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Juan Andrés

Publications and source records attributed to Juan Andrés.

17 recordsLinked to original sources
PubMed2006

New findings on the Diels-Alder reactions. An analysis based on the bonding evolution theory.

Two Diels-Alder type reactions, i.e., normal electron demand (NED) between 1,3-butadiene (BD) and acrolein (Acr) and inverse electron demand (IED) between 2,4-pentadienal (PDA) and methyl vinyl ether (MVE), have been investigated using the bonding evolution theory (BET). BET combines topological analysis of the electron localization function (ELF) and catastrophe theory. Catalyst effect has been incorporated through Lewis acid BH3. The B3LYP hybrid HF/DFT method along with 6-31G(d), 6-311++G(d,p) basis sets have been used. All reactions yield two-stage mechanism and there is no topological evidence that they might be concerted with two bonds partially formed during transition structure. A formation of six-membered ring requires 10 (or 11) steps separated by two types of catastrophes: fold and cusp. The first "intermolecular" bond (C1-C6) is formed at 1.93, 1.92 A (NED) and 1.92, 1.97 A (IED). The six-membered ring is "closed" at 2.11, 2.13 A (NED) and 2.5, 2.6 A (IED) via formation of the second bond C4-C5. All reactions begin with "reduction" of C=C bonds to single C-C (cusp catastrophes). Subsequently, the nonbonding electron density is concentrated (fold catastrophes) on terminal C atoms. Finally the new bonds, C1-C6 and C4-C5, are established (cusp catastrophes). Both magnitude and regularity of the electron redistribution, happening during reactions enable us to distinguish two effects: (1) the "ring effect", where a large amount of electron density is regularly transferred from double C=C bonds to intermolecular regions and single C-C bonds, (2) the "side chain effect"--usually weaker and irregular--involving substituents' bonds. In the transition structure, well formed bonding basin V(C1,C6), is observed only for the PDA...BH3/MVE reaction. For other reactions only the nonbonding basins: V(C1) and V(C6), are found in the interaction region C1...C6.

Journal Article↗
PubMed2006

Catalysis in glycine N-methyltransferase: testing the electrostatic stabilization and compression hypothesis.

Glycine N-methyltransferase (GNMT) is an S-adenosyl-l-methionine dependent enzyme that catalyzes glycine transformation to sarcosine. Here, we present a hybrid quantum mechanics/molecular mechanics (QM/MM) computational study of the reaction compared to the counterpart process in water. The process takes place through an SN2 mechanism in both media with a transition state in which the transferring methyl group is placed in between the donor (SAM) and the acceptor (the amine group of glycine). Comparative analysis of structural, electrostatic, and electronic characteristics of the in-solution and enzymatic transition states allows us to get a deeper insight into the origins of the enzyme's catalytic power. We found that the enzyme is able to stabilize the substrate in its more active basic form by means of a positively charged residue (Arg175) placed in the active site. However, the maximum stabilization is attained for the transition state. In this case, the enzyme is able to form stronger hydrogen bonds with the positively charged amine group. Finally, we show that in agreement with previous computational studies on other methyltransferases, there is no computational evidence for the compression hypothesis, as was formulated by Schowen (Hegazi, M. F., Borchardt, R. T., and Schowen, R. L. (1979) J. Am. Chem. Soc. 101, 4359-4365).

Catalysis↗
PubMed2006

Better understanding of the ring-cleavage process of cyanocyclopropyl anionic derivatives. A theoretical study based on the electron localization function.

[reaction: see text] Theoretical calculations at the B3LYP/6-31+G(d), MP2/6-31+G(d), and G3(MP2) levels have been carried out to understand the alternative reaction pathways (the cyclopropyl ring cleavage (RC) and the retrocycloaddition reaction (rCA)) of a constrained tricyanocyclopropyl anionic derivative. The more energetically favorable path is found to be the RC process, a formally "forbidden" rearrangement (Leiviers, M.; Tam, I.; Groves, K.; Leung, D.; Xie, Y.; Breslow, R. Org. Lett. 2003, 5, 19, 3407) yielding an allylic anion system via a concerted transition structure, in agreement with experimental outcomes. rCA is more energetically favorable along a two-stage mechanism, via an intermediate, than a synchronous concerted process. By using isodesmic reactions, we have found that B3LYP presents limitations when it calculates carbon-carbon bond-breaking processes along the present rCA reaction. A detailed analysis of the nature of the topology of the reactive potential energy surface for the RC process points out the presence of a valley-ridge inflection point in the uphill part. An explanation for the low-energy barrier associated with RC is furnished on the analysis of the evolution of the twisting (dis-/conrotatory) motions of cyano substituents in the cyclopropyl ring as well as on the number and type of electron pairs provided by the electron localization function (ELF).

Journal Article↗
PubMed2006

Stereoselectivity behavior of the AZ28 antibody catalyzed oxy-Cope rearrangement.

Catalytic antibodies are very interesting not only because of the rate enhancement of the reactions that they catalyze but also because of the selectivities they can achieve that are sometimes not present in natural enzyme processes. We have selected the study of the stereoselectivity of the matured AZ28 that catalyzes an oxy-Cope rearrangement. For this particular case, the presence of a chiral center in the substrate provokes the existence of two different enantiomers, R and S. Furthermore, it is also possible to locate two different orientations for the hydroxyl group in the central ring of the substrate in the transition state, equatorial and axial, rendering two different conformers. In this paper we present the free energy profiles obtained for different substrate isomers in the cavity created by the matured catalytic antibody. Our simulations have reproduced the stereoselectivity of the matured AZ28, differentiating between the axial or equatorial orientations and preferentially stabilizing the S forms, at a qualitative level. Finally, the inclusion of the substrate-CA interactions in a flexible molecular model has allowed us to observe the different pattern of interactions that are related to different interaction energies, which seem to be crucial in the stereoselectivity behavior of the catalytic antibody.

Antibodies, Catalytic↗
PubMed2005

Toward an understanding of the catalytic role of hydrogen-bond donor solvents in the hetero-Diels-Alder reaction between acetone and butadiene derivative.

A detailed theoretical investigation of the catalytic role of hydrogen-bond- (HB-) donor molecules (water, methanol, chloroform, dichloromethane, and chloromethane) in the hetero-Diels-Alder reaction between acetone and N,N-dimethyl-1-amino-3-methoxy-1,3-butadiene is presented. This work extends a previous study (Domingo, L. R.; Andres, J. J. Org. Chem. 2003, 68, 8662) in which the importance of weak HB-donor solvents to catalyze more effectively than solvents with a higher dielectric constant but no HB-donor capability was analyzed. Now, based on density functional theory (DFT) at B3LYP/6-31+G(d) level calculations, different techniques for analyzing the nature of HB interaction, namely, natural bond orbital (NBO) theory, topological analysis of the electron density (atoms in molecules, AIM, theory), and the electron localization function (ELF) and decomposition of the interaction energy between monomers (energy decomposition analysis, EDA), have been applied to understand why only some HB-donor solvents are able to catalyze the reaction. The catalytic effect of the solvent arises from the improved HB-acceptor capability of the oxygen atom at the transition structure (TS) due to the strong polarization of the carbonyl group. The HB acceptor presents three lone pairs (NBO analysis), and the ELF shows an increment of the electronic charge of the lone pairs of 0.50e with respect to the reactant. All solvent molecules form stronger HB interactions at the TS, but only those presenting larger charge-transfer interactions (water, methanol, chloroform) benefit more from the polarization of the carbonyl group than other solvents (dichloromethane, chloromethane) with less "covalent" character.

Acetone↗
PubMed2005

A joint study based on the electron localization function and catastrophe theory of the chameleonic and centauric models for the Cope rearrangement of 1,5-hexadiene and its cyano derivatives.

A novel interpretation of the chameleonic and centauric models for the Cope rearrangements of 1,5-hexadiene (A) and different cyano derivatives (B: 2,5-dicyano, C: 1,3,4,6-tetracyano, and D: 1,3,5-tricyano) is presented by using the topological analysis of the electron localization function (ELF) and Thom's catastrophe theory (CT) on the reaction paths calculated at the B3LYP/6-31G(d,p) level. The progress of the reaction is monitorized by the changes of the ELF structural stability domains (SSD), each being change controlled by a turning point derived from CT. The reaction mechanism of the parent reaction A is characterized by nine ELF SSDs. All processes occur in the vicinity of the transition structure and corresponding to a concerted formation/breaking of C(1)-C(6) and C(3)-C(4) bonds, respectively, together with an accumulation of charge density onto C(2) and C(5) atoms. Reaction B presents the same number of ELF SSDs as A, but a different order appears; the presence of 2,5-dicyano substituents favors the formation of C(1)-C(6) bonds over the breaking of C(3)-C(4) bond process, changing the reaction mechanism from a concerted towards a stepwise, via a cyclohexane biradical intermediate. On the other side, reaction C presents the same type of turning points but two ELF SSD less than A or B; there is an enhancement of the C(3)-C(4) bond breaking process at an earlier stage of the reaction by delocalizing the electrons from the C(3)-C(4) bond among the cyano groups. In the case of competitive effects of cyano subsituents on each moiety, as it is for reaction D, seven different ELF SSDs have been identified separated by eight turning points (two of them occur simultaneously). Both processes, formation/breaking of C(1)-C(6) and C(3)-C(4) bonds, are slightly favored with respect to the parent reaction (A), and the TS presents mixed electronic features of both B and C. The employed methodology provides theoretical support for the centauric nature (half-allyl, half-radical) for the TS of D.

Journal Article↗
PubMed2005

On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations.

The way in which enzymes influence the rate of chemical processes is still a question of debate. The protein promotes the catalysis of biochemical processes by lowering the free energy barrier in comparison with the reference uncatalyzed reaction in solution. In this article we are reporting static and dynamic aspects of the enzyme catalysis in a bimolecular reaction, namely a methyl transfer from S-adenosylmethionine to the hydroxylate oxygen of a substituted catechol catalyzed by catechol O-methyltransferase. From QM/MM optimizations, we will first analyze the participation of the environment on the transition vector. The study of molecular dynamics trajectories will allow us to estimate the transmission coefficient from a previously localized transition state as the maximum in the potential of mean force profile. The analysis of the reactive and nonreactive trajectories in the enzyme environment and in solution will also allow studying the geometrical and electronic changes, with special attention to the chemical system movements and the coupling with the environment. The main result, coming from both analyses, is the approximation of the magnesium cation to the nucleophilic and the hydroxyl group of the catecholate as a result of a general movement of the protein, stabilizing in this way the transition state. Consequently, the free energy barrier of the enzyme reaction is dramatically decreased with respect to the reaction in solution.

Catechol O-Methyltransferase↗
PubMed2004

Understanding the nature of the molecular mechanisms associated with the competitive Lewis acid catalyzed [4+2] and [4+3] cycloadditions between arylidenoxazolone systems and cyclopentadiene: a DFT analysis.

The molecular mechanisms of the reactions between aryliden-5(4H)-oxazolone 1, and cyclopentadiene (Cp), in presence of Lewis acid (LA) catalyst to obtain the corresponding [4+2] and [4+3] cycloadducts are examined through density functional theory (DFT) calculations at the B3LYP/6-31G* level. The activation effect of LA catalyst can be reached by two ways, that is, interaction of LA either with carbonyl or carboxyl oxygen atoms of 1 to render [4+2] or [4+3] cycloadducts. The endo and exo [4+2] cycloadducts are formed through a highly asynchronous concerted mechanism associated to a Michael-type addition of Cp to the beta-conjugated position of alpha,beta-unsaturated carbonyl framework of 1. Coordination of LA catalyst to the carboxyl oxygen yields a highly functionalized compound, 3, through a domino reaction. For this process, the first reaction is a stepwise [4+3] cycloaddition which is initiated by a Friedel-Crafts-type addition of the electrophilically activated carbonyl group of 1 to Cp and subsequent cyclization of the corresponding zwitterionic intermediate to yield the corresponding [4+3] cycloadduct. The next rearrangement is the nucleophilic trapping of this cycloadduct by a second molecule of Cp to yield the final adduct 3. A new reaction pathway for the [4+3] cycloadditions emerges from the present study.

Journal Article↗
PubMed2004

A comparative study of claisen and cope rearrangements catalyzed by chorismate mutase. An insight into enzymatic efficiency: transition state stabilization or substrate preorganization?

In this work we present a detailed analysis of the activation free energies and averaged interactions for the Claisen and Cope rearrangements of chorismate and carbachorismate catalyzed by Bacillus subtilischorismate mutase (BsCM) using quantum mechanics/molecular mechanics (QM/MM) simulation methods. In gas phase, both reactions are described as concerted processes, with the activation free energy for carbachorismate being about 10-15 kcal mol(-)(1) larger than for chorismate, at the AM1 and B3LYP/6-31G levels. Aqueous solution and BsCM active site environments reduce the free energy barriers for both reactions, due to the fact that in these media the two carboxylate groups can be approached more easily than in the gas phase. The enzyme specifically reduces the activation free energy of the Claisen rearrangement about 3 kcal mol(-)(1) more than that for the Cope reaction. This result is due to a larger transition state stabilization associated to the formation of a hydrogen bond between Arg90 and the ether oxygen. When this oxygen atom is changed by a methylene group, the interaction is lost and Arg90 moves inside the active site establishing stronger interactions with one of the carboxylate groups. This fact yields a more intense rearrangement of the substrate structure. Comparing two reactions in the same enzyme, we have been able to obtain conclusions about the relative magnitude of the substrate preorganization and transition state stabilization effects. Transition state stabilization seems to be the dominant effect in this case.

Bacillus subtilis↗
PubMed2003

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.

Bacillus subtilis↗
PubMed2003

Enhancing reactivity of carbonyl compounds via hydrogen-bond formation. A DFT study of the hetero-Diels-Alder reaction between butadiene derivative and acetone in chloroform.

To examine how hydrogen-bond (HB) formation involving chloroform solvent molecules influences the chemical reactivity of ketones, the hetero-Diels-Alder reaction of N,N-dimethyl-1-amino-3-methoxy-1,3-butadiene and acetone has been studied by using density functional theory (DFT) at the B3LYP/6-31G level. The effects of the chloroform on the activation energies have been modeled by means of discrete-continuum models. In the gas phase, the formation of specific HB between acetone and one and two chloroform molecules decreases the activation barriers from 19.3 to 13.6 and 8.5 kcal/mol, respectively. Inclusion of solvent effects by means of combined discrete and polarizable continuum models yields a change of molecular mechanism from a concerted to a two-step mechanism, and the first nucleophilic step is the rate-limiting step. The corresponding values of activation barriers in chloroform are 18.6 kcal/ mol (no HB), 13.5 kcal/mol (one HB), and 9.6 kcal/mol (two HBs). These theoretical results account for the experimental observation that chloroform accelerates the reaction more markedly than more polar aprotic solvent such as acetonitrile. A DFT analysis of the global electrophilicity power of the reagents provides a sound explanation about the catalytic effects of chloroform.

Journal Article↗
PubMed2003

Understanding the mechanism of base-assisted decomposition of (N-halo),N-alkylalcoholamines.

The base-assisted decomposition of (N-X),N-methylethanolamine (X = Cl, Br) takes place mainly through two concurrent processes: a fragmentation and an intramolecular elimination. The global process follows second order kinetics, first order relative to both (N-X),N-methylethanolamine and base. Interaction of the base with the ionizable hydroxylic hydrogen triggers the reaction. The intramolecular elimination pathway leads to formaldehyde and 2-aminoethanol as reaction products via base-assisted proton transfer from the methyl to the partially unprotonated hydroxylic oxygen, with loss of halide. Meanwhile, the fragmentation pathway leads to methylamine and two equivalents of formaldehyde via bimolecular base-promoted concerted breakage of the molecule into formaldehyde, halide ion and N-methylmethanimine. Kinetic evidences allow a crude estimation of the concertedness and characterization of the transition structure for both processes, which are slightly asynchronous, the proton transfer to the base taking place ahead of the rest of the molecular events. The degree of asynchroneity increases as the bases become weaker. Electronic structure calculations, at the B3LYP/6-31++G** level, on the fragmentation pathway support the proposed mechanism.

Journal Article↗
PubMed2003

Theoretical modeling of enzyme catalytic power: analysis of "cratic" and electrostatic factors in catechol O-methyltransferase.

A comparative theoretical study of a bimolecular reaction in aqueous solution and catalyzed by the enzyme catechol O-methyltransferase (COMT) has been carried out by a combination of two hybrid QM/MM techniques: statistical simulation methods and internal energy minimizations. In contrast to previous studies by other workers, we have located and characterized transition structures for the reaction in the enzyme active site, in water and in a vacuum, and our potential of mean force calculations are based upon reaction coordinates obtained from features of the potential energy surfaces in the condensed media, not from the gas phase. The AM1/CHARMM calculated free energy of activation for the reaction of S-adenosyl methionine (SAM) with catecholate catalyzed by COMT is 15 kcal mol(-1) lower the AM1/TIP3P free-energy barrier for the reaction of the trimethylsulfonium cation with the catecholate anion in water at 300 K, in agreement with previous estimates. The thermodynamically preferred form of the reactants in the uncatalyzed model reaction in water is a solvent-separated ion pair (SSIP). Conversion of the SSIP into a contact ion pair, with a structure resembling that of the Michaelis complex (MC) for the reaction in the COMT active site, is unfavorable by 7 kcal mol(-1), largely due to reorganization of the solvent. We have considered alternative ways to estimate the so-called "cratic" free energy for bringing the reactant species together in the correct orientation for reaction but conclude that direct evaluation of the free energy of association by means of molecular dynamics simulation with a simple standard-state correction is probably the best approach. The latter correction allows for the fact that the size of the unit cell employed with the periodic boundary simulations does not correspond to the standard state concentration of 1 M. Consideration of MC-like species allows a helpful decomposition of the catalytic effect into preorganization and reorganization phases. In the preorganization phase, the substrates are brought together into the MC-like species, either in water or in the enzyme active site. In the reorganization phase, the roles of the enzymic and aqueous environments may be compared directly because reorganization of the substrate is about the same in both cases. Analysis of the electric field along the reaction coordinate demonstrates that in water the TS is destabilized with respect to the MC-like species because the polarity of the solute diminishes and consequently the reaction field is also decreased. In the enzyme, the electric field is mainly a permanent field and consequently there is only a small reorganization of the environment. Therefore, destabilization of the TS is lower than in solution, and the activation barrier is smaller.

Catalysis↗
PubMed2003

Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case.

In this paper a deeper insight into the chorismate-to prephenate-rearrangement, catalyzed by Bacillus subtilis chorismate mutase, is provided by means of a combination of statistical quantum mechanics/molecular mechanics simulation methods and hybrid potential energy surface exploration techniques. The main aim of this work is to present an estimation of the preorganization and reorganization terms of the enzyme catalytic rate enhancement. To analyze the first of these, we have studied different conformational equilibria of chorismate in aqueous solution and in the enzyme active site. Our conclusion is that chorismate mutase preferentially binds the reactive conformer of the substrate--that presenting a structure similar to the transition state of the reaction to be catalyzed--with shorter distances between the carbon atoms to be bonded and more diaxial character. With respect to the reorganization effect, an energy decomposition analysis of the potential energies of the reactive reactant and of the reaction transition state in aqueous solution and in the enzyme shows that the enzyme structure is better adapted to the transition structure. This means not only a more negative electrostatic interaction energy with the transition state but also a low enzyme deformation contribution to the energy barrier. Our calculations reveal that the structure of the enzyme is responsible for stabilizing the transition state structure of the reaction, with concomitant selection of the reactive form of the reactants. This is, the same enzymatic pattern that stabilizes the transition structure also promotes those reactant structures closer to the transition structure (i.e., the reactive reactants). In fact, both reorganization and preorganization effects have to be considered as the two faces of the same coin, having a common origin in the effect of the enzyme structure on the energy surface of the substrate.

Bacillus subtilis↗
PubMed1999

Theoretical Study on the Molecular Mechanism of the Domino Cycloadditions between Dimethyl Acetylenedicarboxylate and Naphthaleno- and Anthracenofuranophane.

AM1, B3LYP/6-31G//AM1, and B3LYP/6-31G computational studies were performed to select the reaction pathway controlling the reactions between dimethyl acetylenedicarboxylate (DMAD) and two furanophanes, naphthalenofuranophane and anthracenofuranophane. For these domino reactions, several pathways have been characterized on the potential energy surface corresponding to two consecutive cycloadditions. The first step corresponds to a [4 + 2] intermolecular cycloaddition of DMAD with the furan ring or with the naphthalene or anthracene ring of both furanophane systems to yield an oxabicyclo[2.2.1]heptadiene or a bicyclo[2.2.2]octadiene intermediate, respectively. The second step corresponds to [4 + 2] intramolecular cycloadditions of these intermediates. For the naphthalenofuranophane, the most favorable reaction pathway takes place along the initial [4 + 2] intermolecular cycloaddition involving the nonsubstituted ring of the naphthalene system to give a benzobicyclo[2.2.2]octadiene intermediate, which by a [4 + 2] intramolecular cycloaddition between the substituted double bond of this intermediate and the furan ring affords the final cycloadduct. For the anthracenofuranophane, the most favorable reaction pathway takes place along the initial [4 + 2] intermolecular cycloaddition involving the furan ring to give an oxabicyclo[2.2.1]heptadiene intermediate, which by a [4 + 2] intramolecular cycloaddition between the nonsubtituted double bond of the bicyclic system and the naphthalene system affords the final cycloadduct. An analysis of energetic contributions to the potential energy barriers identifies the different factors controlling the competitive reaction pathways. The present theoretical results are able to explain the available experimental data.

Journal Article↗
PubMed1996

On Transition Structures for Hydride Transfer Step in Enzyme Catalysis. A Comparative Study on Models of Glutathione Reductase Derived from Semiempirical, HF, and DFT Methods.

As a model of the chemical reactions that take place in the active site of gluthatione reductase, the nature of the molecular mechanism for the hydride transfer step has been characterized by means of accurate quantum chemical characterizations of transition structures. The calculations have been carried out with analytical gradients at AM1 and PM3 semiempirical procedures, ab initio at HF level with 3-21G, 4-31G, 6-31G, and 6-31G basis sets and BP86 and BLYP as density functional methods. The results of this study suggest that the endo relative orientation on the substrate imposed by the active site is optimal in polarizing the C4-Ht bond and situating the system in the neighborhood of the quadratic region of the transition structure associated to the hydride transfer step on potential energy surface. The endo arrangement of the transition structure results in optimal frontier HOMO orbital interaction between NADH and FAD partners. The geometries of the transition structures and the corresponding transition vectors, that contain the fundamental information relating reactive fluctuation patterns, are model independent and weakly dependent on the level of theory used to determine them. A comparison between simple and complex molecular models shows that there is a minimal set of coordinates describing the essentials of hydride transfer step. The analysis of transition vector components suggests that the primary and secondary kinetic isotope effects can be strongly coupled, and this prompted the calculation of deuterium and tritium primary, secondary, and primary and secondary kinetic isotope effects. The results obtained agree well with experimental data and demonstrate this coupling.

Journal Article↗