of the structural water molecules interact via a hydrogen bond with the C=O or N-H groups of indigo. Micro-Raman spectra clearly evidenced the presence of indigo both in original and in freshly synthesized Maya Blue. The nu(C=O) symmetric mode of Maya Blue red-shifts with respect to pure indigo, as the result of the formation of H-bonds with the nearest clay structural water. Ab initio quantum methods were applied on the indigo molecule, both isolated and linked through H-bonds with water, to calculate the magnitude of the expected vibrational shifts. Calculated and experimental vibrational shifts appeared to be in good agreement. The presence of a peak at 17.8 ppm and the shift of the N-H signal in the 1H MAS NMR spectrum of Maya Blue provide evidence of hydrogen bond interactions between indigo and palygorskite in agreement with IR and ab initio methods.     

A computational study of the thermochemistry of bromine- and iodine-containing methanes and methyl radicals

Bromo- and iodomethanes and the corresponding halogenated methyl radicals have been investigated by ab initio methods. Geometries and vibrational frequencies were derived with quadratic configuration interaction methods at the QCISD/6-311G(d,p) level of theory, and energies via QCISD(T)/6-311+G(3df,2p). Core electrons were represented with relativistic effective potentials. Anharmonicity of the out-of-plane bending modes in the methyl radicals was taken into account by numerical integration of the Schr?dinger equation with potentials derived from relaxed scans of these modes. The results are in good accord with experimental data where available. Thermochemistry derived via isodesmic reactions referenced to CH3, CH4, and monohalomethanes yields excellent accord with new experiments on dihalomethanes and provides recommendations for the more poorly characterized tri- and tetrahalomethanes and halomethyl radicals. For the methanes CH2Br2, CHBr3, CBr4, CH2I2, CHI3, CI4, CH2BrI, CHBr2I, and CHBrI2 we compute DeltafH degrees (298) values of 4.3, 51.6, 110.6, 108.1, 208.5, 321.3, 56.8, 104.8, and 157.1 kJ mol(-1), respectively. For the methyl radicals CH2Br, CHBr2, CBr3, CH2I, CHI2, CI3, CHBrI, CBr2I, and CBrI2 we compute DeltafH degrees (298) values of 166.6, 191.7, 224.0, 217.2, 290.4, 369.1, 241.6, 320.8, and 272.3 kJ mol(-1), respectively. Recommended confidence limits are +/-3 kJ mol(-1) per Br or I atom. Trends in these values and the corresponding C-H bond strengths are discussed and compared with prior experiments, empirical estimation schemes, and ab initio calculations.     

A computational study of the reaction kinetics of methyl radicals with trifluorohalomethanes

Ab initio calculations have been used to characterize the transition states for halogen abstraction by CH₃ in reactions with CF₄, CF₃Cl, CF₃Br, and CF₃I (1–4). Geometries and frequencies were obtained at the HF/6-31G(d) and MP2=full/6-31G(d) levels of theory. Energy barriers were computed via the Gaussian-2 methodology, and the results were employed in transition state theory analyses to obtain the rate constants over 298–2500 K. There is good accord with literature measurements in the approximate temperature range 360–500 K for reactions (2–4), and the computed activation energies are accurate to within ±6 kJ mol⁻¹. Recommended rate constant expressions for use in combustion modeling are k;₁=1.6×10⁻¹⁹ (T/K)^2.41 exp(−13150 K/T), k₂=8.4×10⁻²⁰(T/K)^2.34 exp(−5000 K/T), k₃=4.6×10⁻¹⁹ (T/K)^2.05 exp(−3990 K/T), and k₄=8.3×10⁻¹⁹ (T/K)^2.18 exp(−1870 K/T) cm³ molecule⁻¹ s⁻¹. The results are discussed in the context of flame suppression chemistry. © 1998 John Wiley & Sons, Inc. Int J Chem Kinet 30: 179–184, 1998.     

Experimental and computational thermochemical study of 2- and 3-thiopheneacetic acid methyl esters

Thiophene-based compounds have widespread use in modern drug design, biodiagnostics, electronic and optoelectronic devices, and conductive polymers. The present study reports an experimental and computational thermochemical study on the relative stabilities of 2- and 3-thiopheneacetic acid methyl esters. The enthalpies of combustion and vaporization were measured by a rotating-bomb combustion calorimeter, Calvet microcalorimetry, and correlation gas chromatography, and the gas-phase enthalpies of formation at T=298.15 K were determined. Standard ab initio molecular orbital calculations at the G3 level were performed, and a theoretical study of the molecular and electronic structure of the compounds studied was carried out. Calculated enthalpies of formation, using atomization and isodesmic reactions are in very good agreement with the experimental results.     

The SAMP alkylation: a computational study

In a computational study of a stereoselective C-C bond formation, the SAMP alkylation, a previously proposed S(E)2'-front mechanism is evaluated taking into account all current experimental evidence. Using semiempirical, density functional and perturbation theoretical methods, the structure of the key intermediate is revealed and the metalloretentive nature of the mechanism is explained. The experimental ee values of a range of reactions with different electrophiles and carbonyl sources can be correlated with calculated differences in activation energies. Furthermore, it can be concluded that the selectivity derives from the internal stabilization of the transition state 3_syn (corresponding to an electrophilic attack from above the lithiohydrazone plane) by electrophile-lithium interactions. The fast computational approach can be used best as a screening method which excludes less promising candidates to guide this synthetic method.     

Homolysis of N-alkoxyamines: a computational study.

During nitroxide-mediated polymerization (NMP) in the presence of a nitroxide R2(R1)NO*, the reversible formation of N-alkoxyamines [P-ON(R1)R2] reduces significantly the concentration of polymer radicals (P*) and their involvement in termination reactions. The control of the livingness and polydispersity of the resulting polymer depends strongly on the magnitude of the bond dissociation energy (BDE) of the C-ON(R1)R2 bond. In this study, theoretical BDEs of a large series of model N-alkoxyamines are calculated with the PM3 method. In order to provide a predictive tool, correlations between the calculated BDEs and the cleavage temperature (Tc), and the dissociation rate constant (k(d)), of the N-alkoxyamines are established. The homolytic cleavage of the N-OC bond is also investigated at the B3P86/6-311++G(d,p)//B3LYP/6-31G(d), level. Furthermore, a natural bond orbital analysis is carried out for some N-alkoxyamines with a O-C-ON(R1)R2 fragment, and the strengthening of their C-ON(R1)R2 bond is interpreted in terms of stabilizing anomeric interactions.     

The generation of diazirinone: a computational study

Computational studies indicate that the reaction of p-nitrophenoxyfluorodiazirine with fluoride ion should generate diazirinone. However, fluoride ion also catalyzes the decomposition of diazirinone to carbon monoxide and nitrogen, so that the diazirinone is likely to be unstable to the conditions used to generate it.