Treatment of Substitution and Rearrangement Mechanisms of Transition Metal Complexes with Quantum Chemical Methods

Supramolecular delivery of dinuclear ruthenium and osmium MCU inhibitors

The transmembrane protein known as the mitochondrial calcium uniporter (MCU) mediates the influx of calcium ions (Ca2+) into the mitochondrial matrix. An overload of mitochondrial Ca2+ ( m Ca2+) is directly linked to damaging effects in pathological conditions. Therefore, inhibitors of the MCU are important chemical biology tools and therapeutic agents. Here, two new analogues of previously reported Ru- and Os-based MCU inhibitors Ru265 and Os245, of the general formula [(C10H15CO2)M(NH3)4(μ-N)M(NH3)4(O2CC10H15)](CF3SO3)3, where M = Ru (1) or Os (2), are reported. These analogues bear adamantane functional groups, which were installed to act as guests for the host molecule cucurbit-[7]-uril (CB[7]). These complexes were characterized and analyzed for their efficiency as guests for CB[7]. As shown through a variety of spectroscopic techniques, each adamantane ligand is encapsulated into one CB[7], affording a supramolecular complex of 1 : 2 stoichiometry. The biological effects of these compounds in the presence and absence of two equiv. CB[7] were assessed. Both complexes 1 and 2 exhibit enhanced cellular uptake compared to the parent compounds Ru265 and Os245, and their uptake is increased further in the presence of CB[7]. Compared to Ru265 and Os245, 1 and 2 are less potent as m Ca2+ uptake inhibitors in permeabilized cell models. However, in intact cell systems, 1 and 2 inhibit the MCU at concentrations as low as 1 μM, marking an advantage over Ru265 and Os245 which require an order of magnitude higher doses for similar biological effects. The presence of CB[7] did not affect the inhibitory properties of 1 and 2. Experiments in primary cortical neurons showed that 1 and 2 can elicit protective effects against oxygen-glucose deprivation at lower doses than those required for Ru265 or Os245. At low concentrations, the protective effects of 1 were modulated by CB[7], suggesting that supramolecular complex formation can play a role in these biological conditions. The in vivo biocompatibility of 1 was investigated in mice. The intraperitoneal administration of these compounds and their CB[7] complexes led to time-dependent induction of seizures with no protective effects elicited by CB[7]. This work demonstrates the potential for supramolecular interactions in the development of MCU inhibitors.

Alkane C-H activation and ligand exchange on silica supported d0 metal alkylidenes: relevance to alkane metathesis

In this work, we study the ligand exchange process between an alkane and a series of silica supported metal alkylidenes, which may occur by different pathways: C-H addition, σ-bond metathesis, and α-H abstraction. The results indicate that the α-H abstraction pathway is the preferred one, regardless of the catalyst and ligands. This is in contrast to the expected preference for the C-H addition route. When looking for the origin of this preference, our calculations revealed that the α-H abstraction pathway is driven by entropy, which favors the initial dissociation of the alkyl ligand from the catalyst.

Role of the Enzymatic Environment in the Reactivity of the AuIII-C^N^C Anticancer Complexes

The action mechanism of anticancer gold(III) complexes is a multi-step process and depends on their redox stability. First, the gold(III) complex undergoes a ligand exchange reaction in the presence of cellular thiols, such as those available in the active site of the enzyme TrxR, and then, the Au^III → Au^I reduction occurs. Most experimental and theoretical studies describe these processes under chemical conditions without considering the enzyme structure effect. In the present study, molecular models are proposed for the [Au^III(C^N^C)(SHCys-R)]⁺ adduct, with the [Au^III(C^N^C)]⁺ moiety bonded to the Cys498 residue in the C-terminal arm of the TrxR. This one represents the product of the first ligand exchange reaction. Overall, our results suggest that the exchange of the auxiliary ligand (for instance, Cl^- to S-R) plays a primary role in increasing the reduction potential, with the enzyme structure having a small effect. The parent compound [Au^III(C^N^C)Cl] has E° = -1.20 V, which enlarges to -0.72 V for [Au^III(C^N^C)CH₃SH]⁺ and to -0.65 V for the largest model studied, Au-trx. In addition to the effect of the enzyme structure on the redox stability, we also analyze the Au transfer to the enzyme using a small peptide model (a tetramer). This reaction is dependent on the Cys497 protonation state. Thermodynamics and kinetic analysis suggests that the C^N^C ligand substitution by Cys497 is an exergonic process, with an energy barrier estimated at 20.2 kcal mol^-1. The complete transfer of the Au ion to the enzyme's active site would lead to a total loss of enzyme activity, generating oxidative damage and, consequently, cancer cell death.

The solvation effect on the rattling behaviour of the hydrated excess proton in water

The solvation effect on the kinetic rattling behaviour of the hydrated excess proton H⁺(aq) in water is theoretically modeled by using density functional theory (DFT) and the quantum chemical cluster model (CM). To test the solvation effects on the proton morphology and rattling kinetics, different solvation models for the proton are constructed based on the gas phase (GP) Zundel cation, which include the gas phase-polarizable continuum model (GP-PCM), the gas phase-supermolecule model (GP-SM), and the gas phase-supermolecule-polarizable continuum model (GP-SM-PCM). These solvation models consider either one or both of the short- and long-range solute-solvent interactions. Meanwhile, 1 to 6 explicit solvent water molecules (N_m' = 1-6) are added around the GP Zundel cation to test different explicit solvation environments. The calculation results show that the solvation environment has an important influence on the morphology and rattling kinetics of H⁺(aq). The proton rattling pathways are obtained only under the condition that both symmetrical explicit solvation environments and implicit bulk solvents are present. The zero-point contribution reduces the reaction energy barrier and enables the rattling to occur spontaneously at room temperature. The theoretical modeling results provide new insights into the microscopic kinetic behaviour of proton rattling in water at the molecular level, which are helpful in studying the proton transfer mechanism in aqueous systems.

Hierarchy of Commonly Used DFT Methods for Predicting the Thermochemistry of Rh-Mediated Chemical Transformations

The accuracy and reliability of 17 commonly used density functionals in conjunction with Poisson-Boltzmann finite solvation model were gauged for predicting the free energy of Rh(I)- and Rh(III)-mediated chemical transformations such as ligand exchange, hydride elimination, dihydrogen elimination, chloride affinity, and silyl hydride bond activation reactions. In total, six Rh-mediated reactions were examined, and the computed density functional theory results were then subjected to comparison with the experimentally reported values. For reaction A, involving replacement of N₂ with η²-H₂ over Rh(I), MPWB1K-D3, B3PW91, B3LYP, and BHandHYLP emerged to be the best functionals of all the tested methods in terms of their deviations ≤2 kcal mol^-1 from experimental data. For reaction B, in which exchange of η²-C₂H₄ with N₂ over Rh(I) takes place, MPWB1K-D3 and M06-2X-D3 functionals performed the best, while as for reaction C (hydride elimination reaction in Rh(III) complex), it is PBE functional that showed impressive performance. Similarly, for reaction D (H₂ elimination reaction in Rh(III) complex), PBE0-D3 and PBE-D3 showed exceptional results compared to other functionals. For reaction E (H₂O/Cl^- exchange), the PBE0 again shows impressive performance as compared to other functionals. For reaction F (Si-H activation), M06-2X-D3, PBE0-D3, and MPWB1K-D3 functionals are undoubtedly the best functionals. Overall, PBE0-D3 and MPWB1K-D3 functionals were impressive in all cases with lowest mean unsigned errors (3.2 and 3.4 kcal mol^-1, respectively) with respect to experimental Gibbs free energies. Thus, these two functionals are recommended for studying Rh-mediated chemical transformations.

Density functional theory studies on the solvent effects in Al(H2O)63+ water-exchange reactions: the number and arrangement of outer-sphere water molecules

Density functional theory (DFT) calculations combined with cluster models are performed at the B3LYP/6-311+G(d,p) level for investigating the solvent effects in Al(H₂O)₆³⁺ water-exchange reactions. A "One-by-one" method is proposed to obtain the most representative number and arrangement of explicit H₂Os in the second hydration sphere. First, all the possible ways to locate one explicit H₂O in second sphere (N_m' = 1) based on the gas phase structure (N_m' = 0) are examined, and the optimal pathway (with the lowest energy barrier) for N_m' = 1 is determined. Next, more explicit H₂Os are added one by one until the inner-sphere is fully hydrogen bonded. Finally, the optimal pathways with N_m' = 0-7 are obtained. The structural and energetic parameters as well as the lifetimes of the transition states are compared with the results obtained with the "Independent-minimum" method and the "Independent-average" method, and all three methods show that the pathway with N_m' = 6 may be representative. Our results give a new idea for finding the representative pathway for water-exchange reactions in other hydrated metal ion systems.

Pressure Dependence of Carbonate Exchange with [NpO2(CO3)3]4- in Aqueous Solutions

The rates of ligand exchange into the geochemically important [NpO₂(CO₃)₃]^4- aqueous complex are measured as a function of pressure in order to complement existing data on the isostructural [UO₂(CO₃)₃]^4- complex. Experiments are conducted at pH conditions where the rate of exchange is independent of the proton concentration. Unexpectedly, the experiments show a distinct difference in the pressure dependencies of rates of exchange for the uranyl and neptunyl complexes.

Pivotal Role of a Pentacoordinate (3)MC State on the Photocleavage Efficiency of a Thioether Ligand in Ruthenium(II) Complexes: A Theoretical Mechanistic Study

A mechanistic study of the photocleavage of the methylthioethanol ligand (Hmte) in the series of ruthenium complexes [Ru(tpy)(N-N)(Hmte)](2+) (tpy = 2,2':6',2″-terpyridine, N-N = bpy (2,2'-bipyridine), biq (2,2'-biquinoline), dcbpy (6,6'-dichloro-2,2'-bipyridine), dmbpy (6,6'-dimethyl-2,2'-bipyridine)) was performed using density functional theory. These studies reveal the decisive role of two quasi-degenerate triplet metal-centered states, denoted (3)MChexa and (3)MCpenta, on the lowest triplet potential energy surface. It also shows how the population of the specific pentacoordinate (3)MCpenta state, characterized by a geometry more accessible for the attack of a solvent molecule, is a key step for the efficiency of the photosubstitution reaction. The difference in the photosubstitution quantum yields experimentally observed for this series of complexes (from φ = 0.022 for N-N = bpy up to φ = 0.30 for N-N = dmbpy) is rationalized by the existence of this (3)MCpenta photoreactive state and by the different topologies of the triplet excited-state potential energy surfaces, rather than by the sole steric properties of these polypyridinyl ligands.

Moving from Classical Ru-NHC to Neutral or Charged Rh-NHC Based Catalysts in Olefin Metathesis

Considering the versatility of oxidation states of rhodium together with the successful background of ruthenium-N-heterocyclic carbene based catalysts in olefin metathesis, it is envisaged the exchange of the ruthenium of the latter catalysts by rhodium, bearing an open-shell neutral rhodium center, or a +1 charged one. In the framework of in silico experiments, density functional theory (DFT) calculations have been used to plot the first catalytic cycle that as a first step includes the release of the phosphine. DFT is, in this case, the tool that allows the discovery of the less endergonic reaction profile from the precatalytic species for the neutral catalyst with respect to the corresponding ruthenium one; increasing the endergonic character when dealing with the charged system.

New perspectives in organolanthanide chemistry from redox to bond metathesis: insights from theory

A fifteen year contribution of computational studies carried out in close synergy with experiments is summarized.

Identification of an Isothiocyanate on the HypEF Complex Suggests a Route for Efficient Cyanyl-Group Channeling during [NiFe]-Hydrogenase Cofactor Generation

[NiFe]–hydrogenases catalyze uptake and evolution of H₂ in a wide range of microorganisms. The enzyme is characterized by an inorganic nickel/ iron cofactor, the latter of which carries carbon monoxide and cyanide ligands. In vivo generation of these ligands requires a number of auxiliary proteins, the so–called Hyp family. Initially, HypF binds and activates the precursor metabolite carbamoyl phosphate. HypF catalyzes removal of phosphate and transfers the carbamate group to HypE. In an ATP–dependent condensation reaction, the C–terminal cysteinyl residue of HypE is modified to what has been interpreted as thiocyanate. This group is the direct precursor of the cyanide ligands of the [NiFe]–hydrogenase active site cofactor. We present a FT–IR analysis of HypE and HypF as isolated from E. coli. We follow the HypF–catalyzed cyanation of HypE in vitro and screen for the influence of carbamoyl phosphate and ATP. To elucidate on the differences between HypE and the HypEF complex, spectro–electrochemistry was used to map the vibrational Stark effect of naturally cyanated HypE. The IR signature of HypE could ultimately be assigned to isothiocyanate (–N=C=S) rather than thiocyanate (–S–C≡N). This has important implications for cyanyl–group channeling during [NiFe]–hydrogenase cofactor generation.

Mechanism of Formation of Copper(II) Chloro Complexes Revealed by Transient Absorption Spectroscopy and DFT/TDDFT Calculations

Copper(II) complexes are extremely labile with typical ligand exchange rate constants on the order of 10(6)-10(9) M(-1) s(-1). As a result, it is often difficult to identify the actual formation mechanism of these complexes. In this work, using UV-vis transient absorption when probing in a broad time range (20 ps to 8 μs) in conjunction with DFT/TDDFT calculations, we studied the dynamics and underlying reaction mechanisms of the formation of extremely labile copper(II) CuCl4(2-) chloro complexes from copper(II) CuCl3(-) trichloro complexes and chloride ions. These two species, produced via photochemical dissociation of CuCl4(2-) upon 420 nm excitation into the ligand-to-metal-charge-transfer electronic state, are found to recombine into parent complexes with bimolecular rate constants of (9.0 ± 0.1) × 10(7) and (5.3 ± 0.4) × 10(8) M(-1) s(-1) in acetonitrile and dichloromethane, respectively. In dichloromethane, recombination occurs via a simple one-step addition. In acetonitrile, where [CuCl3](-) reacts with the solvent to form a [CuCl3CH3CN](-) complex in less than 20 ps, recombination takes place via ligand exchange described by the associative interchange mechanism that involves a [CuCl4CH3CN](2-) intermediate. In both solvents, the recombination reaction is potential energy controlled.

Comparative Assessment of DFT Performances in Ru- and Rh-Promoted σ-Bond Activations

In this work, the performances of 19 density functional theory (DFT) methods are calibrated comparatively on Ru- and Rh-promoted σ-bond (C-H, O-H, and H-H) activations. DFT calibration reference is generated from explicitly correlated coupled cluster CCSD(T)-F12 calculations, and the 4s4p core-valence correlation effect of the two 4d platinum group transition metals is also included. Generally, the errors of DFT methods for calculating energetics of Ru-/Rh-mediated reactions appear to correlate more with the magnitude of energetics itself than other factors such as metal identity. For activation energy calculations, the best performing functionals for both Ru and Rh systems are MN12SX < CAM-B3LYP < M06-L < MN12L < M06 < ωB97X < B3LYP < LC-ωPBE (in the order of increasing mean unsigned deviations, MUDs, of less than 2 kcal/mol). For reaction energy calculations, best functionals with MUDs less than 2 kcal/mol are PBE0 < CAM-B3LYP ≈ N12SX. The effect of the DFT empirical dispersion correction on the performance of the DFT methods is beneficial for most density functionals tested in this work, reducing their MUDs to different extents. After including empirical dispersion correction, ωB97XD, B3LYP-D3, and CAM-B3LYP-D3 (PBE0-D3, B3LYP-D3, and ωB97XD) are the three best performing DFs for activation energy (reaction energy) calculations, from which B3LYP-D3 and ωB97XD can notably be recommended uniformly for both the reaction energy and reaction barrier calculations. The good performance of B3LYP-D3 in quantitative description of the energetic trends further adds value to B3LYP-D3 and singles this functional out as a reasonable choice in the Ru/Rh-promoted σ-bond activation processes.

Structure and properties of the precursor/successor complex and transition state of the CrCl²⁺/Cr²⁺ electron self-exchange reaction via the inner-sphere pathway

The electron self-exchange reaction CrCl(OH2)5(2+) + Cr(OH2)6(2+) → Cr(OH2)6(2+) + CrCl(OH2)5(2+), proceeding via the inner-sphere pathway, was investigated with quantum-chemical methods. Geometry and vibrational frequencies of the precursor/successor (P/S) complex, (H2O)5Cr(III)ClCr(II)(OH2)5(4+)/(H2O)5Cr(II)ClCr(III)(OH2)5(4+), and the transition state (TS), (H2O)5CrClCr(OH2)5(4+‡), were computed with density functional theory (DFT) and conductor polarizable continuum model hydration. Consistent data were obtained solely with long-range-corrected functionals, whereby in this study, LC-BOP was used. Bent and linear structures were computed for the TS and P/S. The electronic coupling matrix element (H(ab)) and the reorganizational energy (λ) were calculated with multistate extended general multiconfiguration quasi-degenerate second-order perturbation theory. The nuclear tunneling factor (Γ(n)), the nuclear frequency factor (ν(n)), the electronic frequency factor (ν(el)), the electron transmission coefficient (κ(el)), and the first-order rate constant (k(et)) for the electron-transfer step (the conversion of the precursor complex into the successor complex) were calculated based on the imaginary frequency (ν(‡)) of the TS, the Gibbs activation energy (ΔG(‡)), H(ab), and λ. The formation of the precursor complex via water substitution at Cr(OH2)6(2+) was also investigated with DFT and found to be very fast. Thus, the electron-transfer step is rate-determining. For the substitution reaction, only a bent TS structure could be obtained. The overall rate constant (k) was estimated as the product K(A)k(et), whereby K(A) is the equilibrium constant for the formation of the ion aggregate of the reactants Cr(OH2)6(2+) and CrCl(OH2)5(2+), Cr(H2O)6·CrCl(OH2)5(4+) (IAR). k calculated for the bent and linear isomers agrees with the experimental value.

Understanding the rates and molecular mechanism of water-exchange around aqueous ions using molecular simulations

Solvation processes occurring around aqueous ions are of fundamental importance in physics, chemistry, and biology. Over the past few decades, several experimental and theoretical studies were devoted to understanding ion solvation and the processes involved in it. In this article, we present a summary of our recent efforts that, through computer simulations, focused on providing a comprehensive understanding of solvent-exchange processes around aqueous ions. To accomplish these activities, we have looked at the mechanistic properties associated with the water-exchange process, such as potentials of mean force, time-dependent transmission coefficients, and the corresponding rate constants using transition state theory, the reactive flux method, and Grote-Hynes treatments of the dynamic response of the solvent.

Photooxidation and photoaquation of iron hexacyanide in aqueous solution: A picosecond X-ray absorption study

We present a picosecond Fe K-edge absorption study of photoexcited ferrous and ferric hexacyanide in water under 355 and 266 nm excitation. Following 355 nm excitation, the transient spectra for the ferrous and ferric complexes exhibit a red shift of the edge reflecting an increased electron density at the Fe atom. For the former, an enhanced pre-edge transition is also observed. These observations are attributed to the aquated [Fe(CN)5OH2](3-) species, based on quantum chemical calculations which also provide structural parameters. Upon 266 nm excitation of the ferric complex, a transient reminiscent of the aquated species is observed (appearance of a pre-edge feature and red shift of the edge) but it is different from that obtained under 355 nm excitation. This points to a new reaction channel occurring through an intermediate state lying between these two excitation energies. Finally, 266 nm excitation of the ferrous species is dominated by the photooxidation channel with formation of the ferric complex as main photoproduct. However, we observe an additional minor photoproduct, which is identical to the 266 nm generated photoproduct of the ferric species, suggesting that under our experimental conditions, the pump pulse photooxidises the ferrous complex and re-excites the primary ferric photoproduct.

1H and 17O NMR relaxometric and computational study on macrocyclic Mn(II) complexes

Herein we report a detailed 1H and 17O relaxometric investigation of Mn(II) complexes with cyclen-based ligands such as 2-(1,4,7,10-tetraazacyclododecan-1-yl)acetic acid (DO1A), 2,2'-(1,4,7,10-tetraazacyclododecane-1,4-diyl)diacetic acid (1,4-DO2A), 2,2'-(1,4,7,10-tetraazacyclododecane-1,7-diyl)diacetic acid (1,7-DO2A), and 2,2',2"-(1,4,7,10-tetraazacyclododecane-1,4,7-triyl)triacetic acid (DO3A). The Mn(II) complex with the heptadentate ligand DO3A does not have inner sphere water molecules (q = 0), and therefore, the metal ion is most likely seven-coordinate. The hexadentate DO2A ligand has two isomeric forms: 1,7-DO2A and 1,4-DO2A. The Mn(II) complex with 1,7-DO2A is predominantly six-coordinate (q = 0). In aqueous solutions of [Mn(1,4-DO2A)], a species with one coordinated water molecule (q = 1) prevails largely, whereas a q = 0 form represents only about 10% of the overall population. The Mn(II) complex of the pentadentate ligand DO1A also contains a coordinated water molecule. DFT calculations (B3LYP model) are used to obtain information about the structure of this family of closely related complexes in solution, as well as to determine theoretically the 17O and 1H hyperfine coupling constants responsible for the scalar contribution to 17O and 1H NMR relaxation rates and 17O NMR chemical shifts. These calculations provide 17O A/ħ values of ca. 40 × 10(6) rad s(-1), in good agreement with experimental data. The [Mn(1,4-DO2A)(H2O)] complex is endowed with a relatively fast water exchange rate (k(ex)298 = 11.3 × 10(8) s(-1)) in comparison to the [Mn(EDTA)(H2O)]2- analogue (k(ex)298 = 4.7 × 10(8) s(-1)), but about 5 times lower than that of the [Mn(DO1A)(H2O)]+ complex (k(ex)298 = 60 × 10(8) s(-1)). The water exchange rate measured for the latter complex represents the highest water exchange rate ever measured for a Mn(II) complex.

Computational insight into the initial steps of the Mars-van Krevelen mechanism: electron transfer and surface defects in the reduction of polyoxometalates

Metal oxides as a rule oxidize and oxygenate substrates via the Mars-van Krevelen mechanism. A well-defined α-Keggin polyoxometalate, H(5)PV(2)Mo(10)O(40), can be viewed as an analogue of discrete structure that reacts via the Mars-van Krevelen mechanism both in solution and in the gas phase. Guided by previous experimental observations, we have studied the key intermediates on the reaction pathways of its reduction by various compounds using high-level DFT calculations. These redox reactions of polyoxometalates require protons, and thus such complexes were explicitly considered. First, the energetics of outer-sphere proton and electron transfer as well as coupled proton and electron transfer were calculated for seven substrates. This was followed by identification of possible key intermediates on the subsequent reaction pathways that feature displacement of the metal atom from the Keggin structure and coordinatively unsaturated sites on the H(5)PV(2)Mo(10)O(40) surface. Such metal defects are favored at vanadium sites. For strong reducing agents the initial outer-sphere electron transfer, alone or possibly coupled with proton transfer, facilitates formation of metal defects. Subsequent coordination allows for formation of reactive ensembles on the catalyst surface, for which the selective oxygen-transfer step becomes feasible. Weak reducing agents do not facilitate defect formation by outer-sphere electron and/or proton transfers, and thus formation of metal defect structures prior to the substrate activation is suggested as an initial step. Calculated geometries and energies of metal defect structures support experimentally observed intermediates and demonstrate the complex nature of the Mars-van Krevelen mechanism.