From Ligand- to Metal-centered Reactivity: Metal Substitution Effect in Thiosemicarbazone-based Complexes for H2 Production.

The quest to develop and optimize catalysts for H2 production requires a thorough understanding in the possible catalytic mechanisms involved. Transition metals are very often the centers of reactivity in the catalysis, although this can change in the presence of a redox-active ligand. Investigating the differences in catalysis when considering ligand- and metal-centered reactivity is important to find the most optimal mechanisms for hydrogen evolution reaction. Here, we investigated this change of reactivity in two versions of a thiosemicarbazone-based complex, using Co and Ni metal centers. While the Ni version has a ligand-centered reactivity, Co switches it toward a metal-centered one. Comparison between the mechanisms show differences in rate-limiting steps, and shows the importance of identifying those steps in order to optimize the system for hydrogen production.

Unraveling the catalytic mechanisms of H2 production with thiosemicarbazone nickel complexes.

Thiosemicarbazone-based complexes have been explored as a new class of redox-active catalysts H2 production due to their flexibility for extensive optimization. To rationalize the process, we need to understand how these complexes function. In this work, we used DFT calculations to investigate the various mechanisms that could take place for three previously characterized Ni complexes. We found that two possible mechanisms are compatible with previously published experimental data, involving protonation of two adjacent N atoms close to the metal center. The first step likely involves a proton-coupled electron transfer process from a proton source to one of the distal N atoms in the ligand. From here, a second proton can be transferred either to the coordinating N atom situated in between the first protonated atom and the Ni atom, or to the second distal N atom. The former case then has the protons in close distance for H2 production. However, the latter will require a third protonation event to occur, which would fall in one of the N atoms adjacent to the Ni center, resulting in a similar mechanism. Finally, we show that the H-H bond formation is the rate-limiting step, and suggest additional strategies that can be taken into account to further optimize these complexes.

Hydrogen evolution reaction mediated by an all-sulfur trinuclear nickel complex.

We report the synthesis and the characterization of a trinuclear nickel complex. Solid state and solution studies using X-ray diffraction, NMR and UV-vis spectroscopy highlight the square planar geometries around the metal centers and an all-sulfur coordination sphere. It exhibits significant electrocatalytic activity for hydrogen evolution in DMF using Et3NHCl as the proton source. DFT studies suggest that sulfur atoms act as proton relay, as proposed in [NiFe] hydrogenases.

Ligand-based electronic effects on the electrocatalytic hydrogen production by thiosemicarbazone nickel complexes.

This work reports on the synthesis and characterization of a series of mononuclear thiosemicarbazone nickel complexes that display significant catalytic activity for hydrogen production in DMF using trifluoroacetic acid as the proton source. The ligand framework was chemically modified by varying the electron-donating abilities of the para substituents on the phenyl rings, which was expected to impact the capability of the resulting complexes to reduce protons into hydrogen. Over the four nickel complexes that were obtained, the one with the thiomethyl substituent, NiSCH3, was found to overtake the catalytic performances of the parent complex NiOCH3 featuring lower overpotential values and similar maximum turnover frequencies. These results confirm the electronic effects of the ligand on HER when using thiosemicarbazone nickel complexes and support that chemical modifications can tune the catalytic performances of such systems.

Molecular Electrocatalysts for the Hydrogen Evolution Reaction: Input from Quantum Chemistry.

In the pursuit of carbon-free fuels, hydrogen can be considered as an apt energy carrier. The design of molecular electrocatalysts for hydrogen production is important for the development of renewable energy sources that are abundant, inexpensive, and environmentally benign. Over the last 20 years, a large number of electrocatalysts have been developed, and considerable efforts have been directed toward the design of earth-abundant, first-row transition-metal complexes capable of promoting electrocatalytic hydrogen evolution reaction (HER). In this context, numerical approaches have emerged as powerful tools to study the catalytic performances of these complexes. This review covers some of the most significant theoretical mechanistic studies of biomimetic and bioinspired homogeneous HER catalysts. The approaches employed to study the free energy landscapes are discussed and methods used to obtain accurate estimates of relevant observables required to study the HER are presented. Furthermore, the structural and electronic parameters that govern the reactivity, and are necessary to achieve efficient hydrogen production, are discussed in view of future research directions.

To Be or Not To Be a Molecular Ion: The Role of the Solvent in Photoionization of Arginine.

Application of photoionization mass spectroscopy, a technique capable of assessing protonation states in complex molecules in the gas phase, is challenging for arginine due to its fragility. We report photoionization efficiencies in the valence region of aqueous aerosol particles produced from arginine solutions under various pH and vaporization conditions. By using ab initio calculations, we investigate the stability of different conformers. Our results show that neutral arginine fragments upon ionization in the gas phase but solvation stabilizes the molecular ion, resulting in different photoionization dynamics. We also report the valence-band photoelectron spectra of the aerosol solutions obtained at different pH values.

Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes.

Genetic variation among orthologous proteins can cause cryptic phenotypic properties that only manifest in changing environments. Such variation may impact the evolvability of proteins, but the underlying molecular basis remains unclear. Here, we performed comparative directed evolution of four orthologous metallo-ß-lactamases toward a new function and found that different starting genotypes evolved to distinct evolutionary outcomes. Despite a low initial fitness, one ortholog reached a significantly higher fitness plateau than its counterparts, via increasing catalytic activity. By contrast, the ortholog with the highest initial activity evolved to a less-optimal and phenotypically distinct outcome through changes in expression, oligomerization and activity. We show how cryptic molecular properties and conformational variation of active site residues in the initial genotypes cause epistasis, that could lead to distinct evolutionary outcomes. Our work highlights the importance of understanding the molecular details that connect genetic variation to protein function to improve the prediction of protein evolution.

Multiheme Cytochrome Mediated Redox Conduction through Shewanella oneidensis MR-1 Cells.

Multiheme cytochromes function as extracellular electron transfer (EET) conduits that extend the metabolic reach of microorganisms to external solid surfaces. These conduits are also proposed to facilitate long-distance electron transport along cellular membranes and across multiple cells. Here we report electrochemical gating measurements of Shewanella oneidensis MR-1 cells linking interdigitated electrodes. The dependence of the source-drain current on gate potential demonstrates a redox conduction mechanism, which we link to the presence of multiheme cytochromes of the Mtr pathway. We also find that the measured thermal activation energy of 0.29 ± 0.03 eV is consistent with these obtained from electron hopping calculations through the S. oneidensis Mtr outer-membrane decaheme cytochromes. Our measurements and calculations have implications for understanding and controlling micrometer-scale electron transport in microbial systems.

Distinct Electron Conductance Regimes in Bacterial Decaheme Cytochromes.

Shewanella oneidensis MR-1 gains energy by extracellular electron transfer to solid surfaces. They employ c-type cytochromes in two Mtr transmembrane complexes, forming a multiheme wire for electron transport across the cellular outer membrane. We investigated electron- and hole-transfer mechanisms in the external terminal of the two complexes, MtrC and MtrF. Comparison of computed redox potentials with previous voltammetry experiments in distinct environments (isolated and electrode-bound conditions of PFV or in vivo) suggests that these systems function in different regimes depending on the environment. Analysis of redox potential shifts in different regimes indicates strong coupling between the hemes via an interplay between direct Coulomb and indirect interactions through local structural reorganization. The latter results in the screening of Coulomb interactions and explains poor correlation of the strength of the heme-to-heme interactions with the distance between the hemes.

Computer simulations of the catalytic mechanism of wild-type and mutant ß-phosphoglucomutase.

ß-Phosphoglucomutase (ß-PGM) has served as an important model system for understanding biological phosphoryl transfer. This enzyme catalyzes the isomerization of ß-glucose-1-phosphate to ß-glucose-6-phosphate in a two-step process proceeding via a bisphosphate intermediate. The conventionally accepted mechanism is that both steps are concerted processes involving acid-base catalysis from a nearby aspartate (D10) side chain. This argument is supported by the observation that mutation of D10 leaves the enzyme with no detectable activity. However, computational studies have suggested that a substrate-assisted mechanism is viable for many phosphotransferases. Therefore, we carried out empirical valence bond (EVB) simulations to address the plausibility of this mechanistic alternative, including its role in the abolished catalytic activity of the D10S, D10C and D10N point mutants of ß-PGM. In addition, we considered both of these mechanisms when performing EVB calculations of the catalysis of the wild type (WT), H20A, H20Q, T16P, K76A, D170A and E169A/D170A protein variants. Our calculated activation free energies confirm that D10 is likely to serve as the general base/acid for the reaction catalyzed by the WT enzyme and all its variants, in which D10 is not chemically altered. Our calculations also suggest that D10 plays a dual role in structural organization and maintaining electrostatic balance in the active site. The correct positioning of this residue in a catalytically competent conformation is provided by a functionally important conformational change in this enzyme and by the extensive network of H-bonding interactions that appear to be exquisitely preorganized for the transition state stabilization.

The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis.

Despite the numerous experimental and theoretical studies on phosphate monoester hydrolysis, significant questions remain concerning the mechanistic details of these biologically critical reactions. In the present work we construct a linear free energy relationship for phosphate monoester hydrolysis to explore the effect of modulating leaving group pKa on the competition between solvent- and substrate-assisted pathways for the hydrolysis of these compounds. Through detailed comparative electronic-structure studies of methyl phosphate and a series of substituted aryl phosphate monoesters, we demonstrate that the preferred mechanism is dependent on the nature of the leaving group. For good leaving groups, a strong preference is observed for a more dissociative solvent-assisted pathway. However, the energy difference between the two pathways gradually reduces as the leaving group pKa increases and creates mechanistic ambiguity for reactions involving relatively poor alkoxy leaving groups. Our calculations show that the transition-state structures vary smoothly across the range of pKas studied and that the pathways remain discrete mechanistic alternatives. Therefore, while not impossible, a biological catalyst would have to surmount a significantly higher activation barrier to facilitate a substrate-assisted pathway than for the solvent-assisted pathway when phosphate is bonded to good leaving groups. For poor leaving groups, this intrinsic preference disappears.

Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily.

It is becoming widely accepted that catalytic promiscuity, i.e., the ability of a single enzyme to catalyze the turnover of multiple, chemically distinct substrates, plays a key role in the evolution of new enzyme functions. In this context, the members of the alkaline phosphatase superfamily have been extensively studied as model systems in order to understand the phenomenon of enzyme multifunctionality. In the present work, we model the selectivity of two multiply promiscuous members of this superfamily, namely the phosphonate monoester hydrolases from Burkholderia caryophylli and Rhizobium leguminosarum. We have performed extensive simulations of the enzymatic reaction of both wild-type enzymes and several experimentally characterized mutants. Our computational models are in agreement with key experimental observables, such as the observed activities of the wild-type enzymes, qualitative interpretations of experimental pH-rate profiles, and activity trends among several active site mutants. In all cases the substrates of interest bind to the enzyme in similar conformations, with largely unperturbed transition states from their corresponding analogues in aqueous solution. Examination of transition-state geometries and the contribution of individual residues to the calculated activation barriers suggest that the broad promiscuity of these enzymes arises from cooperative electrostatic interactions in the active site, allowing each enzyme to adapt to the electrostatic needs of different substrates. By comparing the structural and electrostatic features of several alkaline phosphatases, we suggest that this phenomenon is a generalized feature driving selectivity and promiscuity within this superfamily and can be in turn used for artificial enzyme design.

How valence bond theory can help you understand your (bio)chemical reaction.

Almost a century has passed since valence bond (VB) theory was originally introduced to explain covalent bonding in the H2 molecule within a quantum mechanical framework. The past century has seen constant improvements in this theory, with no less than two distinct Nobel prizes based on work that is essentially developments in VB theory. Additionally, ongoing advances in both methodology and computational power have greatly expanded the scope of problems that VB theory can address. In this Tutorial Review, we aim to give the reader a solid understanding of the foundations of modern VB theory, using a didactic example of a model SN2 reaction to illustrate its immediate applications. This will be complemented by examples of challenging problems that at present can only be efficiently addressed by VB-based approaches. Finally, the ongoing importance of VB theory is demonstrated. It is concluded that VB will continue to be a major driving force for chemistry in the century to come.

Challenges in computational studies of enzyme structure, function and dynamics.

In this review we give an overview of the field of Computational enzymology. We start by describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel Laureates. We then present key features of the state-of-the-art in the field, showing what theory, accompanied by experiments, has taught us so far about enzymes. We also briefly describe computational methods, such as quantum mechanics-molecular mechanics approaches, reaction coordinate treatment, and free energy simulation approaches. We finalize by discussing open questions and challenges.

Force field independent metal parameters using a nonbonded dummy model.

The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn(2+), Zn(2+), Mg(2+), and Ca(2+), as well as providing new parameters for Ni(2+), Co(2+), and Fe(2+). In all the cases, we are able to reproduce both M(2+)-O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase I as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers.

Computational protein engineering: bridging the gap between rational design and laboratory evolution.

Enzymes are tremendously proficient catalysts, which can be used as extracellular catalysts for a whole host of processes, from chemical synthesis to the generation of novel biofuels. For them to be more amenable to the needs of biotechnology, however, it is often necessary to be able to manipulate their physico-chemical properties in an efficient and streamlined manner, and, ideally, to be able to train them to catalyze completely new reactions. Recent years have seen an explosion of interest in different approaches to achieve this, both in the laboratory, and in silico. There remains, however, a gap between current approaches to computational enzyme design, which have primarily focused on the early stages of the design process, and laboratory evolution, which is an extremely powerful tool for enzyme redesign, but will always be limited by the vastness of sequence space combined with the low frequency for desirable mutations. This review discusses different approaches towards computational enzyme design and demonstrates how combining newly developed screening approaches that can rapidly predict potential mutation "hotspots" with approaches that can quantitatively and reliably dissect the catalytic step can bridge the gap that currently exists between computational enzyme design and laboratory evolution studies.