Correcting the Experimental Enthalpies of Formation of Some Members of the Biologically Significant Sulfenic Acids Family.

Sulfenic acids are important intermediates in the oxidation of cysteine thiol groups in proteins by reactive oxygen species. The mechanism is influenced heavily by the presence of polar groups, other thiol groups, and solvent, all of which determines the need to compute precisely the energies involved in the process. Surprisingly, very scarce experimental information exists about a very basic property of sulfenic acids, the enthalpies of formation. In this Article, we use high level quantum chemical methods to derive the enthalpy of formation at 298.15 K of methane-, ethene-, ethyne-, and benzenesulfenic acids, the only ones for which some experimental information exists. The methods employed were tested against well-known experimental data of related species and extensive CCSD(T) calculations. Our best results consistently point out to a much lower enthalpy of formation of methanesulfenic acid, CH3SOH (ΔfH0(298.15K) = -35.1 ± 0.4 kcal mol-1), than the one reported in the NIST thermochemical data tables. The enthalpies of formation derived for ethynesulfenic acid, HC≡CSOH, +32.9 ± 1.0 kcal/mol, and benzenesulfenic acid, C6H5SOH, -2.6 ± 0.6 kcal mol-1, also differ markedly from the experimental values, while the enthalpy of formation of ethenesulfenic acid CH2CHSOH, not available experimentally, was calculated as -11.2 ± 0.7 kcal mol-1.

Degradation mechanism of 2-fluoropropene by Cl atoms: experimental and theoretical products distribution studies.

The gas-phase reaction products of 2-fluoropropene (2FP) with Cl atoms have been determined for the first time at 298 K and atmospheric pressure using a 1080 L quartz-glass photoreactor coupled with in situ FTIR spectroscopy to monitor reactants and products. Acetyl fluoride and formyl chloride were observed as the main products with yields of (106 ± 10)% and (100 ± 11)%, respectively. Electronic structure calculations of reactants, intermediates, products and transition states on a detailed mechanism of the reaction were performed by DFT procedures (BMK, M06, M062X/D3), as well as accurate composite methods on both the addition and abstraction reaction channels. From the joint experimental and theoretical studies, we concluded that the reaction occurs primarily via addition to the Cα carbon, with a smaller participation of the addition on the Cß carbon, which is not produced directly from the separated reactants but from the CH3CFCH2Cl intermediate radical through a submerged transition state. The abstraction channel occurs at larger energies than the addition ones, and also presents a submerged transition state, with a lower barrier. No products arising from this channel are expected. The proposed mechanism explains also why formaldehyde, predicted as a product by former theoretical studies, is not found among the experimental products. The atmospheric implications of the reaction products are assessed.

Reinvestigation of the Deceptively Simple Reaction of Toluene with OH and the Fate of the Benzyl Radical: The "Hidden" Routes to Cresols and Benzaldehyde.

In a previous work, we have investigated the initial steps of the reaction of toluene with the hydroxyl radical using several quantum chemical approaches including density functional and composite post-Hartree-Fock models. Comparison of H-abstraction from the methyl group and additions at different positions of the phenyl ring showed that the former reaction channel is favored at room temperature. This conclusion appears at first sight incompatible with the experimental observation of a lower abundance of the product obtained from abstraction (benzaldehyde) with respect to those originating from addition (cresols). Further reactions of the intermediate radicals with oxygen, water, and additional OH radicals are explored in this paper through theoretical calculations on more than 120 species on the corresponding potential energy surface. The study of the addition reactions, to obtain the cresols through hydroxy methylcyclodienyl intermediate radicals, showed that only in the case of o-cresol the reaction proceeds by addition of O2 to the ring, internal H-transfer, and hydroperoxyl abstraction and not through direct H-abstraction. For both p- and m-cresol, instead, the reaction occurs through a higher-energy direct H-abstraction, thus explaining in part the observed larger concentration of the ortho isomer in the final products. It was also found that the benzyl radical, formed by H-abstraction from the methyl group, is able to react further if additional OH is present. Two reaction paths leading to o-cresol, two leading to p-cresol, and one leading to m-cresol were determined. Moreover, in this situation, the benzyl radical is predicted to produce benzyl alcohol, as was found in some experiments. The commonly accepted route to benzaldehyde was found to be not the energetically favored one. Instead, a route leading to the benzoyl radical (and ultimately to benzoic acid) with the participation of one water molecule was clearly more favorable, both thermodynamically and kinetically.

Calculation of the Geometries and Infrared Spectra of the Stacked Cofactor Flavin Adenine Dinucleotide (FAD) as the Prerequisite for Studies of Light-Triggered Proton and Electron Transfer.

Flavin cofactors, like flavin adenine dinucleotide (FAD), are important electron shuttles in living systems. They catalyze a wide range of one- or two-electron redox reactions. Experimental investigations include UV-vis as well as infrared spectroscopy. FAD in aqueous solution exhibits a significantly shorter excited state lifetime than its analog, the flavin mononucleotide. This finding is explained by the presence of a "stacked" FAD conformation, in which isoalloxazine and adenine moieties form a π-complex. Stacking of the isoalloxazine and adenine rings should have an influence on the frequency of the vibrational modes. Density functional theory (DFT) studies of the closed form of FAD in microsolvation (explicit water) were used to reproduce the experimental infrared spectra, substantiating the prevalence of the stacked geometry of FAD in aqueous surroundings. It could be shown that the existence of the closed structure in FAD can be narrowed down to the presence of only a single water molecule between the third hydroxyl group (of the ribityl chain) and the N7 in the adenine ring of FAD.

Theoretical study of the reactions of the hydroselenyl radical (HSe●) with the selenenic radical (HSeO●).

The formation of selenium species in some biological processes involves the generation of ionic and radical intermediates such as RSe●, RSe-, RSeO●, and RSeO-, among others. We performed a theoretical study of the possible mechanisms for the reaction of the two simplest Se radicals-the hydroselenyl (HSe●) and selenenic (HSeO●) radicals, in which the possible products, intermediates, and transition-state structures were investigated. Density functional theory (DFT) was applied at the B3LYP/6-311++G(3df,3pd) level and the Ahlrichs Coulomb fitting basis sets were employed with an effective core potential (ECP) for both Se atoms. The same procedure was used to calculate the electronic density. All calculations were also performed using the M06-2X functional, which describes weaker bonds better than B3LYP does. In the reaction of interest, the so-called CR complex (HSe····SeOH) is formed initially. After passing through the transition state TS1, cis-HSeSeOH is obtained as a product. If a low barrier is then overcome (passing through the transition state TS32), the trans-HSeSeOH species is obtained. The CR complex can also rearrange into the intermediate INT after overcoming the barrier presented by the transition state TS2. Additionally, the decomposition of INT to H2O and 1Se2 is possible through another transition state. This reaction is not included in this study. We also observed a second possible route for the conversion of INT to one of the HSeSeOH species; this route occurs through two pathways (with transition states TS31 and TS32). A comparison of some of the results with those obtained for sulfur analogs along the same pathways is also presented in this work. Graphical abstract Electronic envelopes for HSeO● and HSe● radicals.

A new perspective in the Lewis acid catalyzed ring opening of epoxides. Theoretical study of some complexes of methanol, acetic acid, dimethyl ether, diethyl ether, and ethylene oxide with boron trifluoride.

Several 1:1, 1:2, and 2:2 complexes between BF3 and CH3OH (Met), CH3COOH (AcA), (CH3)2O (DME), (CH3CH2)2O (DEE), and (CH2)2O (EOX) have been studied using ab initio (MP2) and density functional theory (DFT) (PBE, B3LYP) methods and the 6-311++G(3df,2pd) basis set. Geometrical structures and vibrational frequencies are reported, in most cases, for the first time. A detailed comparison of the vibrational frequencies for the O...BF3 vibrational modes, as well as for the nu(OH) band in the methanol and acetic acid complexes with BF3, is performed, and the theoretical frequency shifts are compared with the available experimental information. Thermochemical properties are calculated by employing counterpoise correction to alleviate the basis set superposition error. The DFT enthalpy of complexation of the 1:1 complexes results in the order of stability (AcA)2>AcA:BF3>DEE:BF3>DME:BF3>Met:BF3>EOX:BF3>(Met)2; in contrast, MP2 shows the noticeable difference that the AcA:BF3 complex is much less stable (similar to Met:BF3). The order of stability shows that, even though acetic acid prefers dimerization to complexation with BF3, the case is exactly the opposite for methanol. In both cases, the interaction of BF3 with the dimer gives rise to very stable trimers. However, in contrast to the interaction of BF3 with the methanol dimer being stronger than that with the monomer, the interaction of BF3 with the acetic acid dimer is weaker than that with the monomer. The relative strength of the complexes, discussed in the context of BF3-catalyzed ring opening of epoxides, suggests that the effect of the catalyst in a nonprotogenic solvent should be more properly ascribed to activation of the nucleophile instead of activation of the epoxide.

Molecular structure and internal rotation in 2,3,5,6-tetrafluoroanisole as studied by gas-phase electron diffraction and quantum chemical calculations.

The geometric structure of 2,3,5,6-tetrafluoroanisole and the potential function for internal rotation around the C(sp2)-O bond were determined by gas electron diffraction (GED) and quantum chemical calculations. Analysis of the GED intensities with a static model resulted in near-perpendicular orientation of the O-CH3 bond relative to the benzene plane with a torsional angle around the C(sp2)-O bond of tau(C-O) = 67(15) degrees. With a dynamic model, a wide single-minimum potential for internal rotation around the C(sp2)-O bond with perpendicular orientation of the methoxy group [tau(C-O) = 90 degrees] and a barrier of 2.7 +/- 1.6 kcal/mol at planar orientation [tau(C-O) = 0 degrees] was derived. Calculated potential functions depend strongly on the computational method (HF, MP2, or B3LYP) and converge adequately only if large basis sets are used. The electronic energy curves show internal structure, with local minima appearing because of the interplay between electron delocalization, changes in the hybridization around the oxygen atom, and the attraction between the positively polarized hydrogen atoms in the methyl group and the fluorine atom at the ortho position. The internal structure of the electronic energy curves mostly disappears if zero-point energies and thermal corrections are added. The calculated free energy barrier at 298 K is 2.0 +/- 1.0 kcal/mol, in good agreement with the experimental determination.