Biomedical subjects

Angels González-Lafont

Publications and source records attributed to Angels González-Lafont.

11 recordsLinked to original sources

PubMed2007

Kinetic study on the reaction of OH radical with dimethyl sulfide in the absence of oxygen.

A variational transition-state theory calculation for the reaction of OH radical with dimethyl sulfide (DMS) in the absence of oxygen is presented. The potential energy surface was previously studied and the effects of different levels of theory were analyzed. Here we propose a kinetic model for the atmospheric DMS oxidation in the absence of oxygen. For the first time, addition of OH to DMS and CH(3)SOH elimination channels are connected, and the equilibrium approximation in the high-pressure regime is applied to the DMS-OH adduct in the absence of oxygen. Both low- and high-pressure limits are considered to analyze the two different mechanisms of the H-abstraction channel, and two different kinetic approaches are applied to study them. The rate constants for the addition-elimination and H-abstraction routes are compared and the branching ratios are also studied. Tunneling contributions and kinetic isotope effects are analyzed. We conclude, in agreement with experimental observations, that in the absence of oxygen DMS oxidation takes place via H-abstraction with a branching ratio of 1.0 at atmospheric temperatures.

Free Radicals↗

PubMed2007

Methyl vinyl ketone+OH and methacrolein+OH oxidation reactions: a master equation analysis of the pressure- and temperature-dependent rate constants.

High-level electronic structure calculations and master equation analyses were carried out to obtain the pressure- and temperature-dependent rate constants of the methyl vinyl ketone+OH and methacrolein+OH reactions. The balance between the OH addition reactions at the high-pressure limit, the OH addition reactions in the fall-off region, and the pressure-independent hydrogen abstractions involved in these multiwell and multichannel systems, has been shown to be crucial to understand the pressure and temperature dependence of each global reaction. In particular, the fall-off region of the OH addition reactions contributes to the inverse temperature dependence of the rate constants in the Arrhenius plots, leading to pressure-dependent negative activation energies. The pressure dependence of the methyl vinyl ketone+OH reaction is clearly more important than in the case of the methacrolein+OH reaction owing to the weight of the hydrogen abstraction process in this second system. Comparison of the theoretical rate constants and the experimental measurements shows quite good agreement.

Journal Article↗

PubMed2006

Variational transition-state theory study of the dimethyl sulfoxide (DMSO) and OH reaction.

The mechanism for the atmospheric oxidation of DMSO has been studied. For the first time, all the possible channels in the DMSO + OH reaction are studied together theoretically, and their corresponding rate constants have been evaluated under the variational transition-state formalism. Three different channels have been characterized: an addition-elimination process to form MSIA (CH3SOOH) and CH3, a H-abstraction pathway to give CH3SOCH2 and H2O, and a nonkinetically relevant S(N)2-type reaction to form methanol and CH3SO. In agreement with previous experimental and theoretical works, the main product in the DMSO + OH reaction turns out to be the MSIA, with a branching ratio at 298.15 K around 97%. The effects of pressure in the global rate constant have also been analyzed.

Journal Article↗

PubMed2006

On the ionization state of the substrate in the active site of glutamate racemase. A QM/MM study about the importance of being zwitterionic.

Computer simulations on a QM/MM potential energy surface have been carried out to gain insights into the catalytic mechanism of glutamate racemase (MurI). Understanding such a mechanism is a challenging task from the chemical point of view because it involves the deprotonation of a low acidic proton by a relatively weak base to give a carbanionic intermediate. First, we have examined the dependency of the kinetics and thermodynamics of the racemization process catalyzed by MurI on the ionization state of the substrate (glutamate) main chain. Second, we have employed an energy decomposition procedure to study the medium effect on the enzyme-substrate electrostatic and polarization interactions along the reaction. Importantly, the present theoretical results quantitatively support the mechanistic proposal by Rios et al. [J. Am. Chem. Soc. 2000, 122, 9373-9385] for the PLP-independent amino acid racemases.

Amino Acid Isomerases↗

PubMed2005

Pressure dependence in the methyl vinyl ketone + OH and methacrolein + OH oxidation reactions: an electronic structure study.

High-level electronic structure calculations were carried out for the study of the reaction pathways in the OH-initiated oxidations of methyl vinyl ketone (MVK) and methacrolein (MACR). For the two conformers of MVK (called synperiplanar and antiperiplanar), the addition channels of OH to the terminal and central carbon atom of the double bond dominate the overall rate constant, whereas the abstraction of the methyl hydrogen atoms has no significant kinetic role. In the case of MACR, only the antiperiplanar conformer is important in its reactivity. In addition, the lower Gibbs free energy barrier for MACR corresponds to the aldehydic hydrogen abstraction reaction, which will be somewhat more favorable than the addition processes. The subtle balance between the different pathways (additions versus abstractions) serves to give an understanding of the pressure dependence of the rate constants of these tropospheric oxidation processes.

Acrolein↗

PubMed2005

Electronic structure study of the initiation routes of the dimethyl sulfide oxidation by OH.

In the present work the potential energy surface (PES) corresponding to the different initiation routes of the oxidation mechanism of DMS by hydroxyl radical in the absence of O(2) has been studied, and connections among the different stationary points have been established. Single-point high level electronic structure calculations at lower level optimized geometries have been shown to be necessary to assure convergence of energy barriers and reaction energies. Our results demonstrate that the oxidation of DMS by OH turns out to be initiated via three channels: a hydrogen abstraction channel that through a saddle point structure finally leads to CH(3)SCH(2) + H(2)O, an addition-elimination channel that firstly leads to an adduct complex (AD) and then via an elimination saddle point structure finally gives CH(3)SOH and CH(3) products, and a third channel that through a concerted pathway leads to CH(3)OH and CH(3)S. The H-abstraction and the addition-elimination channels initiate by a common pathway that goes through the same reactant complex (RC). Our theoretical results agree quite well with the branching ratios experimentally assigned to the formation of the different products. Finally, the calculated equilibrium constants of the formation of the complex AD and the hexadeuterated complex AD from the corresponding reactants, as a function of the temperature, are in good accordance with the experimental values.

Journal Article↗

PubMed2005

A fast radical chain mechanism in the polyfluoroalkoxylation of aromatics through NO2 group displacement. Mechanistic and theoretical studies.

Introduction of polyfluoroalkoxy and polyfluoroalkylthio substituents in aromatic rings can be achieved with mild conditions and short times thorough reaction of concentrated solutions of dinitrobenzenes in DMF with polyfluoro alcohols and polyfluoro thiols in moderate excess, in the presence of excess tetrabutylammonium fluoride as a base. Mechanistic studies suggest that under these conditions a fast radical chain mechanism operates. This mechanism is elicited by oxidation of a Meisenheimer complex and proceeds through a radical aromatic substitution with the polyfluoroalkoxy or the polyfluoroalkylthio radicals as key intermediates. At low concentrations, entrainment can be achieved with superoxide anion. A rationale for this effect is discussed. Answers to particular questions about the proposed mechanism are achieved through a theoretical study at the B3LYP/6-31+G(d,p) level. Specifically, the competition between the radical mechanism and the corresponding polar one (classical S(N)Ar reaction) is studied in that way, with the conclusion that the key steps of the radical mechanism in our reaction conditions (polar aprotic solvent) are at least as efficient as the ones of the polar one, thus justifying the observed kinetic advantage for the chain reaction in the conditions where an efficient initiation occurs.

Alcohols↗

PubMed2005

A theoretical study of the competitive homolytic/heterolytic aniomesolytic cleavages of C-O alkyl ether bonds.

Density functional theory electronic structure calculations of the homolytic/heterolytic aniomesolytic C-O fragmentations in the gas phase of a series of radical anions of substituted-phenyl benzyl ethers and substituted-benzyl phenyl ethers have been carried out. Along the series, the electron-withdrawing strength of the substituents increases. An intramolecular electron transfer from the pi system to the sigma molecular orbital of the scissile C-O bond is required to produce the fragmentation. As the electron-withdrawing strength of the substituents increases, the transition-state structures appear later with higher potential energy and Gibbs free energy barriers. The homolytic mesolytic cleavages are always thermodynamically favored versus the corresponding heterolytic mesolytic ones. The heterolytic mesolytic fragmentations in radical anions containing only weak electron-withdrawing groups are faster than the corresponding homolytic mesolytic ones. Conversely, in radical anions supporting strong electron-withdrawing groups the homolytic mesolytic fragmentations are faster in terms of potential energy barriers. However, the entropic contribution makes it comparable the homolytic and the heterolytic Gibbs free energy barriers in this case. The main factors that determine the relative rates of those kind of aniomesolytic cleavages are discussed.

Journal Article↗

PubMed2004

Testing electronic structure methods for describing intermolecular H...H interactions in supramolecular chemistry.

In this article a wide variety of computational approaches (molecular mechanics force fields, semiempirical formalisms, and hybrid methods, namely ONIOM calculations) have been used to calculate the energy and geometry of the supramolecular system 2-(2'-hydroxyphenyl)-4-methyloxazole (HPMO) encapsulated in beta-cyclodextrin (beta-CD). The main objective of the present study has been to examine the performance of these computational methods when describing the short range H. H intermolecular interactions between guest (HPMO) and host (beta-CD) molecules. The analyzed molecular mechanics methods do not provide unphysical short H...H contacts, but it is obvious that their applicability to the study of supramolecular systems is rather limited. For the semiempirical methods, MNDO is found to generate more reliable geometries than AM1, PM3 and the two recently developed schemes PDDG/MNDO and PDDG/PM3. MNDO results only give one slightly short H...H distance, whereas the NDDO formalisms with modifications of the Core Repulsion Function (CRF) via Gaussians exhibit a large number of short to very short and unphysical H...H intermolecular distances. In contrast, the PM5 method, which is the successor to PM3, gives very promising results. Our ONIOM calculations indicate that the unphysical optimized geometries from PM3 are retained when this semiempirical method is used as the low level layer in a QM:QM formulation. On the other hand, ab initio methods involving good enough basis sets, at least for the high level layer in a hybrid ONIOM calculation, behave well, but they may be too expensive in practice for most supramolecular chemistry applications. Finally, the performance of the evaluated computational methods has also been tested by evaluating the energetic difference between the two most stable conformations of the host(beta-CD)-guest(HPMO) system.

Journal Article↗

PubMed2003

Dependence of the rate constants on the treatment of internal rotation modes: the reaction OH + CH3SH --> CH3S + H2O as an example.

The title reaction has been used as an example to test the importance of using a hindered rotor treatment instead of a harmonic oscillator model for calculating vibrational partition functions corresponding to low-frequency internal rotation modes. First, a normal-mode analysis according to the Ayala and Schlegel's algorithm has been used to identify the internal rotation modes of methanethiol and the transition state structure. Then, after calculation of the energy barrier for each internal rotation, the corresponding hindered rotor partition functions have been calculated following the CW scheme of Chuang and Truhlar. The results show that the anharmonic treatment produces a rather modest improvement of the rate constants at room temperature or below.

Journal Article↗

PubMed2002

Thermodynamics, kinetics, and dynamics of the two alternative aniomesolytic fragmentations of C-O bonds: an electrochemical and theoretical study.

Fragmentation reactions of radical anions (mesolytic cleavages) of cyanobenzyl alkyl ethers (intramolecular dissociative electron transfer, heterolytic cleavages) have been studied electrochemically. The intrinsic barriers for the processes have been established from the experimental thermodynamic and kinetic parameters. These values are more than 3 kcal/mol lower as an average than the related homolytic mesolytic fragmentations of radical anions of 4-cyanophenyl ethers. In the particular case of isomers 4-cyanobenzyl phenyl ether and 4-cyanophenyl benzyl ether, the difference in intrinsic barriers amounts to 5.5 kcal/mol, and this produces an energetic crossing where the thermodynamically more favorable process (homolytic) is the kinetically slower one. The fundamental reasons for this behavior have been established by means of theoretical calculations within the density functional theory framework, showing that, in this case, the factors that determine the kinetics are clearly different (mainly present in the transition state) from those that determine the thermodynamics and they are not related to the regioconservation of the spin density ("spin regioconservation principle"). Our theoretical results reproduce quite well the experimental energetic difference of barriers and demonstrate the main structural origin of the difference.

Journal Article↗