Unraveling reaction mechanisms by means of Quantum Chemical Topology Analysis

A chemical reaction can be understood in terms of geometrical changes of the molecular structures and reordering of the electronic densities involved in the process; therefore, identifying structural and electronic density changes taking place along the reaction coordinate renders valuable information on reaction mechanism. Understanding the atomic rearrangements that occur during chemical reactions is of great importance, and this perspective aims to highlight the major developments in quantum chemical topology analysis, based on the combination of electron localization function and catastrophe theory as useful tools in elucidating the bonding and reactivity patterns of molecules. It reveals all the expected, but still ambiguous, elements of electronic structure extensively used by chemists. The chemical bonds determine chemical reactivity, and this technique offers the possibility of their visualization, allowing chemists to understand how atoms bond, how and where bonds are broken/formed along a given reaction pathway at a most fundamental level, and so, better following and understanding the changes in the bond pattern. Their results clearly herald a new era, in which the atomic imaging of chemical bonds will constitute a new method for examining chemical structures and reaction mechanisms. The important feature of this procedure is that in practice the scope of its values is system-independent. In addition, from a practical point of view, it is cheap to calculate and implement because wave functions are the required input, which are easily available from standard calculations. To capture these results two reaction mechanisms: isomerization of C(BH)2 carbene and the thermal cycloheptatriene-norcaradiene isomerizations have been selected, indicating both the generality and utility of this type of analysis

A bonding evolution analysis for the thermal Claisen rearrangement: an experimental and theoretical exercise for testing the electron density flow

A comprehensive theoretical investigation of the thermal Claisen rearrangement of allyl vinyl ether (AVE) to allylacetaldehyde has been carried out. We present the use of the electron localization function (ELF) to monitor the bonding evolution aspects in the course of this thermal rearrangement and the results are compared with a photo-impulsive process where instantaneous vibration frequencies are monitored [Phys. Chem. Chem. Phys., 2011, 12, 5546-5555]. Our results reveal an asynchronous electron density rearrangement inasmuch that the breaking of the C3-O bond and the formation of the C1- C5 do not take place simultaneously. We also demonstrate how the bonding evolution brings about the natural appearance of the curly arrows representing the electronic flow in molecular rearrangements. This holds the key to gaining an unprecedented insight into the mapping of the electron density flow while the bonds change throughout the reaction progress

Curly arrows, electron flow, and reaction mechanisms from the perspective of the bonding evolution theory

Despite the usefulness of curly arrows in chemistry, their relationship with real electron density flows is still imprecise, and even their direct connection to quantum chemistry is still controversial. The paradigmatic description – from first principles – of the mechanistic aspects of a given chemical process is based mainly on the relative energies and geometrical changes at the stationary points of the potential energy surface along the reaction pathway; however, it is not sufficient to describe chemical systems in terms of bonding aspects. Probing the electron density distribution during a chemical reaction can provide important insights, enabling us to understand and control chemical reactions. This aim has required an extension of the relationships between the concepts of traditional chemistry and those of quantum mechanics. Bonding evolution theory (BET), which combines the topological analysis of the electron localization function (ELF) and Thom’s catastrophe theory (CT), provides a powerful method that offers insight into the molecular mechanism of chemical rearrangements. In agreement with the laws of physical and aspects of quantum theory, BET can be considered an appropriate tool to tackle chemical reactivity with a wide range of possible applications. In this work, BET is applied to address a long-standing problem: the ability to monitor the flow of electron density. BET analysis shows a connection between quantum mechanics and bond making/forming processes. Likewise, the present approach retrieves the classical curly arrows used to describe the rearrangements of chemical bonds and provides detailed physical grounds for this type of representation. We demonstrate this procedure using the test set of prototypical examples of thermal ring apertures, and the degenerated Cope rearrangement of semibullvalene

C3-symmetry Mo3S4 aminophosphino clusters combining three sources of stereogenicity: stereocontrol directed by hydrogen bond interactions and ligand configuration

A diastereoselective synthesis of proline containing aminophosphino cubane-type Mo3S4 clusters, (P)-[Mo3S4Cl3((1S,2R)-PPro)3]Cl ((P)-[Mo-(SN,RC)]Cl) and (P)-[Mo3S4Cl3((1S,2S)-PPro)3]Cl ((P)-[Mo-(SN,SC)] Cl), has been achieved in high yields by reacting the corresponding enantiomerically pure PPro ((R)- and (S)-2-[(diphenylphosphino)methyl]pyrrolidine) ligands with the Mo3S4Cl4(PPh3)3(H2O)2 complex. Circular dichroism, nuclear magnetic resonance and X-ray techniques confirm that the (P)-[Mo-(SN,RC)]Cl and (P)-[Mo-(SN,SC)]Cl cluster cations are diastereoisomers which combine three sources of stereogenicity provided by the cluster framework, one carbon atom of the aminophosphine ligand and the nitrogen stereogenic center. The higher stability of the (P)-[Mo-(SN,SC)]+ cation is due to stabilizing vicinal Cl⋯HN interactions as well as due to the cis-fused conformation of the bicyclic system formed upon coordination of the aminophosphine ligand.The financial support of the Spanish Ministerio de Economía y Competitividad (Grant CTQ2011-23157 and CTQ2015-65207-P), Universitat Jaume I (Research Project P1·1B2013-19) and Generalitat Valenciana (PROMETEOII/2014/022) is gratefully acknowledged. The authors also thank the Servei Central d’Instrumentació Científica (SCIC) of the University Jaume I for providing us with the mass spectrometry, NMR and X-ray facilities. C. A. thanks the Spanish Ministerio de Economía y Competitividad for a predoctoral fellowship (FPI)

A bonding evolution theory study of the reaction between methylidyne radical, CH(X2Π), and cyclopentadiene, C5H6

In the present work, bonding evolution theory (BET) is applied to gain insight about the complex reaction between methylidyne radical, CH (X2 Π) and cyclopentadiene, C5H6. The novelty of this work is that all reaction pathways take place in the doublet electronic state and an unpaired electron is always present. Therefore, taking the aforementioned reaction as explicative example, we have shown how to apply the BET tool to these kinds of open-shell systems, by splitting the wavefunctions into the corresponding alpha and beta parts. As an added value, we have included a point-by-point description of the algorithm we use to make it available for the readers. Hence, a complete analysis of bond breaking/forming and charge redistribution along the multi-channels connecting reactants to products via the transition states and intermediates is presented. We show how the BET brings about the representation of the electronic flow in complex molecular rearrangements like the one herein studied, yielding a transparent rationalization based on the electron density redistribution. The present study allows us to conclude that along the different processes giving rise to the benzene product, the breaking of a C C sigma bond initiates the electronic rearrangement in two cases, but not in the third one. The last step in these processes can be described as an initial weakening of the C H bond with a quasi-hydride formation and a final retro-transfer of electrons from the quasi-hydride to the C H bond. On the other hand, in the way to the fulvene product, the breaking of the C C sigma bond takes place after previous electronic redistribution. Neither the last step of the fulvene formation process nor the interesting H transfer described in the second one, can be explaiFunding for open access charge: CRUE-Universitat Jaume

On the catalytic transfer hydrogenation of nitroarenes by a cubane-type Mo3S4 cluster hydride: disentangling the nature of the reaction mechanism

Cubane-type Mo3S4 cluster hydrides decorated with phosphine ligands are active catalysts for the transfer hydrogenation of nitroarenes to aniline derivatives in the presence of formic acid (HCOOH) and triethylamine (Et3N). The process is highly selective and most of the cluster species involved in the catalytic cycle have been identified through reaction monitoring. Formation of a dihydrogen cluster intermediate has also been postulated based on previous kinetic and theoretical studies. However, the different steps involved in the transfer hydrogenation from the cluster to the nitroarene to finally produce aniline remain unclear. Herein, we report an in-depth computational investigation into this mechanism. Et3N reduces the activation barrier associated with the formation of Mo–HHOOCH dihydrogen species. The global catalytic process is highly exergonic and occurs in three consecutive steps with nitrosobenzene and N-phenylhydroxylamine as reaction intermediates. Our computational findings explain how hydrogen is transferred from these Mo–HHOOCH dihydrogen adducts to nitrobenzene with the concomitant formation of nitrosobenzene and the formate substituted cluster. Then, a b-hydride elimination reaction accompanied by CO2 release regenerates the cluster hydride. Two additional steps are needed for hydrogen transfer from the dihydrogen cluster to nitrosobenzene and N-phenylhydroxylamine to finally produce aniline. Our results show that the three metal centres in the Mo3S4 unit act independently, so the cluster can exist in up to ten different forms that are capable of opening a wide range of reaction paths. This behaviour reveals the outstanding catalytic possibilities of this kind of cluster complexes, which work as highly efficient catalytic machines

Combined kinetic and DFT studies on the stabilization of the pyramidal form of H3PO2 at the heterometal site of [Mo3M’S4(H2O)10]4+ clusters (M’= Pd, Ni)

Kinetic and DFT studies have been carried out on the reaction of the [Mo3M’S4(H2O)10]4+ clusters (M’= Pd, Ni) with H3PO2 to form the [Mo3M’(pyr-H3PO2)S4(H2O)9]4+ complexes, in which the rare pyramidal form of H3PO2 is stabilized by coordination to the M’ site of the clusters. The reaction proceeds with biphasic kinetics, both steps showing a first order dependence with respect to H3PO2. These results are interpreted in terms of a mechanism that involves an initial substitution step in which one tetrahedral H3PO2 molecule coordinates to M’ through the oxygen atom of the P=O bond, followed by a second step that consists in tautomerization of coordinated H3PO2 assisted by a second H3PO2 molecule. DFT studies have been carried out to obtain information on the details of both kinetic steps, the major finding being that the role of the additional H3PO2 molecule in the second step consists in catalysing a hydrogen shift from phosphorus to oxygen in O-coordinated H3PO2, which is made possible by its capability of accepting a proton from P-H to form H4PO2 + and then transfer it to the oxygen. DFT studies have been also carried out on the reaction at the Mo centres to understand the reasons that make these metal centres ineffective for promoting tautomerizatio

Catalytic Hydrogenation of Azobenzene in the Presence of a Cuboidal Mo3S4 Cluster via an Uncommon Sulfur-Based H2 Activation Mechanism

Azobenzene hydrogenation is catalyzed under moderate conditions by a cuboidal Mo3(μ3-S)(μ-S)3 diamino complex via a cluster catalysis mechanism. Dihydrogen activation by the molecular [Mo3(μ3-S)(μ-S)3Cl3(dmen)3]+ cluster cation takes place at the μ-S bridging atoms without direct participation of the metals in clear contrast with classical concepts. The reaction occurs with the formation of 1,2-diphenylhydrazine as an intermediate with similar appearance and disappearance rate constants. On the basis of DFT calculations, a mechanism is proposed in which formation of 1,2-diphenylhydrazine and aniline occurs through two interconnected catalytic cycles that share a common reaction step that involves H2 addition to two of the bridging sulfur atoms of the catalyst to form a dithiolate Mo3(μ3-S)(μ-SH)2)(μ-S) adduct. Both catalytic cycles have similar activation barriers, in agreement with the experimental observation of close rate constant values. Microkinetic modeling of the process leads to computed concentration–time profiles in excellent agreement with the experimental ones providing additional support to the calculated reaction mechanism. Slight modifications on the experimental conditions of the catalytic protocol in combination with theoretical calculations discard a direct participation of the metal on the reaction mechanism. The effect of the ancillary ligands on the catalytic activity of the cluster fully agrees with the present mechanistic proposal. The results herein demonstrate the capability of molybdenum sulfide materials to activate hydrogen through an uncommon sulfur based mechanism opening attractive possibilities toward their applications as catalysts in other hydrogenation processes

How effectively bonding evolution theory retrieves and visualizes curly arrows: The cycloaddition reaction of cyclic nitrones

In the present work, the electron density flows involved throughout the progress of the four reaction pathways associated with the intramolecular [3 + 2] cycloaddition of cyclic nitrones Z-1 and E-1 are analyzed using the bonding evolution theory. The present study highlights the nonconcerted nature of the processes, which can be described as taking place in several stages. The first stage consists in the depopulation of the initial C N and C=C double bonds to render the N lone pair and the corresponding C-N and C-C single bonds, and these electronic flows initiate the reactions. The C-C and C-O sigma bond formations take place later on, once the transition states have been overcome. Along the bridged pathways, the C-C bond formation process precedes the O-C bond formation event, although, along the fused paths, the O-C bond formation process occurs first and the formation of the C-C bond is the last electronic flow to take place. Finally, curly arrow representations accounting for the timing of the electron flows are obtained from the bonding evolution theory results

Base-Free Catalytic Hydrogen Production from Formic Acid Mediated by a Cubane-Type Mo3S4 Cluster Hydride

Formic acid (FA) dehydrogenation is an attractive process in the implementation of a hydrogen economy. To make this process greener and less costly, the interest nowadays is moving toward non-noble metal catalysts and additive-free protocols. Efficient protocols using earth abundant first row transition metals, mostly iron, have been developed, but other metals, such as molybdenum, remain practically unexplored. Herein, we present the transformation of FA to form H2 and CO2 through a cluster catalysis mechanism mediated by a cuboidal [Mo3S4H3(dmpe)3]+ hydride cluster in the absence of base or any other additive. Our catalyst has proved to be more active and selective than the other molybdenum compounds reported to date for this purpose. Kinetic studies, reaction monitoring, and isolation of the [Mo3S4(OCHO)3(dmpe)3]+ formate reaction intermediate, in combination with DFT calculations, have allowed us to formulate an unambiguous mechanism of FA dehydrogenation. Kinetic studies indicate that the reaction at temperatures up to 60 °C ends at the triformate complex and occurs in a single kinetic step, which can be interpreted in terms of statistical kinetics at the three metal centers. The process starts with the formation of a dihydrogen-bonded species with Mo–H···HOOCH bonds, detected by NMR techniques, followed by hydrogen release and formate coordination. Whereas this process is favored at temperatures up to 60 °C, the subsequent β-hydride elimination that allows for the CO2 release and closes the catalytic cycle is only completed at higher temperatures. The cycle also operates starting from the [Mo3S4(OCHO)3(dmpe)3]+ formate intermediate, again with preservation of the cluster integrity, which adds our proposal to the list of the infrequent cluster catalysis reaction mechanisms.Funding for open access charge: CRUE-Universitat Jaume