Theoretical insights in enzyme catalysis

In this tutorial review we show how the methods and techniques of computational chemistry have been applied to the understanding of the physical basis of the rate enhancement of chemical reactions by enzymes. This is to answer the question: Why is the activation free energy in enzyme catalysed reactions smaller than the activation free energy observed in solution? Two important points of view are presented: Transition State (TS) theories and Michaelis Complex (MC) theories. After reviewing some of the most popular computational methods employed, we analyse two particular enzymatic reactions: the conversion of chorismate to prephenate catalysed by Bacillus subtilis chorismate mutase, and a methyl transfer from S-adenosylmethionine to catecholate catalysed by catechol O-methyltransferase. The results and conclusions obtained by different authors on these two systems, supporting either TS stabilisation or substrate preorganization, are presented and compared. Finally we try to give a unified view, where a preorganized enzyme active site, prepared to stabilise the TS, also favours those reactive conformations geometrically closer to the TS.     

Comparison of “bottom-up” and “top-down” strategies for the estimation of the uncertainty in organic elemental analysis

The estimation of uncertainty in organic elemental analysis for C, H, N and S is reported. Both “bottom up” and “top down” strategies are used for uncertainty calculations. The bottom up approach used the results of C, H, N, and S obtained from the homogeneity study of two pure chemicals (toluene-4-sulfonamide and 4(6)-methyl-2-thiouracil). Two calibration systems, K factor and calibration curve, were applied in this study and no significant differences were obtained. For the “top down” approach, we used the data obtained from a proficiency test on both pure chemicals from among 45 Spanish laboratories. Both approaches are compared and discussed below.     

Detection and characterization of hydroxyl radical adducts by mass spectrometry

The study of the influence of free radicals in the biological process depends primarily on the capacity to detect these reactive species. In this work we have studied the application of mass spectrometry to the identification of hydroxyl radical species. The detection and identification by collisional activation mass-analyzed ion kinetic energy spectrometry (CA-MIKES) of a spin adduct of DMPO with the hydroxyl radical [(DMPO + O) + H]+ (m/z 130) has demonstrated that mass spectrometry can be a powerful tool in the detection and identification of spin adducts of DMPO with hydroxyl radical species. We were also able to detect the capture of secondary free radicals using ethanol by detecting and identifying the corresponding adduct [(DMPO + ethanol) + H]+. Other spin adducts have also been detected and identified. We consider that the use of mass spectrometry is a relevant technique for the detection of free hydroxyl radicals, especially in complex mixtures, since mass spectrometry is able to discriminate these adducts in such situations. Moreover, using this approach, it was possible to identify new spin adducts.     

Detection and characterization by mass spectrometry of radical adducts produced by linoleic acid oxidation

The formation of linoleic acid radical species under the oxidative conditions of the Fenton reaction (using hydrogen peroxide and Fe (II)) was monitored by FAB-MS and ES-MS using the spin trap 5,5-dimethyl-1-pyrrolidine-N-oxide, DMPO. Both the FAB and ES mass spectra were very similar and showed the presence of ions corresponding to carbon- and oxygen centered spin adducts (DMPO/L*, DMPO/LO*, and DMPO/LOO*). Cyclic structures, formed between the DMPO oxygen and the neighboring carbon of the fatty acid, were also observed. Electrospray tandem mass spectrometry of these ions was performed to confirm the proposed structure of these adducts. All MS/MS spectra showed an ion at m/z 114, correspondent to the [DMPO + H]+, and a fragment ion due to loss of DMPO (loss of 113 Da), confirming that they are DMPO adducts. ES-MS/MS spectra of alkoxyl radical adducts (DMPO/LO*) showed an additional ion at m/z 130 [DMPO - O + H]+, while ES MS/MS of peroxyl radical adducts (DMPO/LOO*) showed a fragment ion at m/z 146 [DMPO - OO + H]+, confirming both structures. Other fragment ions were observed, such as alkyl acylium radical ions, formed by cleavage of the alkyl chain after loss of water and the DMPO molecule. The identification of fragment ions observed in the MS/MS spectra of the different DMPO adducts suggests the occurrence of structural isomers containing the DMPO moiety both at C9 and C13. The use of ES tandem mass spectrometry, associated with spin trapping experiments, has been shown to be a valuable tool for the structural characterization of carbon and oxygen-centered spin adducts of lipid radicals.     

On the relationship of the scaled phase space and Skyrme-coherent state treatments of proton antiproton annihilation at rest

We discuss pion multiplicities and single pion momentum spectra from proton antiproton annihilation at rest. Both the scaled phase space model and the Skyrmecoherent state approach describe these observables well. In the coherent state approach the puzzling size of the scale parameter relating the phase space integrals for different multiplicities is replaced by a well defined weight function. The strength of this function is determined by the intensity of the classical pion field and its spatial extent is of order 1 fm.     

Using Grote-Hynes theory to quantify dynamical effects on the reaction rate of enzymatic processes. The case of methyltransferases

Dynamical effects have recently received much attention in the context of the theoretical investigation of enzymatic catalysis. In this paper we use a combination of Grote-Hynes theory with quantum mechanical/molecular mechanical modeling that is a powerful tool to understand and quantify these dynamical effects in a particular enzyme, the glycine N-methyltransferase (GNMT). Comparison of the results obtained for this enzyme with another methyltransferase (catechol O-methyltransferase, COMT) allows us to understand the different nature of the coupling of the environment to the reaction coordinate as a function of the electrostatic interaction established by the reactive subsystem. The transmission coefficients obtained using Grote-Hynes theory are in excellent agreement with molecular dynamics estimations and show that the coupling is higher in GNMT than in COMT. The larger friction observed in GNMT is explained on the basis of the interaction established by the substrate in the active site. The larger value of the friction leads to a smaller value of the reaction frequency and thus also to a larger disagreement with the estimation of the transmission coefficient based on the frozen environment approach.     

On the Multiplicity of Algebraic Limit Cycles

In the present paper we tackle the problem of determining the multiplicity of periodic orbit as limit cycle of a planar differential system. We consider the particular case of a circumference as periodic orbit. We show that the conditions of multiplicity can be almost algebraically solvable. There are parameters in which these conditions depend transcendentally, as happens in the degenerate center-focus problem. Even though this difficulty, these transcendental dependence can be, in some sense, controlled because only a basis of fundamental functions appear. The appearance of this fundamental basis opens the path to approach these types of problems. We present several examples of families for which these conditions can be computed.     

Magnetic and transport studies of σ-phase Fe50V50 alloys with different thermal history

The influence of the formation conditions of the sigma phase in an equiatomic FeV alloy on the magnetic and electric transport properties is studied. It is found that a sigma phase sample with higher resistivity (subject to a previous long annealing) has a much sharper magnetic transition than one formed after a shorter heat treatment and quenching, although both have very similar magnetic moments and ferromagnetic transition temperatures (T_c ～ 15 K from minimum dM/dT).