Catalytic Effect of Electric Fields on the Kemp Elimination Reactions with Neutral Bases.

The effect of solvent reaction fields and oriented electric fields on the Kemp elimination reaction between methylamine or imidazole and 5-nitrobenzisoxazole has been theoretically studied. The Kemp reaction is the most widely used for the design of new enzymes. Our results, using the SMD continuous model for solvents, are in quite good agreement with the experimental fact that the rate of the analogous reaction with butylamine is one order of magnitude smaller in water than in acetonitrile. In the case of external electric fields, our results show that they can increase or decrease the energy barrier depending on the magnitude and orientation of the field. A duly oriented electric field may have a notable catalytic effect on the reaction. So, external electric fields and reaction fields due to the medium can contribute to the design of new enzymes. Several factors that must be taken into account to increase the catalytic effect are discussed.

Kemp Elimination Reaction Catalyzed by Electric Fields.

The Kemp elimination reaction is the most widely used in the de novo design of new enzymes. The effect of two different kinds of electric fields in the reactions of acetate as a base with benzisoxazole and 5-nitrobenzisoxazole as substrates have been theoretically studied. The effect of the solvent reaction field has been calculated using the SMD continuum model for several solvents; we have shown that solvents inhibit both reactions, the decrease of the reaction rate being larger as far as the dielectric constant is increased. The diminution of the reaction rate is especially remarkable between aprotic organic solvents and protic solvents as water, the electrostatic term of the hydrogen bonds being the main factor for the large inhibitory effect of water. The presence of an external electric field oriented in the direction of the charge transfer (z axis) increases it and, so, the reaction rate. In the reaction of the nitro compound, if the electric field is oriented in an orthogonal direction (x axis) the charge transfer to the NO2 group is favored and there is a subsequent increase of the reaction rate. However, this increase is smaller than the one produced by the field in the z axis. It is worthwhile mentioning that one of the main effects of external electric fields of intermediate intensity is the reorientation of the reactants. Finally, the implications of our results in the de novo design of enzymes are discussed.

Phosphoryl-Transfer Reaction in RNA under Alkaline Conditions.

The phosphoryl-transfer reaction in RNA under alkaline conditions by exploring the influence of several solvents theoretically was studied. The calculations were carried out by using the M06-2X functional and the solvents were taken as a continuum by using the solvent model density (SMD) method. The main findings show that the O2'-P-O5' angle in the reactants, the free activation energies, and the reaction mechanism are clearly dependent on the dielectric constant of the environment, thus showing that the electrostatic term is the determining factor for this chemical system with two negative charges. Our study seems to indicate that water, the solvent with the greatest dielectric constant, would be the solvent that increases the reaction rate the most. As this outcome was not the case in enzymatic catalysis, one has to conclude that, in the case of proteins as well as for ribozymes, the enzymatic catalysis is not mainly due to the solvent reaction field, but to local electrical fields as a result of enzyme preorganization.

Phosphoryl Transfer Reaction in RNA: Is the Substrate-Assisted Catalysis a Possible Mechanism in Certain Solvents?

A proton shuttle mechanism for the phosphoryl transfer reaction in RNA, in which a proton is transferred from the nucleophile to the leaving group through a nonbridged oxygen atom of the phosphate, was explored using the MO6-2X density functional method and the solvent continuum model. This reaction is the initial step of the RNA hydrolysis. We used different solvents characterized by their dielectric constant, and, for each of them, we studied the nuclear and electronic relaxation, produced by the solvent reaction field, for the stationary points. Given that RNA has a poor leaving group, the bond breaking corresponds to the rate-determining step. If the O atom is substituted by a S atom, the leaving group is now good, and the rate-determining step is now the nucleophilic attack concerted with the proton transfer. The most relevant result we found is that none of the solvents we studied has a free energy of activation that is smaller than the one in water. This suggests that the enzyme catalysis following this mechanism must be due to the permanent electric field that is created by a preorganized charge distribution but not to the solvent reaction field.

Theoretical Insights on the Mechanism of the GTP Hydrolysis Catalyzed by the Elongation Factor Tu (EF-Tu).

The purpose of this work is to have a better understanding of the mechanism of GTP hydrolysis catalyzed by the elongation factor Tu. Two main aspects are being discussed in the literature: the associative or dissociative character of the process and the nature of nucleophile activation. The calculations of the QM subsystem have been done by means of the M06-2X density functional and the split valence triple-ζ 6-311+G(d,p) basis set. The environmental effect has been introduced through the continuum SMD method. We have studied three models of increasing complexity in order to analyze the different factors that intervene in the catalytic action. The results obtained in this paper confirm that the protonated His84 plays a fundamental role in the catalytic mechanism, but we have also found that the crystallographic sodium ion has a notable effect in the catalysis. So, our work has permitted a new insight, complementary to those obtained with QM/MM calculations, into this very complex process.

Theoretical study on two-step mechanisms of peptide release in the ribosome.

A quantum mechanical study of different two-step mechanisms of peptide release in the ribosome has been carried out using the M06-2X density functional. Reoptimization with MP2 has also been carried out for the stationary points of some selected mechanisms. The uncatalyzed processes in solution have been treated with the SMD solvation model. From the results obtained in this paper for the peptide release process we can conclude that the energy barriers for the two-step mechanisms are lower than the ones for the concerted process, that the 2'OH plays also an important role in the catalytic process and that the side chain does not only accommodate a nucleophilic water molecule in the PTC, but it also contributes to activate this molecule through electron transfer to the water oxygen. We have also found that the second step is the rate-determining one, and that the two most favorable mechanisms, in which a water or a formamide molecule is added, follow a quite different strategy to catalyze the reaction. The main conclusion of our work is that the two-step mechanisms cannot be disregarded, since they can contribute to clarify the complex and yet unsolved problem of the mechanism of the peptide release process.

Quantum mechanical study on the mechanism of peptide release in the ribosome.

A quantum mechanical study of different concerted mechanisms of peptide release in the ribosome has been carried out using the M06-2X density functional. Reoptimization with MP2 has also been carried out for the stationary points of some selected mechanisms. The uncatalyzed processes in solution have been treated with the SMD solvation model. We conclude that the 2'-OH plays an important catalytic role and that it takes place via a zwitterionic transition state, this TS being stabilized by the presence of oxyanion holes or by the solvent. The comparison with our previous study on the peptide bond formation shows that both processes proceed via two different mechanisms, in such a way that the TS of the aminolysis has an ion-pair instead of a zwitterionic character. So, despite the limitations of the model we have used, we can conclude that there is catalytic promiscuity at the peptidyl transferase center (PTC) of the ribosome.

Quantum-mechanical study on the mechanism of peptide bond formation in the ribosome.

Ribosomes transform the genetic information encoded within genes into proteins. In recent years, there has been much progress in the study of this complex molecular machine, but the mechanism of peptide bond formation and the origin of the catalytic power of this ancient enzymatic system are still an unsolved puzzle. A quantum-mechanical study of different possible mechanisms of peptide synthesis in the ribosome has been carried out using the M06-2X density functional. The uncatalyzed processes in solution have been treated with the SMD solvation model. Concerted and two-step mechanisms have been explored. Three main points suggested in this work deserve to be deeply analyzed. First, no zwitterionic intermediates are found when the process takes place in the ribosome. Second, the proton shuttle mechanism is suggested to be efficient only through the participation of the A2451 2'-OH and two crystallographic water molecules. Finally, the mechanisms in solution and in the ribosome are very different, and this difference may help us to understand the origin of the efficient catalytic role played by the ribosome.

Synthesis and structural study of highly constrained hybrid cyclobutane-proline γ,γ-peptides.

Two diastereomeric series of hybrid γ,γ-peptides derived from conveniently protected derivatives of (1R,2S)- and (1S,2R)-3-amino-2,2-dimethylcyclobutane-1-carboxylic acid and cis-4-amino-L: -proline joined in alternation have efficiently been prepared through convergent synthesis. High-resolution NMR experiments show that these compounds present defined conformations in solution affording very compact structures as the result of intra and inter residue hydrogen-bonded ring formation. (R,S)-cyclobutane containing peptides adopt more twisted conformations than (S,R) diastereomers. In addition, all these γ-peptides have high tendency to aggregation providing vesicles of nanometric size, which were stable when allowed to stand for several days, as verified by transmission electron microscopy.

Mutual relationship between stacking and hydrogen bonding in DNA. Theoretical study of guanine-cytosine, guanine-5-methylcytosine, and their dimers.

The mutual relationship between stacking and hydrogen-bonding and the possible influence of stacking in the different behavior of cytosine (C) and 5-methylcytosine (C') in DNA have been studied through complete DFT optimization of different structures of G-C and G-C' dimers (i.e., G-C/C-G and G-C'/C'-G), using four different functionals. Our results show that stacking leads to an increase of the O(6)...H-N(4) hydrogen bond length and to a simultaneous decrease of the N(2)-H...O(2) one, in such a way that both lengths approach each other and, in some cases, an inversion occurs. These results suggest that stacking can be a factor to explain the disparity between theory and experiment on the relative strength of the two lateral hydrogen bonds. Regarding the difference between cytosine and 5-methylcytosine, we have shown that methylation enhances the stacking interactions, mainly due to the increase of polarizability. Methylation also favors the existence of slid structures which can produce local distortions of DNA.

Borylated methylenephosphonium salts: precursors of elusive boryl(phosphino)carbenes.

The synthesis of a new family of boryl-substituted methylenephosphonium derivatives, the phosphorus analogues of iminium salts, has been developed. They were used in the preparation of the first stable boryl(phosphino)carbene, which has been fully characterized by NMR spectroscopy and X-ray crystallography. Density functional theory calculations indicate that these carbenes can be classified as push-pull carbenes with a relatively small singlet-triplet energy gap.

Comparison of density functionals for reactions of sulfur ylides with aldehydes and olefins.

The reactions of a model sulfur ylide with formaldehyde and 1,1-dicianoethylene, leading to the formation of an epoxyde and a cyclopropane, respectively, have been studied using different computational methods, and the results have been compared to those obtained with the CBS-QB3 method. The second step of these reactions presents transition states similar to that of an SN2 reaction. Depending on the degree of electron delocalization at the transition state, a different amount of exact exchange is necessary in the exchange functional to obtain accurate energy barriers. This amount is larger for the reaction of formaldehyde, in which the transition state is more delocalized, than for the reaction of 1,1-dicianoethylene. Similar results have been obtained for symmetric and non-symmetric SN2 reactions. The calculation of the reaction path has shown that the error relative to CBS-QB3 tends to increase when approaching the transition state. Among the different computational methods, PBE1PBE is the one to provide the most accurate energy barriers and reaction energies, whereas BB1K leads to the best results for the reaction path before the transition state.