Determination of sulfite radical (SO 3 ⋅ −) reaction rate constants by means of competition kinetics

Summary The sulfite radical anion (SO ₃ ^–) was found to react rapidly with the flavonoid quercetin (k = 2.5 × 10⁸ dm³mol^–1 s^–1) and the carotenoids crocin (k = 1.0 × 10⁹ dm³mol^–1 s^1–) and crocetin (k = 1.5 × 10⁹ dm³mol^1– s^1–). The reactions can easily be monitored due to the strong absorptions of the substrates and, in the case of quercetin, the formation of a strongly absorbing transient species. Using these substances, we determined by means of competition kinetics rate constants of SO ₃ ^– reactions with nucleic acid components, polyunsaturated fatty acids, and glutathione.Abbreviations ABTS 2,2-azinobis(3-ethyl-6-benzothiazolinesulfonate) - cmc critical micellization concentration - GSH Glutathione - PUFA polyunsaturated fatty acids Preliminary results were presented at the Third Biennial Meeting of the Society for Free Radical Research in Düsseldorf in July, 1986     

Theoretical study on rate constants for the reactions of CF3CH2NH2 (TFEA) with the hydroxyl radical at 298 K and atmospheric pressure

Theoretical investigations are carried out on reaction mechanism of the reactions of CF₃CH₂NH₂ (TFEA) with the OH radical by means of ab initio and DFT methods. The electronic structure information on the potential energy surface for each reaction is obtained at MPWB1K/6-31+G(d,p) level and energetic information is further refined by calculating the energy of the species with a Gaussian-2 method, G2(MP2). The existence of transition states on the corresponding potential energy surface is ascertained by performing intrinsic reaction coordinate (IRC) calculation. Our calculation indicates that the H abstraction from –NH₂ group is the dominant reaction channel because of lower energy barrier. The rate constants of the reaction calculated using canonical transition state theory (CTST) utilizing the ab initio data. The agreement between the theoretical and experimental rate constants is good at the measured temperature. From the comparison with CH₃CH₂NH₂, it is shown that the fluorine substution decreases the reactivity of the C-H bond.     

A density functional theory study of phenyl formation initiated by ethynyl radical (C2H•) and ethyne (C2H2)

An ab initio computational density functional theory (DFT) was used to study the formation of the first cyclic molecule (phenyl) initiated by the ethynyl radical (C₂H•). The study covers a competition reaction between the addition reactions of C₂H• with ethyne (C₂H₂) and some molecular re-arrangement schemes. The minimum energy paths of the preferred cyclic formation route were characterized. A thorough thermochemical analysis was performed by evaluating the differences in the energy of activation (ΔE), enthalpy (ΔH), and Gibb's free energy (ΔG) of the optimized stable and transition state (TS) molecules. The reaction temperatures were set to normal (T = 298 K) and combustion (T = 1,200 K) conditions.

Do parallel β-strands have dipole moments? An ab initio molecular-orbital-direct reaction field study

Recently, it was suggested that parallel β-sheets have a significant dipole moment, in contrast to antiparallel sheets. Ab initio molecular-orbital (MO) calculations on parallel and antiparallel β-strands of tetra(Gly) show that they have very similar charge distributions. Interaction energies between two and three strands of tetra(Gly), obtained using the direct reaction field Hamiltonian, show that a particular choice of point charges is probably not crucial for calculating interactions within β-sheets, but that it might be for calculating interactions between these sheets and other parts of a protein, in particular, α-helices. The point-charge representation of our MO-SCF results will probably reduce the hazard of introducing artefacts in electrostatic calculations of protein conformational energies, provided the short-range interactions are treated in a more realistic way, i.e., such that intra- and interchain induction effects are included.     

Further quasi-classical trajectory studies on the C++ H2O reaction

Further trajectory studies on the C⁺ + H₂O reaction have been performed using a potential energy surface described through a finite element method in its p version. In former trajectory studies [Y. Ishikawa, T. Ikegami and R.C. Binning Jr., Direct ab initio molecular dynamics study of C⁺+H₂O: angular distribution of products and distribution of product kinetic energies, Chem. Phys. Lett. 370 (2003), pp. 490–495; J.R. Flores, Quasichemical trajectories on a finite element density functional potential energy surface: the C⁺+H₂O reaction revisited, J. Chem. Phys. 125 (2006), 164309], tunnelling was not taken into account. The present results together with the analysis of the electronic excited states [J.R. Flores and A.B. González, The role of the excited electronic states in the C⁺+H₂O reaction, J. Chem. Phys. 128 (2008), 144310] are useful to interpret the mechanism of the title reaction, which has been the subject of crossed beam experiments [D.M. Sonnenfroh, R.A. Curtiss and J.M. Farrar, Collision complex formation in the reaction of C⁺ with H₂O, J. Chem. Phys. 83 (1985), pp. 3958–3964] and can be considered a prototypical ion–molecule reaction.     

Conformation and tautomerizm of the 2-methyl-4-pyridin-2′-yl-1,5-benzodiazepine molecule. An ab initio study

The protomeric tautomerizm and conformation of the 2-methyl-4-pyridin-2′-yl-1,5-benzodiazepine molecule were investigated, and its three neutral tautomers (B₁,B₂,B₃) and their rotamers (C₁,C₂,C₃) were considered. Full geometry optimizations were carried out at the HF/6-31G* and B3LYP/6-31G* levels in gas phase and in water. The tautomerization processes in water (ɛ = 78.54) were studied by using self-consistent reaction field theory. The calculation showed that the boat conformation is dominant for the seven-membered diazepine ring in all of the structures, even with different double bond positions. The calculated relative free energies (ΔG) showed that the tautomer C₁ was the most stable structure, and its conformer B₁ was the second most stable in the gas phase and in water. Figure 2-Methyl-4-pyridin-2′-yl-1,5-benzodiazepine     

Exhaust gas purification using biocatalysts (fixed bacteria monocultures) — the influence of biofilm diffusion rate (O2) on the overall reaction rate

Summary This paper presents results of experiments on the influence of O₂ and substrate (pollutant) concentration on the overall reaction rate of a trickle-bed reactor used for biological waste gas purification. The biocatalyst was a pollutant-specific bacterial monoculture fixed on porous glass carriers. The conversion of acetone and propionaldehyde, as model pollutants that are easily soluble in water, was measured. Under constant hydrodynamic conditions (gas and liquid flow rates) the inlet pollutant concentration was varied. The O₂ partial pressure in the model gas was increased to investigate the influence of O₂ supply on pollutant conversion. At higher pollutant concentrations (>117 mg acetone.m^-3 gas and > 150 mg propionaldehyde.m^-3 gas) higher concentrations of dissolved O₂ led to a significant rise in the maximum degradation capacity of the reactor. This maximum reaction rate was independent of the pollutant mass flow. It seems that the diffusion of O₂ in the biofilm is rate-determining. The reaction rate at lower inlet concentrations was not affected by the improved O₂ supply. Here the external mass transfer through the liquid film limits the reaction rate and the maximum separation efficiency of about 80% at a residence time of 1.2s (space velocity 3000h^-1) is achieved.     

Direct dynamics simulations of the hydrogen abstraction reaction Cl + CF3CF2CH2OH

The mechanism and kinetics of 2,2,3,3,3-pentafluoropropanol (CF₃CF₂CH₂OH) reaction with Chlorine atom (Cl) is investigated in this work. Two hydrogen abstraction channels of the title reaction are identified. The geometries of all the stationary points in the potential energy surface are obtained at the BHandHLYP/6-311G** level, and the energies of the selected points along the minimum energy path (MEP) are improved by the CCSD(T) method. A dual-level direct dynamics method is employed to study the kinetic nature of the hydrogen-abstraction reaction channels. The calculated rate coefficients show that the hydrogen abstraction from the CH₂ group is the primary channel. The calculated total rate coefficients are in best agreement with the experimental values. The four-parameter rate coefficients expression of the title reaction between the temperatures 200 K and 1000 K is provided.     

An ab initio study of cis/trans isomerization in the XONO systems (X  F,Cl)

Hartree-Fock level and post Hartree-Fock level molecular orbital calculations are reported for the cis and trans isomers of the FONO and ClONO molecules in their electronic ground states for the transition states which are associated with their isomerization from the cis to trans forms.Geometries have been determined together with respective vibrational frequencies, and the energy barrier for the isomerization reaction calculated. The barrier was found to be 67 kJ/mol for FONO and 67 kJ/mol for ClONO. The calculated isomerization energies are 16 kJ/mol and 20 kJ/mol respectively. We also report certain spectroscopic properties for the molecules.     

Measurement of 2J(H,C)- and 3J(H,C)-coupling constants by α/β selective HC(C)H-TOCSY

A new heteronuclear NMR pulse sequence for the measurement of ⁿJ(C,H) coupling constants, the /selective HC(C)H-TOCSY, is described. It is shown that the S³E element (Meissner et al., 1997a,b) can be used to obtain spin state selective coherence transfer in molecules, in which adjacent CH moieties are labeled with ¹³C. Application of the / selective HC(C)H-TOCSY to a 10nt RNA tetraloop 5-CGCUUUUGCG-3, in which the four uridine residues are ¹³C labeled in the sugar moiety, allowed measurement of two bond and three bond J(C,H) coupling constants, which provide additional restraints to characterize the sugar ring conformation of RNA in cases of conformational averaging.     

DFT study on the reactions of ClO–/BrO– with RCl (R = CH3, C2H5, and C3H7) in gas phase

Gas-phase reactions of ClO^–/BrO^– with RCl (R = CH₃, C₂H₅, and C₃H₇) have been investigated in detail using the popular DFT functional BHandHLYP/aug-cc-pVDZ level of theory. As a result, our findings strongly suggest that the type of reaction is firstly initiated by a typical S_N2 fashion. Subsequently, two competitive substitution steps, named as S_N2-induced substitution and S_N2-induced elimination, respectively, would proceed before the initial S_N2 product ion-dipole complex separates, in which the former exhibits less reactivity than the latter. Those are consistent with relevant experimental results. Moreover, we have also explored reactivity difference for the title reactions in term of some factors derived from methyl group, p-π electronic conjugation, ionization energy (IE), as well as molecular orbital (MO) analysis.

Effect of Zn ion on the structure and electronic states of Aβ nonamer: molecular dynamics and ab initio molecular orbital calculations

Aggregates of amyloid-beta proteins (Aβ) have been recognised to be intimately related to pathogenesis of Alzheimer’s disease (AD). Indeed, Aβ aggregates of various sizes from dimers to fibrils were found in the brains of AD patients, and these aggregates can be self-organised. Since abnormal accumulation of metal ions such as Zn, Cu and Fe was also observed in the brains, the association between Aβ aggregations and these metal ions has been studied widely. In the present study, to elucidate the influence of Zn ions on the stability of Aβ aggregates, we performed molecular dynamics (MD) simulations and ab initio fragment molecular orbital (FMO) calculations on the Aβ nonamers with and without Zn ions and investigated the change in its structure and electronic states induced by Zn ions at atomic and electronic levels. The MD simulations revealed that Aβ nonamer cannot keep its symmetry structure, whereas Aβ nonamer with Zn ions keeps the structure. The FMO results indicated that electrostatic interactions among the charged amino-acid residues of Aβ nonamer are significantly changed by the influence of Zn ions to stabilise Aβ nonamer. These results provide useful information for proposing novel compounds, which binds specifically to Aβ and inhibits the Aβ aggregation.     

Microsolvation and hydration enthalpies of CaC2O4(H2O) n (n = 0-16) and C2O4 2-(H2O) n (n = 0-14): an ab initio study

We studied hydrated calcium oxalate and its ions at the restricted Hartree–Fock RHF/6-31G* level of theory. Performing a configurational search seems to improve the fit of the HF/6-31G* level to experimental data. The first solvation shell of calcium oxalate contains 13 water molecules, while the first solvation shell of oxalate ion is formed by 14 water molecules. The first solvation shell of Ca(II) is formed by six water molecules, while the second shell contains five. At 298.15 K, we estimate the asymptotic limits (infinite dilution) of the total standard enthalpies of hydration for Ca(II), oxalate ion and calcium oxalate as ?480.78, –302.78 and –312.73 kcal mol^?1, resp. The dissociation of hydrated calcium oxalate is an endothermic process with an asymptotic limit of +470.84 kcal mol^?1.