Stabilizing σ-hole Dimethyl Interactions.

Methyl groups bound to electronegative atoms, such as N or O, are recognized to participate in tetrel bonding as Lewis acids. On the other hand, the capability of methyl groups bound to electropositive atoms, such as B or Al, to act as Lewis bases has been recently reported. Herein, we analyze the combination of these two behaviors to establish attractive methyl···methyl interactions. We have explored the Cambridge Structural Database to find experimental examples of these dimethyl-bound systems, finding a significant degree of directionality in the relative disposition of the two methyl groups. Moreover, we have carried out a comprehensive computational analysis at the DFT level of the dimethyl interactions, including the natural bond orbital, energy decomposition analysis, and topological analysis of the electron density (QTAIM and NCI). The dimethyl interaction is characterized as weak yet attractive and based on electrostatics, with a non-negligible contribution from orbital charge transfer and polarization.

Riboflavin kinase and pyridoxine 5'-phosphate oxidase complex formation envisages transient interactions for FMN cofactor delivery.

Enzymes catalysing sequential reactions have developed different mechanisms to control the transport and flux of reactants and intermediates along metabolic pathways, which usually involve direct transfer of metabolites from an enzyme to the next one in a cascade reaction. Despite the fact that metabolite or substrate channelling has been widely studied for reactant molecules, such information is seldom available for cofactors in general, and for flavins in particular. Flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) act as cofactors in flavoproteins and flavoenzymes involved in a wide range of physiologically relevant processes in all type of organisms. Homo sapiens riboflavin kinase (RFK) catalyses the biosynthesis of the flavin mononucleotide cofactor, and might directly interplay with its flavin client apo-proteins prior to the cofactor transfer. Non-etheless, none of such complexes has been characterized at molecular or atomic level so far. Here, we particularly evaluate the interaction of riboflavin kinase with one of its potential FMN clients, pyridoxine-5'-phosphate oxidase (PNPOx). The interaction capacity of both proteins is assessed by using isothermal titration calorimetry, a methodology that allows to determine dissociation constants for interaction in the micromolar range (in agreement with the expected transient nature of the interaction). Moreover, we show that; i) both proteins become thermally stabilized upon mutual interaction, ii) the tightly bound FMN product can be transferred from RFK to the apo-form of PNPOx producing an efficient enzyme, and iii) the presence of the apo-form of PNPOx slightly enhances RFK catalytic efficiency. Finally, we also show a computational study to predict likely RFK-PNPOx binding modes that can envisage coupling between the FMN binding cavities of both proteins for the potential transfer of FMN.

Exploring the Potential Energy Surface of Pt6 Sub-Nano Clusters Deposited over Graphene.

Catalytic systems based on sub-nanoclusters deposited over different supports are promising for very relevant chemical transformations such as many electrocatalytic processes as the ORR. These systems have been demonstrated to be very fluxional, as they are able to change shape and interconvert between each other either alone or in the presence of adsorbates. In addition, an accurate representation of their catalytic activity requires the consideration of ensemble effects and not a single structure alone. In this sense, a reliable theoretical methodology should assure an accurate and extensive exploration of the potential energy surface to include all the relevant structures and with correct relative energies. In this context, we applied DFT in conjunction with global optimization techniques to obtain and analyze the characteristics of the many local minima of Pt6 sub-nanoclusters over a carbon-based support (graphene)-a system with electrocatalytic relevance. We also analyzed the magnetism and the charge transfer between the clusters and the support and paid special attention to the dependence of dispersion effects on the ensemble characteristics. We found that the ensembles computed with and without dispersion corrections are qualitatively similar, especially for the lowest-in-energy clusters, which we attribute to a (mainly) covalent binding to the surface. However, there are some significant variations in the relative stability of some clusters, which would significantly affect their population in the ensemble composition.

Mechanism Insights into the Iridium(III)- and B(C6F5)3-Catalyzed Reduction of CO2 to the Formaldehyde Level with Tertiary Silanes.

The catalytic system [Ir(CF3CO2)(κ2-NSiMe)2] [1; NSiMe = (4-methylpyridin-2-yloxy)dimethylsilyl]/B(C6F5)3 promotes the selective reduction of CO2 with tertiary silanes to the corresponding bis(silyl)acetal. Stoichiometric and catalytic studies evidenced that species [Ir(CF3COO-B(C6F5)3)(κ2-NSiMe)2] (3), [Ir(κ2-NSiMe)2][HB(C6F5)3] (4), and [Ir(HCOO-B(C6F5)3)(κ2-NSiMe)2] (5) are intermediates of the catalytic process. The structure of 3 has been determined by X-ray diffraction methods. Theoretical calculations show that the rate-limiting step for the 1/B(C6F5)3-catalyzed hydrosilylation of CO2 to bis(silyl)acetal is a boron-promoted Si-H bond cleavage via an iridium silylacetal borane adduct.

Peel Diffusion and Antifungal Efficacy of Different Fungicides in Pear Fruit: Structure-Diffusion-Activity Relationships.

Fungal pathogens can invade not only the fruit peel but also the outer part of the fruit mesocarp, limiting the efficacy of fungicides. In this study, the relationships between fungicide structure, diffusion capacity and in vivo efficacy were evaluated for the first time. The diffusion capacity from pear peel to mesocarp of 11 antifungal compounds, including p-aminobenzoic acid, carbendazim, difenoconazole, dipicolinic acid, flusilazole, gentamicin, kojic acid, prochloraz, quinolinic acid, thiophanate methyl and thiram was screened. The obtained results indicated that size and especially polarity were negatively correlated with the diffusion capacity. Although some antifungal compounds, such as prochloraz and carbendazim, were completely degraded after a few days in peel and mesocarp, other compounds, such as p-aminobenzoic acid and kojic acid, showed high stability. When applying the antifungal compounds at the EC50 concentrations, it was observed that the compounds with high diffusion capacity showed higher in vivo antifungal activity against Alternaria alternata than compounds with low diffusion capacity. In contrast, there was no relationship between stability and in vivo efficacy. Collectively, the obtained results indicated that the diffusion capacity plays an important role in the efficacy of fungicides for the control of pear fruit diseases.

Nucleophilic Reactivity at a ═CH Arm of a Lutidine-Based CNC/Rh System: Unusual Alkyne and CO2 Activation.

Reaction of an amido pincer complex [(CNC)*Rh(CO)] (1) (CNC* is the deprotonated form of CNC) with carbon dioxide gave a neutral complex [(CNC-CO2)Mes*Rh(CO)] (2), which is the result of a C-C bond-forming reaction between the deprotonated arm of the CNC* ligand and CO2. The molecular structure of 2 showed a zwitterionic complex, where the CO2 moiety is covalently connected to the former ═CH arm of the CNC* pincer ligand. The unusual structure of 1 allowed us to explore the reactivity of the CO2 moiety with selected primary amines RNH2 (benzylamine and ammonia), which afforded cationic complexes [(CNC)MesRh(CO)][HRNC(O)O] (R = Bz (3), H (4)). Compounds 3 and 4 are the result of a C-N coupling between the incoming amine and the CO2 fragment covalently connected to the pincer ligand in 2, a process that involves protonation of the "CH-CO2" fragment in 2 from the respective amines. Once revealed the nucleophilic character of the ═CH fragment in 1, we explored its reactivity with alkynes, a study that enlightened a novel reactivity trend in alkyne activation. Reaction of 1 with terminal alkynes RC≡CH (R = Ph, 2-py, 4-C6H4-CF3) yielded neutral complexes [(CNC-CH═CHR)Mes*Rh(CO)] (R = Ph (5), 2-py (6), 4-C6H4-CF3 (7)) in good yields. Deuterium labeling experiments with PhC≡CD confirmed that complex 5 is the product of a formal insertion of the alkyne into the C(sp2)-H bond of the deprotonated arm in 1. This structural proposal was further confirmed by the X-ray molecular structure of phenyl complex 5, which showed the alkyne covalently linked to the pincer ligand. Besides, this novel transformation was analyzed by DFT methods and showed a metal-ligand cooperative mechanism, based on the initial electrophilic attack of the alkyne to the ═CH arm of the CNCMes* ligand (making a new C-C bond) followed by the action of a protic base (HN(SiMe3)2), which is able to perform a proton rearrangement that leads to the final product 5.

Rhodium-NHC-Catalyzed gem-Specific O-Selective Hydropyridonation of Terminal Alkynes.

The dinuclear complex [Rh(µ-Cl)(η2 -coe)(IPr)]2 is an efficient catalyst for the O-selective Markovnikov-type addition of 2-pyridones to terminal alkynes. DFT calculations support a hydride-free pathway entailing intramolecular oxidative protonation of a π-alkyne by a κ1 N-hydroxypyridine ligand. Subsequent O-nucleophilic attack on a metallacyclopropene species affords an O-alkenyl-2-oxypyridine chelate rhodium intermediate as the catalyst resting state. The release of the alkenyl ether is calculated as the rate-determining step.

Dehydrogenation of formic acid using iridium-NSi species as catalyst precursors.

Using a low loading of the iridium(III) complexes [Ir(CF3SO3)(κ2-NSiiPr)2] (1) (NSiiPr = (4-methylpyridin-2-yloxy)diisopropylsilyl) and [{Ir(κ2-NSiMe)2}2(µ-CF3SO3)2] (2) (NSiMe = (4-methylpyridin-2-yloxy)dimethylsilyl) in the presence of Et3N, it has been possible to achieve the solventless selective dehydrogenation of formic acid. The best catalytic performance (TOF5 min ≈ 2900 h-1) has been achieved with 2 (0.1 mol%) and Et3N (40 mol% to FA) at 373 K. Kinetic studies at variable temperatures show that the activation energy of the 2-catalyzed process at 353 K is 22.8 ± 0.8 kcal mol-1. KIE values of 1.33, 2.86, and 3.33 were obtained for the 2-catalyzed dehydrogenation of HCOOD, DCOOH, and DCOOD, respectively, in the presence of 10 mol% of Et3N at 353 K. These data show that the activation of the C-H bond of FA is the rate-determining step of the process. A DFT mechanistic study for the catalytic cycle involving hydride abstraction from the formate anion by the metal, assisted by a molecule of formic acid, and heterolytic H2 formation has been performed. Moreover, the presence of Ir-formate intermediates was identified by means of NMR studies of the catalytic reactions in thf-d8 at 323 K. In all the cases, the decomposition of the catalyst to give unactive crystalline iridium NPs was observed.

Impact of Green Cosolvents on the Catalytic Dehydrogenation of Formic Acid: The Case of Iridium Catalysts Bearing NHC-phosphane Ligands.

The catalysts [Ir(COD)(κ3-P,C,P'-PCNHCP)]BF4 and [Ir(COD)(κ2-P,C-PCNHCO)]BF4 proved to be active in the solventless dehydrogenation of formic acid. The impact of various cosolvents on the activity was evaluated, showing an outstanding improvement of the catalytic performance of [Ir(COD)(κ2-P,C-PCNHCO)]BF4] in "green" organic carbonates: namely, dimethyl carbonate (DMC) and propylene carbonate (PC). The TOF1h value for [Ir(COD)(κ2-P,C-PCNHCO)]BF4 increases from 61 to 988 h-1 upon changing from solventless conditions to a 1/1 (v/v) DMC/HCOOH mixture. However, in the case of [Ir(COD)(PCNHCP)]BF4, only a marginal improvement from 156 to 172 h-1 was observed under analogous conditions. Stoichiometric experiments allowed the identification of various key reaction intermediates, providing valuable information on their reactivity. Experimental data and DFT calculations point to the formation of dinuclear species as the catalyst deactivation pathway, which is prevented in the presence of DMC and PC.

2-Pyridone-stabilized iridium silylene/silyl complexes: structure and QTAIM analysis.

Iridium(iii) complexes of the general formula [Ir(X)(κ2-NSiiPr2)2] (NSiiPr2 = (4-methyl-pyridine-2-yloxy)diisopropylsilyl; X = Cl, 3; CF3SO3, 5; CF3CO2, 6) have been prepared and fully characterized, including X-ray diffraction studies and theoretical calculations. The presence of isopropyl substituents at the silicon atom favours the monomeric structure found in complexes 3 and 5. The short Ir-Si bond distances (2.25-2.28 Å) indicate some degree of base-stabilized silylene character of the Ir-Si bond in 3, 5 and 6 assisted by the 2-pyridone moiety. However, the shortening of these Ir-Si bonds might be a consequence of the constrained 2-pyridone geometry, and consequently the silyl character of these bonds can not be excluded. A DFT theoretical study on the nature of the Ir-Si bonds has been performed for complex 3 as well as for four other iridium complexes finding representative examples of different bonding situations between Ir and Si atoms: silylene, base-assisted silylene (both with an anionic base and with a neutral base), and silyl bonds, using the topological properties of the electron charge density. The results of these studies show that the Ir-Si bonds in Ir-NSiiPr2 complexes can be considered as an intermediate between the base-stabilized silylene and silyl cases, and therefore they have been proposed as 2-pyridone-stabilized iridium silylene/silyl bonds.

Magnetism and Heterogeneous Catalysis: In Depth on the Quantum Spin-Exchange Interactions in Pt3M (M = V, Cr, Mn, Fe, Co, Ni, and Y)(111) Alloys.

Bimetallic Pt-based alloys have drawn considerable attention in the last decades as catalysts in proton-exchange membrane fuel cells (PEMFCs) because they closely fulfill the two major requirements of high performance and good stability under operating conditions. Pt3Fe, Pt3Co, and Pt3Ni stand out as major candidates, given their good activity toward the challenging oxygen reduction reaction (ORR). The common feature across catalysts based on 3d-transition metals and their alloys is magnetism. Ferromagnetic spin-electron interactions, quantum spin-exchange interactions (QSEIs), are one of the most important energetic contributions in allowing milder chemisorption of reactants onto magnetic catalysts, in addition to spin-selective electron transport. The understanding of the role played by QSEIs in the properties of magnetic 3d-metal-based alloys is important to design and develop novel and effective electrocatalysts based on abundant and cheap metals. We present a detailed theoretical study (via density functional theory) on the most experimentally explored bimetallic alloys Pt3M (M = V, Cr, Mn, Fe, Co, Ni, and Y)(111). The investigation starts with a thorough structural study on the composition of the layers, followed by a comprehensive physicochemical description of their resistance toward segregation and their chemisorption capabilities toward hydrogen and oxygen atoms. Our study demonstrates that Pt3Fe(111), Pt3Co(111), and Pt3Ni(111) possess the same preferential multilayered structural organization, known for exhibiting specific magnetic properties. The specific role of QSEIs in their catalytic behavior is justified via comparison between spin-polarized and non-spin-polarized calculations.

Tunable from Blue to Red Emissive Composites and Solids of Silver Diphosphane Systems with Higher Quantum Yields than the Diphosphane Ligands.

PMMA composites and solids of complexes of formulas [AgX(P-P)]n [n = 1 and 2; X = Cl, NO3, ClO4, CF3COO, and OTf; P-P = dppb, xantphos, (PR2)2C2B10H10 (R = Ph and iPr)] display the whole palette of colors from blue to red upon selection of the anionic ligand (X) and the diphosphane (P-P). The diphosphane seems to play the most important role in tuning the emission energy and thermally activated delayed fluorescence (TADF) behavior. The PMMA composites of the complexes exhibit higher quantum yields than that of the diphosphane ligands and those with dppb are between 28 and 53%. Remarkably, instead of blue-green emissions which dominate the luminescence of silver diphosphane complexes in rigid phases, those with carborane diphosphanes are yellow-orange or orange-red emitters. Theoretical studies have been carried out for complexes with P-P = dppb, X = Cl; P-P = dppic, X = NO3; P-P = dppcc, X = Cl, NO3, and OTf and the mononuclear complexes [AgX(xantphos)] (X = Cl, Br). Optimization of the first excited triplet state was only possible for [AgX(xantphos)] (X = Cl and Br). A mixed MLCT and MC nature could be attributed to the S0 → T1 transition in these three-coordinated complexes.

Human riboflavin kinase: Species-specific traits in the biosynthesis of the FMN cofactor.

Human riboflavin kinase (HsRFK) catalyzes vitamin B2 (riboflavin) phosphorylation to flavin mononucleotide (FMN), obligatory step in flavin cofactor synthesis. HsRFK expression is related to protection from oxidative stress, amyloid-ß toxicity, and some malignant cancers progression. Its downregulation alters expression profiles of clock-controlled metabolic-genes and destroys flavins protection on stroke treatments, while its activity reduction links to protein-energy malnutrition and thyroid hormones decrease. We explored specific features of the mechanisms underlying the regulation of HsRFK activity, showing that both reaction products regulate it through competitive inhibition. Fast-kinetic studies show that despite HsRFK binds faster and preferably the reaction substrates, the complex holding both products is kinetically most stable. An intricate ligand binding landscape with all combinations of substrates/products competing with the catalytic complex and exhibiting moderate cooperativity is also presented. These data might contribute to better understanding the molecular bases of pathologies coursing with aberrant HsRFK availability, and envisage that interaction with its client-apoproteins might favor FMN release. Finally, HsRFK parameters differ from those of the so far evaluated bacterial counterparts, reinforcing the idea of species-specific mechanisms in RFK catalysis. These observations support HsRFK as potential therapeutic target because of its key functions, while also envisage bacterial RFK modules as potential antimicrobial targets.

A Bond Charge Model Ansatz for Intrinsic Bond Energies: Application to C-C Bonds.

A simple bond charge model is proposed to predict intrinsic bond energies. Model parameters can be derived from the topology of the electron localization function and equilibrium geometries through classic considerations. Results for carbon-carbon covalent bonds are shown to be very accurate in different chemical environments. Insight can be extracted from the application of the model due to its elementary construction and simple mathematical formulation. The remarkable robustness of the fitted model highlights how different density functional approximations relate geometries, densities, and energies.

Localizing electron density errors in density functional theory.

The accuracy of different density functional approximations is assessed through the use of quantum chemical topology on molecular electron densities. In particular, three simple yet ever-important systems are studied: N2, CO and ethane. Our results exemplify how real-space descriptors can help understand the sources of errors in density functional theory, avoiding unwanted error compensation present in simplified statistical metrics. Errors in "well-built" functionals are shown to be concentrated in chemically meaningful regions of space, and hence they are predictable. Conversely, strongly parametrized functionals show isotropic errors that cannot be traced back to chemically transferable units. Moreover, we will show that energetic corrections are mapped back into improvements in the density in chemically meaningful regions. These results point at the relevance of real-space perspectives when parametrizing or relating energy and density errors.

Towards the competent conformation for catalysis in the ferredoxin-NADP+ reductase from the Brucella ovis pathogen.

Brucella ovis encodes a bacterial subclass 1 ferredoxin-NADP(H) reductase (BoFPR) that, by similarity with other FPRs, is expected either to deliver electrons from NADPH to the redox-based metabolism and/or to oxidize NADPH to regulate the soxRS regulon that protects bacteria against oxidative damage. Such potential roles for the pathogen survival under infection conditions make of interest to understand and to act on the BoFPR mechanism. Here, we investigate the NADP+/H interaction and NADPH oxidation by hydride transfer (HT) to BoFPR. Crystal structures of BoFPR in free and in complex with NADP+ hardly differ. The latter shows binding of the NADP+ adenosine moiety, while its redox-reactive nicotinamide protrudes towards the solvent. Nonetheless, pre-steady-state kinetics show formation of a charge-transfer complex (CTC-1) prior to the hydride transfer, as well as conversion of CTC-1 into a second charge-transfer complex (CTC-2) concomitantly with the HT event. Thus, during catalysis nicotinamide and flavin reacting rings stack. Kinetic data also identify the HT itself as the rate limiting step in the reduction of BoFPR by NADPH, as well as product release limiting the overall reaction. Using all-atom molecular dynamics simulations with a thermal effect approach we are able to visualise a potential transient catalytically competent interaction of the reacting rings. Simulations indicate that the architecture of the FAD folded conformation in BoFPR might be key in catalysis, pointing to its adenine as an element to orient the reactive atoms in conformations competent for HT.

Synthesis and reactivity at the Ir-MeTpm platform: from κ1-N coordination to κ3-N-based organometallic chemistry.

Reaction of [Ir(µ-Cl)(COE)2]2 (COE = cis-cyclooctene) with tris(3,5-dimethylpyrazol-1-yl)methane (MeTpm) affords [IrCl(κ1-N-MeTpm)(COD)] (1) (COD = 1,5-cyclooctadiene). The formation of 1 implies the transfer dehydrogenation of a COE ligand to give COD and COA (cyclooctane). A mechanistic proposal based on DFT calculations that explains this iridium promoted process has been disclosed. Additionally, reactivity studies have allowed the preparation and characterization, including determination of the molecular structures of a number of iridium complexes with the MeTpm ligand in κ1, κ2 or κ3-N coordination modes. Moreover, the first example of an Ir-cyclooctyl complex featuring hydride and carbonyl ligands, whose solid state structure has been determined by X-ray diffraction methods, is reported.

On the Role of Ferromagnetic Interactions in Highly Active Mo-Based Catalysts for Ammonia Synthesis.

Reactions involving nitrogen fixation and transfer are of great industrial interest. In this regard, unveiling all the physical principles that determine their activity would be enormously beneficial for the rational design of novel catalysts with improved performance. Within this context, this work explores the activity of bulk molybdenum-based transition metal nitrides in ammonia synthesis. Our results highlight that the most active compositions show increasing ferromagnetism in the metal-nitrogen bonds, which constitute the active sites. We observe that the total spin accumulated in the bonds at the active sites is a physically meaningful descriptor to discriminate optimum catalysts. Higher activities are associated with ferromagnetic phases, and the underlying reason is an enhanced overlapping of the electronic wavefunctions; which also make the reaction steps spin-sensitive. These finding provides strong evidence of the general influence of electrons magnetic moment in catalysis, being part of the specific field of spintro-catalysis.

Proteasome versus Thioredoxin Reductase Competition as Possible Biological Targets in Antitumor Mixed Thiolate-Dithiocarbamate Gold(III) Complexes.

New mixed gold(III) derivatives with dithiocarbamate and thiolate ligands have been synthesized and characterized. They display high anticancer activity against colon cancer cell lines without affecting to differentiated enterocytes, high stability in phosphate-buffered saline solution, and resistance to gold reduction in the presence of reducing agents in the majority of the derivatives. Some of them show interaction with thioredoxin reductase as derived from in vitro analysis and computational studies. However, a competition between this enzyme and proteasome is detected in cells, which is corroborated by the determination of proteasomal chymotrypsin-like activity inhibition. In addition, some of these dithiocarbamate gold(III) derivatives reduce cell viability and proliferation by intrinsic apoptotic pathway, with changes in mitochondrial membrane potential, cytochrome c release and caspase-3 activation. Consequently, our results show new complexes with proteasome as possible target in colorectal cancer.

A well-defined NHC-Ir(iii) catalyst for the silylation of aromatic C-H bonds: substrate survey and mechanistic insights.

A well-defined NHC-Ir(iii) catalyst, [Ir(H)2(IPr)(py)3][BF4] (IPr = 1,3-bis-(2,6-diisopropylphenyl)imidazol-2-ylidene), that provides access to a wide range of aryl- and heteroaryl-silanes by intermolecular dehydrogenative C-H bond silylation has been prepared and fully characterized. The directed and non-directed functionalisation of C-H bonds has been accomplished successfully using an arene as the limiting reagent and a variety of hydrosilanes in excess, including Et3SiH, Ph2MeSiH, PhMe2SiH, Ph3SiH and (EtO)3SiH. Examples that show unexpected selectivity patterns that stem from the presence of aromatic substituents in hydrosilanes are also presented. The selective bisarylation of bis(hydrosilane)s by directed or non-directed silylation of C-H bonds is also reported herein. Theoretical calculations at the DFT level shed light on the intermediate species in the catalytic cycle and the role played by the ligand system on the Ir(iii)/Ir(i) mechanism.