Computational studies of [NiFe] and [FeFe] hydrogenases

Inhibition of [FeFe]-hydrogenases by formaldehyde and wider mechanistic implications for biohydrogen activation

Formaldehyde-a rapid and reversible inhibitor of hydrogen evolution by [FeFe]-hydrogenases-binds with a strong potential dependence that is almost complementary to that of CO. Whereas exogenous CO binds tightly to the oxidized state known as H(ox) but very weakly to a state two electrons more reduced, formaldehyde interacts most strongly with the latter. Formaldehyde thus intercepts increasingly reduced states of the catalytic cycle, and density functional theory calculations support the proposal that it reacts with the H-cluster directly, most likely targeting an otherwise elusive and highly reactive Fe-hydrido (Fe-H) intermediate.

Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives

The development of characterization techniques, advanced synthesis methods, as well as molecular modeling has transformed the study of systems in a well-established research field. The current research challenges in biocatalysis and biotransformation evolve around enzyme discovery, design, and optimization. How can we find or create enzymes that catalyze important synthetic reactions, even reactions that may not exist in nature? What is the source of enzyme catalytic power? To answer these and other related questions, the standard strategies have evolved from trial-and-error methodologies based on chemical knowledge, accumulated experience, and common sense into a clearly multidisciplinary science that allows one to reach the molecular design of tailor-made enzyme catalysts. This is even more so when one refers to enzyme catalysts, for which the detailed structure and composition are known and can be manipulated to introduce well-defined residues which can be implicated in the chemical rearrangements taking place in the active site. The methods and techniques of theoretical and computational chemistry are becoming more and more important in both understanding the fundamental biological roles of enzymes and facilitating their utilization in biotechnology. Improvement of the catalytic function of enzymes is important from scientific and industrial viewpoints, and to put this fact in the actual perspective as well as the potentialities, we recommend the very recent report of Sanderson [Sanderson, K. (2011). Chemistry: enzyme expertise. Nature 471, 397.]. Great fundamental advances have been made toward the ab initio design of enzyme catalysts based on molecular modeling. This has been based on the molecular mechanistic knowledge of the reactions to be catalyzed, together with the development of advanced synthesis and characterization techniques. The corresponding molecular mechanism can be studied by means of powerful quantum chemical calculations. The catalytic active site can be optimized to improve the transition state analogues (TSA) and to enhance the catalytic activity, even improve the active site to favor a desired direction of some promiscuous enzymes. In this chapter, we give a brief introduction, the state of the art, and future prospects and implications of enzyme design. Current computational tools to assist experimentalists for the design and engineering of proteins with desired catalytic properties are described. The interplay between enzyme design, molecular simulations, and experiments will be presented to emphasize the interdisciplinary nature of this research field. This text highlights the recent advances and examples selected from our laboratory are shown, of how the applications of these tools are a first attempt to de novo design of protein active sites. Identification of neutral/advantageous/deleterious mutation platforms can be exploited to penetrate some of Nature's closely guarded secrets of chemical reactivity. In this chapter, we give a brief introduction, the state of the art, and future prospects and implications of enzyme design. The first part describes briefly how the molecular modeling is carried out. Then, we discuss the requirements of hybrid quantum mechanical/molecular mechanics molecular dynamics (QM/MM MD) simulations, analyzing what are the basis of these theoretical methodologies, how we can use them with a view to its application in the study of enzyme catalysis, and what are the best methodologies for assessing its catalytic potential. In the second part, we focus on some selected examples, taking as a common guide the chorismate to prephenate rearrangement, studying the corresponding molecular mechanism in vacuo, in solution and in an enzyme environment. In addition, examples involving catalytic antibodies (CAs) and promiscuous enzymes will be presented. Finally, a special emphasis is made to provide some hints about the logical evolution that can be anticipated in this research field. Moreover, it helps in understanding the open directions in this area of knowledge and highlights the importance of computational approaches in discovering specific drugs and the impact on the rational design of tailor-made enzymes.

Regioselectivity of H cluster oxidation

The H(2)-evolving potential of [FeFe] hydrogenases is severely limited by the oxygen sensitivity of this class of enzymes. Recent experimental studies on hydrogenase from C. reinhardtii point to O(2)-induced structural changes in the [Fe(4)S(4)] subsite of the H cluster. Here, we investigate the mechanistic basis of this observation by means of density functional theory. Unexpectedly, we find that the isolated H cluster shows a pathological catalytic activity for the formation of reactive oxygen species such as O(2)(-) and HO(2)(-). After protonation of O(2)(-), an OOH radical may coordinate to the Fe atoms of the cubane, whereas H(2)O(2) specifically reacts with the S atoms of the cubane-coordinating cysteine residues. Both pathways are accompanied by significant structural distortions that compromise cluster integrity and thus catalytic activity. These results explain the experimental observation that O(2)-induced inhibition is accompanied by distortions of the [Fe(4)S(4)] moiety and account for the irreversibility of this process.

NAD(H)-coupled hydrogen cycling - structure-function relationships of bidirectional [NiFe] hydrogenases

Hydrogenases catalyze the activation or production of molecular hydrogen. Due to their potential importance for future biotechnological applications, these enzymes have been in the focus of intense research for the past decades. Bidirectional [NiFe] hydrogenases are of particular interest as they couple the reversible cleavage of hydrogen to the redox conversion of NAD(H). In this account, we review the current state of knowledge about mechanistic aspects and structural determinants of these complex multi-cofactor enzymes. Special emphasis is laid on the oxygen-tolerant NAD(H)-linked bidirectional [NiFe] hydrogenase from Ralstonia eutropha.

Pentacoordinate iron complexes as functional models of the distal iron in [FeFe] hydrogenases

Mononuclear pentacoordinate iron complexes with a free coordination site were prepared as mimics of the distal Fe (Fe(d)) in the active site of [FeFe] hydrogenases. The complexes catalyze the electrochemical reduction of protons at mild overpotential.

Active-site models for the nickel-iron hydrogenases: effects of ligands on reactivity and catalytic properties

Described are new derivatives of the type [HNiFe(SR)(2)(diphosphine)(CO)(3)](+), which feature a Ni(diphosphine) group linked to a Fe(CO)(3) group by two bridging thiolate ligands. Previous work had described [HNiFe(pdt)(dppe)(CO)(3)](+) ([1H](+)) and its activity as a catalyst for the reduction of protons (J. Am. Chem. Soc. 2010, 132, 14877). Work described in this paper focuses on the effects on properties of NiFe model complexes of the diphosphine attached to nickel as well as the dithiolate bridge, 1,3-propanedithiolate (pdt) vs 1,2-ethanedithiolate (edt). A new synthetic route to these Ni-Fe dithiolates is described, involving reaction of Ni(SR)(2)(diphosphine) with FeI(2)(CO)(4) followed by in situ reduction with cobaltocene. Evidence is presented that this route proceeds via a metastable μ-iodo derivative. Attempted isolation of such species led to the crystallization of NiFe(Me(2)pdt)(dppe)I(2), which features tetrahedral Fe(II) and square planar Ni(II) centers (H(2)Me(2)pdt = 2,2-dimethylpropanedithiol). The new tricarbonyls prepared in this work are NiFe(pdt)(dcpe)(CO)(3) (2, dcpe = 1,2-bis(dicyclohexylphosphino)ethane), NiFe(edt)(dppe)(CO)(3) (3), and NiFe(edt)(dcpe)(CO)(3) (4). Attempted preparation of a phenylthiolate-bridged complex via the FeI(2)(CO)(4) + Ni(SPh)(2)(dppe) route gave the tetrametallic species [(CO)(2)Fe(SPh)(2)Ni(CO)](2)(μ-dppe)(2). Crystallographic analysis of the edt-dcpe compund [2H]BF(4) and the edt-dppe compound [3H]BF(4) verified their close resemblance. Each features pseudo-octahedral Fe and square pyramidal Ni centers. Starting from [3H]BF(4) we prepared the PPh(3) derivative [HNiFe(edt)(dppe)(PPh(3))(CO)(2)]BF(4) ([5H]BF(4)), which was obtained as a ∼2:1 mixture of unsymmetrical and symmetrical isomers. Acid-base measurements indicate that changing from Ni(dppe) (dppe = Ph(2)PCH(2)CH(2)PPh(2)) to Ni(dcpe) decreases the acidity of the cationic hydride complexes by 2.5 pK(a)(PhCN) units, from ∼11 to ∼13.5 (previous work showed that substitution at Fe leads to more dramatic effects). The redox potentials are more strongly affected by the change from dppe to dcpe, for example the [2](0/+) couple occurs at E(1/2) = -820 for [2](0/+) vs -574 mV (vs Fc(+/0)) for [1](0/+). Changes in the dithiolate do not affect the acidity or the reduction potentials of the hydrides. The acid-independent rate of reduction of CH(2)ClCO(2)H by [2H](+) is about 50 s(-1) (25 °C), twice that of [1H](+). The edt-dppe complex [2H](+) proved to be the most active catalyst, with an acid-independent rate of 300 s(-1).

Reversibility and efficiency in electrocatalytic energy conversion and lessons from enzymes

Enzymes are long established as extremely efficient catalysts. Here, we show that enzymes can also be extremely efficient electrocatalysts (catalysts of redox reactions at electrodes). Despite being large and electronically insulating through most of their volume, some enzymes, when attached to an electrode, catalyze electrochemical reactions that are otherwise extremely sluggish (even with the best synthetic catalysts) and require a large overpotential to achieve a useful rate. These enzymes produce high electrocatalytic currents, displayed in single bidirectional voltammetric waves that switch direction (between oxidation and reduction) sharply at the equilibrium potential for the substrate redox couple. Notoriously irreversible processes such as CO(2) reduction are thereby rendered electrochemically reversible--a consequence of molecular evolution responding to stringent biological drivers for thermodynamic efficiency. Enzymes thus set high standards for the catalysts of future energy technologies.

A theoretical study on the enhancement of functionally relevant electron transfers in biomimetic models of [FeFe]-hydrogenases

Recent advances aimed at modeling the chemistry of the active site of [FeFe]-hydrogenases (the H-cluster, composed by a catalytic Fe(2)S(2) subcluster and an Fe(4)S(4) portion) have led to the synthesis of binuclear coordination compounds containing a noninnocent organophosphine ligand [2,3-bis(diphenylphosphino)maleic anhydride, bma] that is able to undergo monoelectron reduction, analogously to the tetranuclear Fe(4)S(4) subcluster portion of the H-cluster. However, such a synthetic model was shown to feature negligible electronic communication between the noninnocent ligand and the remaining portion of the cluster, at variance with the enzyme active site. Here, we report a theoretical investigation that shows why the electron transfer observed in the enzyme upon protonation of the catalytic Fe(2)S(2) subsite cannot take place in the bma-containing cluster. In addition, we show that targeted modifications of the bma ligand are sufficient to restore the electronic communication within the model, such that electron density can be more easily withdrawn from the noninnocent ligand, as a result of protonation of the iron centers. Similar results were also obtained with a ligand derived from cobaltocene. The relevance of our findings is discussed from the perspective of biomimetic reproduction of proton reduction to yield molecular hydrogen.

Towards the computational design of solid catalysts

Over the past decade the theoretical description of surface reactions has undergone a radical development. Advances in density functional theory mean it is now possible to describe catalytic reactions at surfaces with the detail and accuracy required for computational results to compare favourably with experiments. Theoretical methods can be used to describe surface chemical reactions in detail and to understand variations in catalytic activity from one catalyst to another. Here, we review the first steps towards using computational methods to design new catalysts. Examples include screening for catalysts with increased activity and catalysts with improved selectivity. We discuss how, in the future, such methods may be used to engineer the electronic structure of the active surface by changing its composition and structure.

The rate-determining step is dead. Long live the rate-determining state!

The concept of a rate-determining step (RD-Step) is central to the kinetics community, and it is basic knowledge even for the undergraduate chemical student. In spite of this, too many different definitions of the RD-Step appear in the literature, all of them with drawbacks. This dilemma has been thoroughly studied by several authors in the attempt to "patch" the drawbacks and bring the RD-Step to a correct physical meaning. Herein we review with simple models the most notable definitions and some challengers of the RD-Step concept, to conclude with the deduction that there are no rate-determining steps, only rate-determining states.

Favorable Protonation of the (μ-edt)[Fe(2)(PMe(3))(4)(CO)(2)(H-terminal)](+) Hydrogenase Model Complex Over Its Bridging μ-H Counterpart: A Spectroscopic and DFT Study

The mechanism of hydrogen production in [FeFe] hydrogenase remains elusive. However, a species featuring a terminal hydride bound to the distal Fe is thought to be the key intermediate leading to hydrogen production. In this study, density functional theory (DFT) calculations on the terminal (H-term) and bridging (μ-H) hydride isomers of (μ-edt)-[Fe(2)(PMe(3))(4)(CO)(2)H](+) are presented in order to understand the factors affecting their propensity for protonation. Relative to H-term, μ-H is 12.7 kcal/mol more stable, which contributes to its decreased reactivity towards an acid. Potential energy surface (PES) calculations for the reaction of the H-term isomer with 4-nitropyridinium, a proton source, further reveal a lower activation energy barrier (14.5 kcal/mol) for H-term than for μ-H (29 kcal/mol). Besides these energetic considerations, the H-term isomer displays a key molecular orbital (MO <139>) that has a relatively strong hydride (1s) contribution (23%), which is not present in the μ-H isomer. This indicates a potential orbital control of the reaction of the hydride complexes with acid. The lower activation energy barrier and this key MO together control the overall catalytic activity of (μ-edt)[Fe(2)(PMe(3))(4)(CO)(2)(H-term)](+). Lastly, Raman and IR spectroscopy were performed in order to probe the ν(Fe-H) stretching mode of the two isomers and their deuterated counterparts. A ν(Fe-H) stretching mode was observed for the μ-H complex at 1220 cm(-1). However, the corresponding mode is not observed for the less stable H-term isomer.

On understanding proton transfer to the biocatalytic [Fe-Fe](H) sub-cluster in [Fe-Fe]H(2)ases: QM/MM MD simulations

Proton transfer to the [Fe-Fe](H) sub-cluster in the Desulfovibrio desulfuricans (DdH) and Clostridium pasteurianum (CpI) [Fe-Fe] hydrogenases was investigated by a combination of first principles and empirical molecular dynamics simulations. Pathways that can be inferred from the X-ray crystal structures of DdH and CpI, i.e., (Glu159→Ser198→Glu156→water460→Cys178→DTMA([Fe-Fe](H)) and (Glu282→Ser319→Glu279→water612→Cys299), respectively, were considered. Proton transfer from Cys178 to DTMA in the [Fe-Fe](H) sub-cluster in DdH was readily observed in our results, specifically when [Fe-Fe](H) was in the reduced state ([Fe(I)-Fe(I)]) or in the mixed valence state for the protonated distal iron Fe(d) ([Fe(I)-Fe(II)-H(-)](H)). A concerted mechanism is proposed, where proton transfer in DdH from Glu159 to Glu156 via Ser198 and Glu156 to Cys178 via water460 readily occurred, as well as from Glu282 to Glu279 via Ser319 and Glu279 to Cys299 via water612 in CpI. The theoretical prediction of the proton transfer characteristics is consistent with the assumed biocatalytic mechanism of the [Fe-Fe] hydrogenases in which the proton binds at Fe(d), providing confirmation that has not been explored so far. The computational results were qualitatively validated by the agreement with experimental hydrogen production activity data for mutated CpI enzymes, relative to the wild-type protein. Finally, the insight provided by the simulations, combined, in part, with experimental validation, are important for establishing an approach in future exploration of proton transfer to the active site in this class of enzymes, and possibly also for biomimetic analogs.