Spin-Crossing in the (Z)-Selective Alkyne Semihydrogenation Mechanism Catalyzed by Mo3S4 Clusters: A Density Functional Theory Exploration.

Semihydrogenation of internal alkynes catalyzed by the air-stable imidazolyl amino [Mo3S4Cl3(ImNH2)3]+ cluster selectively affords the (Z)-alkene under soft conditions in excellent yields. Experimental results suggest a sulfur-based mechanism with the formation of a dithiolene adduct through interaction of the alkyne with the bridging sulfur atoms. However, computational studies indicate that this mechanism is unable to explain the experimental outcome: mild reaction conditions, excellent selectivity toward the (Z)-isomer, and complete deuteration of the vinylic positions in the presence of CD3OD and CH3OD. An alternative mechanism that explains the experimental results is proposed. The reaction begins with the hydrogenation of two of the Mo3(µ3-S)(µ-S)3 bridging sulfurs to yield a bis(hydrosulfide) intermediate that performs two sequential hydrogen atom transfers (HAT) from the S-H groups to the alkyne. The first HAT occurs with a spin change from singlet to triplet. After the second HAT, the singlet state is recovered. Although the dithiolene adduct is more stable than the hydrosulfide species, the large energy required for the subsequent H2 addition makes the system evolve via the second alternative pathway to selectively render the (Z)-alkene with a lower overall activation barrier.

Exploring the Mechanism of the Intramolecular Diels-Alder Reaction of (2E,4Z,6Z)-2(allyloxy)cycloocta-2,4,6-trien-1-one Using Bonding Evolution Theory.

In the present work, the bond breaking/forming events along the intramolecular Diels-Alder (IMDA) reaction of (2E,4Z,6Z)-2(allyloxy)cycloocta-2,4,6-trien-1-one have been revealed within bonding evolution theory (BET) at the density functional theory level, using the M05-2X functional with the cc-pVTZ basis set. Prior to achieving this task, the energy profiles and stationary points at the potential energy surface (PES) have been characterized. The analysis of the results finds that this rearrangement can proceed along three alternative reaction pathways (a-c). Paths a and b involve two steps, while path c is a one-step process. The first step in path b is kinetically favored, and leads to the formation of an intermediate step, Int-b. Further evolution from Int-b leads mainly to 3-b1. However, 2 is the thermodynamically preferred product and is obtained at high temperatures, in agreement with the experimental observations. Regarding the BET analysis along path b, the breaking/forming process is described by four structural stability domains (SSDs) during the first step, which can be summarized as follows: (1) the breaking of the C-O bond with the transfer of its population to the lone pair (V(O)), (2) the reorganization of the electron density with the creation of two V(C) basins, and (3) the formation of a new C-C single bond via the merger of the two previous V(C) basins. Finally, the conversion of Int-b (via TS2-b1) occurs via the reorganization of the electron density during the first stage (the creation of different pseudoradical centers on the carbon atoms as a result of the depopulation of the C-C double bond involved in the formation of new single bonds), while the last stage corresponds to the non-concerted formation of the two new C-C bonds via the disappearance of the population of the four pseudoradical centers formed in the previous stage. On the other hand, along path a, the first step displays three SSDs, associated with the depopulation of the V(C2,C3) and V(C6,C7) basins, the appearance of the new monosynaptic basins V(C2) and V(C7), and finally the merging of these new monosynaptic basins through the creation of the C2-C7 single bond. The second step is described by a series of five SSDs, that account for the reorganization of the electron density within Int-a via the creation of four pseudoradical centers on the C12, C13, C3 and C6 carbon atoms. The last two SSDs deal with the formation of two C-C bonds via the merging of the monosynaptic basins formed in the previous domains.

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 ß-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.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase.

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase.

The origin of the catalytic power of enzymes has been a question of debate for a long time. In this regard, the possible contribution of protein dynamics in enzymatic catalysis has become one of the most controversial topics. In the present work, the hydride transfer step in the formate dehydrogenase (FDH EC 1.2.1.2) enzyme is studied by means of molecular dynamic (MD) simulations with quantum mechanics/molecular mechanics (QM/MM) potentials in order to explore any correlation between dynamics, tunnelling effects and the rate constant. The temperature dependence of the kinetic isotope effects (KIEs), which is one of the few tests that can be studied by experiments and simulations to shed light on this debate, has been computed and the results have been compared with previous experimental data. The classical mechanical free energy barrier and the number of recrossing trajectories seem to be temperature-independent while the quantum vibrational corrections and the tunnelling effects are slightly temperature-dependent over the interval of 5-45 °C. The computed primary KIEs are in very good agreement with previous experimental data, being almost temperature-independent within the standard deviations. The modest dependence on the temperature is due to just the quantum vibrational correction contribution. These results, together with the analysis of the evolution of the collective variables such as the electrostatic potential or the electric field created by the protein on the key atoms involved in the reaction, confirm that while the protein is well preorganised, some changes take place along the reaction that favour the hydride transfer and the product release. Coordinates defining these movements are, in fact, part of the real reaction coordinate.

Binding Analysis of Some Classical Acetylcholinesterase Inhibitors: Insights for a Rational Design Using Free Energy Perturbation Method Calculations with QM/MM MD Simulations.

In the present study, the binding free energy of some classical inhibitors (DMT, DNP, GNT, HUP, THA) with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation (FEP) method based on hybrid quantum mechanics and molecular mechanics (QM/MM) potentials. The results highlight the key role of the van der Waals interaction for the inhibition process, since the contribution of this term to the binding free energy is almost as decisive as the electrostatic one. The analysis of the geometrical parameters and the interaction energy per residue along the QM/MM molecular dynamics (MD) simulations highlights the most relevant interactions in the different AChE-ligand systems, showing that the charged residues with a more prominent contribution to the interaction energy are Asp72 and Glu199, although the relative importance depends on the molecular size of the ligand. A correlation between the binding free energy and the number of cation-π interactions present in the systems has been established, DMT being the most potent inhibitor, capable of forming four cation-π interactions. A layer of water molecules surrounding the inhibitors has been observed, which act as bridges along a network formed by the ligands and the residues of the gorge and also between different residues. Although several hydrogen bonds between ligands and AChE do appear, no significant values of BIEs have been recorded. This behavior can be accounted for by the special features of AChE, such as the presence of several subsites of different natures in the gorge or the existence of several water molecules that act as bridges in the electrostatic interactions.

Inquiry of the electron density transfers in chemical reactions: a complete reaction path for the denitrogenation process of 2,3-diazabicyclo[2.2.1]hept-2-ene derivatives.

A detailed study on all stages associated with the reaction mechanisms for the denitrogenation of 2,3-diazabicyclo[2.2.1]hept-2-ene derivatives (DBX, with X substituents at the methano-bridge carbon atom, X = H and OH) is presented. In particular, we have characterized the processes leading to cycloalkene derivatives through migration-type mechanisms as well as the processes leading to cyclopentil-1,3-diradical species along concerted or stepwise pathways. The reaction mechanisms have been further analysed within the bonding evolution theory framework at B3LYP and M05-2X/6-311+G(2d,p) levels of theory. Analysis of the results allows us to obtain the intimate electronic mechanism for the studied processes, providing a new topological picture of processes underlying the correlation between the experimental measurements obtained by few-optical-cycle visible pulse radiation and the quantum topological analysis of the electron localization function (ELF) in terms of breaking/forming processes along this chemical rearrangement. The evolution of the population of the disynaptic basin V(N1,N2) can be related to the experimental observation associated with the N=N stretching mode evolution, relative to the N2 release, along the reaction process. This result allows us to determine why the N2 release is easier for the DBH case via a concerted mechanism compared to the stepwise mechanism found in the DBOH system. This holds the key to unprecedented insight into the mapping of the electrons making/breaking the bonds while the bonds change.

A continuous-flow protocol for photoredox-catalyzed multicomponent Petasis reaction.

Here, we present a robust protocol for the facile and rapid synthesis of functionalized secondary amines in continuous flow. More specifically, we describe a detailed guide to perform a photocatalyzed Petasis reaction within 50 min using alkyl boronic acid as radical precursor and a Vapourtec E-series as key equipment. The desired functionalized amine has been synthesized in mmol scale and with a productivity rate of 0.2 mmol/h. The protocol is limited to alkyl boronic acids. For complete details on the generation and use of this protocol, please refer to Oliva et al. (2021).

Galactokinase deficiency: a treatable cause of bilateral cataracts.

Congenital cataract can be caused by several systemic diseases and differential diagnosis should be done between infections, genetic or metabolic diseases. We present a case of a 12-month-old girl with bilateral nuclear cataracts that was referred for investigation. Since she did not present a family history of congenital cataracts or metabolic diseases, and her physical examination was normal, a systemic evaluation was performed. Biochemical studies disclosed abnormal galactose metabolism signs. The diagnosis of galactokinase (GALK1) deficiency was considered and the study of the GALK1 gene allowed identifying a pathogenic genetic variant and a predictably pathogenic missense mutation, previously not described. Dietary measures were imposed with a good evolution.

Photoredox-catalyzed multicomponent Petasis reaction in batch and continuous flow with alkyl boronic acids.

Multicomponent reactions (MCRs) are ideal platforms for the generation of a wide variety of organic scaffolds in a convergent and atom-economical manner. Many strategies for the generation of highly substituted and diverse structures have been developed and among these, the Petasis reaction represents a viable reaction manifold for the synthesis of substituted amines via coupling of an amine, an aldehyde and a boronic acid (BA). Despite its synthetic utility, the inherent drawbacks associated with the traditional two-electron Petasis reaction have stimulated continuous research towards more facile and tolerant methodologies. In this regard, we present the use of free alkyl BAs as effective radical precursors in this MCR through a single-electron transfer mechanism under mild reaction conditions. We have further demonstrated its applicability to photo-flow reactors, facilitating the reaction scale-up for the rapid assembly of complex molecular structures.

Do dynamic effects play a significant role in enzymatic catalysis? A theoretical analysis of formate dehydrogenase.

A theoretical study of the protein dynamic effects on the hydride transfer between the formate anion and nicotinamide adenine dinucleotide (NAD(+)), catalyzed by formate dehydrogenase (FDH), is presented in this paper. The analysis of free downhill molecular dynamic trajectories, performed in the enzyme and compared with the reaction in aqueous solution, has allowed the study of the dynamic coupling between the reacting fragments and the protein or the solvent water molecules, as well as an estimation of the dynamic effect contribution to the catalytic effect from calculation of the transmission coefficient in the enzyme and in solution. The obtained transmission coefficients for the enzyme and in solution were 0.46±0.04 and 0.20±0.03, respectively. These values represent a contribution to catalysis of 0.5 kcal mol(-1), which, although small, is not negligible keeping in mind the low efficiency of FDH. The analysis of the reactive trajectories also reveals how the relative movements of some amino acids, mainly His332 and Arg284, precede and promote the chemical reaction. In spite of these movements, the time-dependent evolution of the electric field created by the enzyme on the key atoms of the reaction reveals a permanent field, which reduces the work required to reach the transition state, with a concomitant polarization of the cofactor. Finally, application of Grote-Hynes theory has allowed the identification of the modes responsible for the substrate-environment coupling, showing how some protein motions take place simultaneously with the reaction. Thus, the equilibrium approach would provide, in this case, an overestimation of the catalyzed rate constant.

Deciphering the Curly Arrow Representation and Electron Flow for the 1,3-Dipolar Rearrangement between Acetonitrile Oxide and (1S,2R,4S)-2-Cyano-7-oxabicyclo[2.2.1]hept-5-en-2-yl Acetate Derivatives.

This study is focused on describing the molecular mechanism beyond the molecular picture provided by the evolution of molecular orbitals, valence bond structures along the reaction progress, or conceptual density functional theory. Using bonding evolution theory (BET) analysis, we have deciphered the mechanism of the 1,3-dipolar rearrangement between acetonitrile oxide and (1S,2R,4S)-2-cyano-7-oxabicyclo[2.2.1]hept-5-en-2-yl acetate derivatives. The BET study revealed that the formation of the C-C bond takes place via a usual sharing model before the O-C one that is also formed in the halogenated species through a not very usual sharing model. The mechanism includes depopulation of the electron density at the N-C triple bond and creation of the V(N) and V(C) monosynaptic basins, depopulation of the former C-C double bond with the creation of V(C,C) basins, and final formation of the V(O,C) basin associated with the O-C bond. The topological changes along the reaction pathway take place in a highly synchronous way. BET provides a convenient quantitative method for deriving curly arrows and electron flow representation to unravel molecular mechanisms.

Origin of the absorption maxima of the photoactive yellow protein resolved via ab initio multiconfigurational methods.

We discuss the role of the protein in controlling the absorption spectra of photoactive yellow protein (PYP), the archetype xanthopsin photoreceptor, using quantum mechanics/molecular mechanics (QM/MM) methods based on ab initio multireference perturbation theory, combined with molecular dynamics (MD) simulations. It is shown that in order to get results in agreement with the experimental data, it is necessary to use a model that allows for a proper relaxation of the whole system and treats the states involved in the electronic spectrum in a balanced way, avoiding biased results due to the effect of nonrepresentative electrostatic interactions on the chromophore.

Dependence of enzyme reaction mechanism on protonation state of titratable residues and QM level description: lactate dehydrogenase.

We have studied the dependence of the chemical reaction mechanism of L-lactate dehydrogenase (LDH) on the protonation state of titratable residues and on the level of the quantum mechanical (QM) description by means of hybrid quantum-mechanical/molecular-mechanical (QM/MM) methods; this methodology has allowed clarification of the timing of the hydride transfer and proton transfer components that hitherto had not been possible to state definitively.

Fish Malodour syndrome in a child.

Body odour can be a manifestation of several metabolic diseases. Diagnosis may be difficult because the disease is often unknown to the doctor. We present a child observed in a general paediatric clinic for bad body odour after eating fish. Given the suspicion of trimethylaminuria, molecular study of flavin mono-oxygenase 3 gene was requested. A pathogenic mutation and polymorphism were identified, which could explain the complaint. Dietary and hygienic measures were imposed with symptom improvement.

Understanding the acylation mechanisms of active-site serine penicillin-recognizing proteins: a molecular dynamics simulation study.

Beta-lactam antibiotics inhibit enzymes involved in the last step of peptidoglycan synthesis. These enzymes, also identified as penicillin-binding proteins (PBPs), form a long-lived acyl-enzyme complex with beta-lactams. Antibiotic resistance is mainly due to the production of beta-lactamases, which are enzymes that hydrolyze the antibiotics and so prevent them reaching and inactivating their targets, and to mutations of the PBPs that decrease their affinity for the antibiotics. In this study, we present a theoretical study of several penicillin-recognizing proteins complexed with various beta-lactam antibiotics. Hybrid quantum mechanical/molecular mechanical potentials in conjunction with molecular dynamics simulations have been performed to understand the role of several residues, and pK(a) calculations have also been done to determine their protonation state. We analyze the differences between the beta-lactamase TEM-1, the membrane-bound PBP2x of Streptococcus pneumoniae, and the soluble DD-transpeptidase of Streptomyces K15.

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.

Topological study of the late steps of the artemisinin decomposition process: modeling the outcome of the experimentally obtained products.

By using 6,7,8-trioxabicyclo[3.2.2]nonane as the artemisinin model and dihydrated Fe(OH)(2) as the heme model, we report a theoretical study of the late steps of the artemisinin decomposition process. The study offers two viewpoints: first, the energetic and geometric parameters are obtained and analyzed, and hence, different reaction paths have been studied. The second point of view uses the electron localization function (ELF) and the atoms in molecules (AIM) methodology, to conduct a complete topological study of such steps. The MO analysis together with the spin density description has also been used. The obtained results agree nicely with the experimental data, and a new mechanistic proposal that explains the experimentally determined outcome of deoxiartemisinin has been postulated.

A topological study of the decomposition of 6,7,8-trioxabicyclo[3.2.2]nonane induced by Fe(II): modeling the artemisinin reaction with heme.

We report a theoretical study on the electronic and topological aspects of the reaction of dihydrated Fe(OH)(2) with 6,7,8-trioxabicyclo[3.2.2]nonane, as a model for the reaction of heme with artemisinin. A comparison is made with the reaction of dihydrated ferrous hydroxide with O(2), as a model for the heme interaction with oxygen. We found that dihydrated Fe(OH)(2) reacts more efficiently with the artemisinin model than with O(2). This result suggests that artemisinin instead of molecular oxygen would interact with heme, disrupting its detoxification process by avoiding the initial heme to hemin oxidation, and killing in this way the malaria parasite. The ELF and AIM theories provide support for such a conclusion, which further clarifies our understanding on how artemisinin acts as an antimalarial agent.

Modeling the decomposition mechanism of artemisinin.

A theoretical study on artemisinin decomposition mechanisms is reported. The calculations have been done at the HF/3-21G and B3LYP/6-31G(d,p) theoretical levels, by using 6,7,8-trioxybicyclo[3.2.2]nonane as the molecular model for artemisinin, and a hydrogen atom, modeling the single electron transfer from heme or Fe(II) in the highly acidic parasite's food vacuole, as inductor of the initial peroxide bond cleavage. All relevant stationary points have been characterized, and the appearance of the final products can be explained in a satisfactory way. Several intermediates and radicals have been found as relatively stable species, thus giving support to the current hypothesis that some of these species can be responsible for the antimalarial action of artemisinin and its derivatives.