Iñaki Tuñón

GEPOL: an improved description of molecular surfaces. III.: a new algorithm for the computation of a solvent-excluding surface

To understand and calculate the interactions of a solute with a solvent, a good method of computing the molecular surface is needed. Three kinds of surfaces may be used: the van der Waals Surface, the Accessible Surface, and the Molecular Surface. The latter is redefined in this article as the Solvent‐Excluding Surface. The new algorithm for computing the Solvent‐Excluding Surface included in the GEPOL93 program is described. GEPOL93 follows the same concept as former versions of GEPOL but with a full new algorithm. Thus, it computes the Solvent‐Excluding Surface by filling the spaces not accessible to the solvent with a set of new spheres. The computation is controlled by three parameters: the number of triangles per sphere, controlled by NDIV; the maximum overlap among the new spheres (OFAC); and the size of the smallest sphere that can be created (RMIN). The changes introduced for the computation of the ESURF make GEPOL93 not just a new version but a new program. An estimation is made of the error in the area and volume obtained in the function of the parameters.

Why is glycine a zwitterion in aqueous solution? A theoretical study of solvent stabilising factors

Abstract In this paper an ab initio study of specific and non-specific solvent effects on the glycine zwitterion energetics and formation mechanism is presented. Calculations are carried out at the HF an MP2 levels with the 6–31 + G ∗∗ basis set. The description of glycine in solution requires the use of continuum models or the inclusion of several discrete water solvent molecules into the calculations. Zwitterion formation in solution occurs by means of an intramolecular proton transfer from oxygen to nitrogen. An analysis of the intermolecular mechanism shows that the addition of one water molecule does not favour the process either geometrically or energetically.

A COUPLED DENSITY FUNCTIONAL-MOLECULAR MECHANICS MONTE CARLO SIMULATION METHOD : THE WATER MOLECULE IN LIQUID WATER

A theoretical model to investigate chemical processes in solution is described. It is based on the use of a coupled density functional/molecular mechanics Hamiltonian. The most interesting feature of the method is that it allows a detailed study of the solutes electronic distribution and of its fluctuations. We present the results for isothermal‐isobaric constant‐NPT Monte Carlo simulation of a water molecule in liquid water. The quantum subsystem is described using a double‐zeta quality basis set with polarization orbitals and nonlocal exchange‐correlation corrections. The classical system is constituted by 128 classical TIP3P or Simple Point Charge (SPC) water molecules. The atom‐atom radial distribution functions present a good agreement with the experimental curves. Differences with respect to the classical simulation are discussed. The instantaneous and the averaged polarization of the quantum molecule are also analyzed.

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.

Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems.

Potential energy surfaces are fundamental tools for the analysis of reaction mechanisms. The accuracy of these surfaces for reactions in very large systems is often limited by the size of the system even if hybrid quantum mechanics/molecular mechanics (QM/MM) strategies are employed. The large number of degrees of freedom of the system requires hundreds or even thousands of optimization steps to reach convergence. Reactions in condensed media (such as enzymes or solutions) are thus usually restricted to be analyzed using low level quantum mechanical methods, thus introducing a source of error in the description of the QM region. In this paper, an alternative method is proposed, coupled to the use of a micro/macroiteration algorithm during the optimization. In these algorithms, the number of microsteps involved in the QM region optimization is usually much smaller than the number of macrosteps required to optimize the MM region. Thus, we define a new potential energy surface in which the gas-phase energy of the QM subsystem and the interaction energy with the MM subsystem are calculated at different computational levels. The high computational level is restricted to the gas-phase energy, which is only requested during the microsteps. The dual level strategy is tested for two reactions in solution (the Menshutkin and the oxy-Cope reactions) and an enzymatic one (the nucleophilic substitution of 1,2-dichloroethane in DhlA). The performance of the proposed computational scheme seems to be quite promising for future applications in other systems.

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

Significance The role of protein dynamics in enzyme catalysis remains a topic of considerable debate. Here, we use a combination of experimental and computational methods to identify the origins of the observed changes in reactivity on isotopic substitution of dihydrofolate reductase from Escherichia coli. Isotopic substitution causes differences in environmental coupling to the hydride transfer step and protein dynamics have therefore a small but measurable effect on the chemical reaction rate. Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis, but identification and analysis of dynamical effects in enzyme-catalyzed reactions have proved very challenging. Here, we tackle this question by comparing an enzyme with its heavy (15N, 13C, 2H substituted) counterpart, providing a subtle probe of dynamics. The crucial hydride transfer step of the reaction (the chemical step) occurs more slowly in the heavy enzyme. A combination of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyses identify the origins of the observed differences in reactivity. The generally slightly slower reaction in the heavy enzyme reflects differences in environmental coupling to the hydride transfer step. Importantly, the barrier and contribution of quantum tunneling are not affected, indicating no significant role for “promoting motions” in driving tunneling or modulating the barrier. The chemical step is slower in the heavy enzyme because protein motions coupled to the reaction coordinate are slower. The fact that the heavy enzyme is only slightly less active than its light counterpart shows that protein dynamics have a small, but measurable, effect on the chemical reaction rate.

Aminoacid zwitterions in solution: Geometric, energetic, and vibrational analysis using density functional theory-continuum model calculations

Glycine and alanine aminoacids chemistry in solution is explored using a hybrid three parameters density functional (B3PW91) together with a continuum model. Geometries, energies, and vibrational spectra of glycine and alanine zwitterions are studied at the B3PW91/6-31+G** level and the results compared with those obtained at the HF and MP2/6-31+G** levels. Solvents effects are incorporated by means of an ellipsoidal cavity model with a multipolar expansion (up to sixth order) of the solute’s electrostatic potential. Our results confirm the validity of the B3PW91 functional for studying aminoacid chemistry in solution. Taking into account the more favorable scaling behavior of density functional techniques with respect to correlated ab initio methods these studies could be extended to larger systems.

MOLECULAR DYNAMICS SIMULATIONS OF ELEMENTARY CHEMICAL PROCESSES IN LIQUID WATER USING COMBINED DENSITY FUNCTIONAL AND MOLECULAR MECHANICS POTENTIALS. I. PROTON TRANSFER IN STRONGLY H-BONDED COMPLEXES

The first molecular dynamics (MD) simulation of a chemical process in solution with an ab initio description of the reactant species and a classical representation of the solvent is presented. We study the dynamics of proton (deuterium) transfer in strongly hydrogen-bonded systems characterized by an energy surface presenting a double well separated by a low activation barrier. We have chosen the hydroxyl-water complex in liquid water to analyze the coupling between the reactive system and the environment. The proton is transferred from one well to the other with a frequency close to 1 ps−1 which is comparable to the low-frequency band associated to hindered translations, diffusional translation and reorientation of water molecules in water. The proton transfer takes place in 20–30 fs whereas the solvent response is delayed by about 50 fs. Therefore, the reaction occurs in an essentially frozen-solvent configuration. In principle, this would produce a barrier increase with respect to the equilibrium react...

Promiscuity in Alkaline Phosphatase Superfamily. Unraveling Evolution through Molecular Simulations

We here present a theoretical study of the alkaline hydrolysis of a phosphodiester (methyl p-nitrophenyl phosphate or MpNPP) in the active site of Escherichia coli alkaline phosphatase (AP), a monoesterase that also presents promiscuous activity as a diesterase. The analysis of our simulations, carried out by means of molecular dynamics (MD) simulations with hybrid quantum mechanics/molecular mechanics (QM/MM) potentials, shows that the reaction takes place through a D(N)A(N) or dissociative mechanism, the same mechanism employed by AP in the hydrolysis of monoesters. The promiscuous activity observed in this superfamily can be then explained on the basis of a conserved reaction mechanism. According to our simulations the specialization in the hydrolysis of phosphomonoesters or phosphodiesters, developed in different members of the superfamily, is a consequence of the interactions established between the protein and the oxygen atoms of the phosphate group and, in particular, with the oxygen atom that bears the additional alkyl group when the substrate is a diester. A water molecule, belonging to the coordination shell of the Mg(2+) ion, and residue Lys328 seem to play decisive roles stabilizing a phosphomonoester substrate, but the latter contributes to increase the energy barrier for the hydrolysis of phosphodiesters. Then, mutations affecting the nature or positioning of Lys328 lead to an increased diesterase activity in AP. Finally, the capacity of this enzymatic family to catalyze the reaction of phosphoesters having different leaving groups, or substrate promiscuity, is explained by the ability of the enzyme to stabilize different charge distributions in the leaving group using different interactions involving either one of the zinc centers or residues placed on the outer side of the catalytic site.

Theoretical Study of Phosphodiester Hydrolysis in Nucleotide Pyrophosphatase/Phosphodiesterase. Environmental Effects on the Reaction Mechanism

We here present a theoretical study of the alkaline hydrolysis of methyl p-nitrophenyl phosphate (MpNPP(-)) in aqueous solution and in the active site of nucleotide pyrophosphatase/phosphodiesterase (NPP). The analysis of our simulations, carried out by means of hybrid quantum mechanics/molecular mechanics (QM/MM) methods, shows that the reaction takes place through different reaction mechanisms depending on the environment. Thus, while in aqueous solution the reaction occurs by means of an A(N)D(N) mechanism, the enzymatic process takes place through a D(N)A(N) mechanism. In the first case, we found associative transition-state (TS) structures, while in the enzyme TS structures have dissociative character. The reason for this change is rationalized in terms of the very different nature of the electrostatic interactions established in each of the environments: while the aqueous solution reduces the repulsion between the negatively charged reacting fragments, assisting their approach, the NPP active site stabilizes the charge distribution of dissociative TS structures, allowing the reaction to proceed with a significantly reduced free energy cost. Interestingly, the NPP active site is able to accommodate different substrates, and it seems that the nature of the TSs depends on their electronic characteristics. So, in the case of the MpNPP(-) substrate, the nitro group establishes hydrogen-bond interactions with water molecules and residues found in the outer part of the catalytic site, while the leaving group oxygen atom does not coordinate directly with any of the zinc atoms of the active site. If methyl phenyl phosphate is used as substrate, then the charge on the leaving group is supported to larger extent by the oxygen atom and the phenolate anion can be then coordinated to one of the two zinc atoms present in the active site.