Mechanism of the Formation of Carboxylate from Alcohols and Water Catalyzed by a Bipyridine-Based Ruthenium Complex: A Computational Study

The catalytic mechanism for oxidizing alcohols to carboxylate in basic aqueous solution by the bipyridine-based ruthenium complex <b>2</b> (BIPY-PNN)­Ru­(H)­(Cl)­(CO) (<i>Nat. Chem.</i> <b>2013</b>, <i>5</i>, 122) is investigated by density functional theory (DFT) with the ωB97X-D functional. Using water as the oxygen donor with liberation of dihydrogen represents a safe and clean process for such oxidations. Under NaOH, the active catalyst is <b>3</b> (BIPY-PNN)­Ru­(H)­(CO). Four steps are involved: dehydrogenation of alcohol to aldehyde (Step 1); coupling of aldehyde and water to form the gem-diol (Step 2); dehydrogenation of gem-diol to carboxylic acid (Step 3); and deprotonation of carboxylic acid to carboxylate anion under base (Step 4). The dehydrogenations of alcohol (Step 1) and gem-diol (Step 3) prefer the double hydrogen transfer mechanism to the β-H elimination mechanism. The coupling of aldehyde and water (Step 2) proceeds through cleavage of water by catalyst <b>3</b> followed by concerted hydroxyl and hydrogen transfer to the aldehyde. The formation of the carboxylate anion occurs via direct deprotonation of the carboxylic acid under base (Step 4), while in the absence of base a stable carboxylic acid-addition complex <b>6</b> was formed. Added base was found to play important roles in the generation of catalyst <b>3</b> from both the stable carboxylic acid-addition complex <b>6</b> and its chloride precursor complex <b>2</b>. The chemoselectivity for the formation of carboxylic acid rather than ester is ascribed to the favorable cleavage of water and the subsequent generation of the stable carboxylate anion that leads to carboxylic acid upon acidification

Molybdenum Trihydride Complexes: Computational Determinations of Hydrogen Positions and Rearrangement Mechanisms

In crystal structures of the molybdenum complexes [(1,2,4-C₅H₂^<i>t</i>Bu₃)­Mo­(PMe₃)₂H₃] (Cp^<i>t</i>Bu₃) and [(C₅H^<i>i</i>Pr₄)­Mo­(PMe₃)₂H₃] (Cp^<i>i</i>Pr₄), the Mo-bound hydrogen positions were resolved for Cp^<i>t</i>Bu₃, but not for Cp^<i>i</i>Pr₄. NMR experiments revealed the existence of an unknown mechanism for hydrogen atom exchange in these molecules, which can be “frozen out” for Cp^<i>t</i>Bu₃ but not for Cp^<i>i</i>Pr₄. Density functional theory calculations of the most stable conformations for both complexes in the gas phase and in a continuum solvent model indicate that the H’s of the Cp^<i>i</i>Pr₄ complex are unresloved because of their disorder, which does not occur for Cp^<i>t</i>Bu₃. A corresponding examination of alternative rearrangement pathways shows that the rearrangements of the H’s could occur by two mechanisms: parallel to the cyclopentadienyl (Cp) ring in a single step and perpendicular to the Cp ring in two steps. The parallel pathway is preferred for both molecules, but it has a lower energy barrier for Cp^<i>i</i>Pr₄ than for Cp^<i>t</i>Bu₃

Molybdenum Trihydride Complexes: Computational Model of Oxidatively Induced Reductive Elimination of Dihydrogen

Recent experimental work shows that the 18-electron molybdenum complexes (1,2,4-C₅H₂<i>t</i>Bu₃)­Mo­(PMe₃)₂H₃ (Cp^<i>t</i>BuMoH₃) and (C₅H<i>i</i>Pr₄)­Mo­(PMe₃)₂H₃ (Cp^<i>i</i>PrMoH₃) undergo oxidatively induced reductive elimination of dihydrogen (H₂), slowly forming the 15-electron monohydride species in tetrahydrofuran and acetonitrile. The 17-electron [Cp^<i>t</i>BuMoH₃]⁺ derivative was stable enough to be characterized by X-ray diffraction, while [Cp^<i>i</i>PrMoH₃]⁺ was not. Density functional theory calculations of the H₂ elimination pathways for both complexes in the gas phase and in a continuum solvent model indicate that H₂ elimination from [Cp^<i>i</i>PrMoH₃]⁺ has a lower barrier than that from [Cp^<i>t</i>BuMoH₃]⁺. Further, a specific solvent association, which is stronger for [Cp^<i>t</i>BuMoH₃]⁺ than for [Cp^<i>i</i>PrMoH₃]⁺, contributes to the stability of the former. In agreement with the experimental observations, the calculations predict that [Cp^<i>t</i>BuMoH₃]⁺ would be in a quartet state at room temperature and a doublet state at 4.2 K, while [Cp^<i>i</i>PrMoH₃]⁺ is in a doublet state even at room temperature

Role of the Chemically Non-Innocent Ligand in the Catalytic Formation of Hydrogen and Carbon Dioxide from Methanol and Water with the Metal as the Spectator

The catalytic mechanism for the production of H₂ and CO₂ from CH₃OH and H₂O by [K­(dme)₂]­[Ru­(H) (trop₂dad)] (K­(dme)₂.<b>1_exp</b>) was investigated by density functional theory (DFT) calculations. Since the reaction occurs under mild conditions and at reasonable rates, it could be considered an ideal way to use methanol to store hydrogen. <i>The predicted mechanism begins with the dehydrogenation of methanol to formaldehyde through a new ligand–ligand bifunctional mechanism, where two hydrogen atoms of CH₃OH eliminate to the ligand’s N and C atoms, a mechanism that is more favorable than the previously known mechanisms, β-H elimination, or the metal–ligand bifunctional</i>. The key initiator of this first step is formed by migration of the hydride in <b>1</b> from the ruthenium to the meta-carbon atom, which generates <b>1</b>″ with a frustrated Lewis pair in the ring between N and C. Hydroxide, formed when <b>1</b>″ cleaves H₂O, reacts rapidly with CH₂O to give H₂C­(OH)­O^–, which subsequently donates a hydride to <b>6</b> to generate HCOOH and <b>5</b>. HCOOH then protonates <b>5</b> to give formate and a neutral complex, <b>4</b>, with a fully hydrogenated ligand. The hydride of formate transfers to <b>6</b>, releasing CO₂. The fully hydrogenated complex, <b>4</b>, is first deprotonated by OH^– to form <b>5</b>, which then releases hydrogen to regenerate the catalyst, <b>1</b>″. <i>In this mechanism, which explains the experimental observations, the whole reaction occurs on the chemically non-innocent ligand with the ruthenium atom appearing as a spectator</i>

Biomimetics of [NiFe]-Hydrogenase: Nickel- or Iron-Centered Proton Reduction Catalysis?

The [NiFe] hydrogenase (H2ase) has been characterized in the Ni-R state with a hydride bridging between Fe and Ni but displaced toward the Ni. In nearly all of the synthetic Ni-R models reported so far, the hydride ligand is either displaced toward Fe, or terminally bound to Fe. Recently, a structural and functional [NiFe]-H2ase mimic (Nat. Chem. 2016, 8, 1054−1060) was reported to produce H₂ catalytically via EECC mechanism through a Ni-centered hydride intermediate like the enzyme. Here, a comprehensive DFT study shows a much lower energy route via an E­[ECEC] mechanism through an Fe-centered hydride intermediate. Although catalytic H₂ production occurs at the potential corresponding to the complex’s second reduction, a third electron is needed to induce the second proton addition from the weak acid. The first two-electron reductions and a proton addition produce a semibridging hydride with a short Fe–H bond like other structured [NiFe]-biomimetics, but this species is not basic enough to add another proton from the weak acid without the third electron. The calculated mechanism provides insight into the origin of this structure in the enzyme

Carbon–Hydrogen Bond Activation in Bis(2,6-dimethylbenzenethiolato)­tris(trimethylphosphine)ruthenium(II): Ligand Dances and Solvent Transformations

Density functional theory (DFT) calculations are used to predict the mechanism for the intramolecular carbon–hydrogen bond activation of an ortho methyl group on the Ru^II(SC₆H₃Me₂-2,6-κ¹S)₂(PMe₃)₃ complex to form the cycloruthenated product <i>cis</i>-Ru­[SC₆H₃-(2-CH₂)­(6-Me)-κ²S₂C]­(PMe₃)₄ and HSC₆H₃Me₂-2,6 in the presence of PMe₃. The DFT calculations also show how changing the solvent from benzene to methanol prevents C–H activation and results in the unactivated six-coordinate product Ru­(SC₆H₃Me₂-2,6-κ¹S)₂(PMe₃)₄ in 100% yield. The reactant was determined to have two plausible σ-bond metathesis pathways in which to react, one for each of the two thiolate ligands. The steps in both mechanisms were influenced by the electronic interactions between the sulfur lone pairs and the Ru 4d orbitals and the steric repulsion between the methyl groups on the five ligands in such a way that the methyl group in the SAr (Ar = SC₆H₃Me₂-2,6) ligand closest to the Ru pirouettes away to activate the other methyl group. The equatorial pathway was calculated to be the lower energy mechanism and, therefore, the dominant pathway for the overall reaction. The difference between reaction mediums was predicted, by both implicit and explicit solvation modeling, to be a result of the polarity and binding of methanol, which transforms the geometry of the reactant from a less polar distorted trigonal-bipyramidal geometry to a more polar distorted square-pyramidal geometry. This change in geometry favors the more rapid addition of a fourth PMe₃ ligand to the more open coordination site, which prevents the C–H activation

Investigating the Electronic Structure of the Atox1 Copper(I) Transfer Mechanism with Density Functional Theory

To maintain correct copper homeostasis, the body relies on ion binding metallochaperones, cuprophilic ligands, and proteins to move copper around as a complexed metal. The most common binding site for Cu­(I) proteins is the CX₁X₂C motif, where X₁ and X₂ are nonconserved residues. Although this binding site motif is well established, the mechanistic and electronic details for the transfer of Cu­(I) between two binding sites have not been fully established, in particular, whether the transfer is dissociative or associative or if the electron-rich Cu­(I)–Cys interactions influence the transfer. In this work, we investigated the electronic structure of the Cu­(I)–S interactions during the copper transfer between Atox1 and a metal binding domain on the ATP7A or ATP7B protein. Initially, three Cu­(I) methylthiolate complexes, [Cu­(SCH₃)₂]⁻¹, [Cu­(SCH₃)₃]⁻², [Cu­(SCH₃)₄]⁻³, were investigated with density functional theory (DFT) to fully elucidate the electronic structure and bonding between Cu­(I) and thiolate species. The two-coordinate, linear species with a C–S–S–C dihedral angle of ∼90° is the lowest energy conformation because the filled π antibonding orbitals are stabilized in this geometry. The importance of π-overlap is also seen with the trigonal planar, three-coordinate Cu­(I) complex, which is similarly stabilized. A corresponding four-coordinate species could not be consistently optimized, so it was concluded that tetrahedral coordination was not likely to be stable. The transfer of Cu­(I) from the Atox1 metallochaperone to a metal binding domain of the ATP7A or ATP7B protein was then modeled by using the CGGC Atox1 binding site for the donor model and the dithiotreitol ligand (DTT) for the acceptor model. The two- and three-coordinate intermediates calculated along the five-step transfer mechanism converged to near optimal Cu–S π-overlap for the respective geometries, which demonstrates that the electronic structure in this electron-rich environment influences the intermediate’s geometries in the transfer mechanism

Understanding the Radical Nature of an Oxidized Ruthenium Tris(thiolate) Complex and Its Role in the Chemistry

The spectroscopically observable tris­(thiolate) complex [Ru­(dppbt)₃]⁺ (<b>1</b>^<b>+</b>) (dppbt = diphenyl­phosphino­benzene­thiolate) is reported to have chemistry based on thiyl-radical character. High-level <i>ab initio</i> methods predict the ground-state electronic structure of <b>1</b>^<b>+</b> to be an open-shell diradical singlet state with antiferromagnetic coupling between (<i>S</i> = 1/2) Ru­(III) and (<i>S</i> = 1/2) S p_<i>z</i>, rather the previous description based on a diradical state involving two S p orbitals. These new results provide an improved understanding of the experimental chemistry of <b>1</b>^<b>+</b> and related species

Influence of the Density Functional and Basis Set on the Relative Stabilities of Oxygenated Isomers of Diiron Models for the Active Site of [FeFe]-Hydrogenase

A series of different density functional theory (DFT) methodologies (24 functionals) in conjunction with a variety of six different basis sets (BSs) was employed to investigate the relative stabilities in the oxygenated isomers of diiron complexes that mimic the active site of [FeFe]-hydrogenase: (μ-pdt)­[Fe­(CO)₂L]­[Fe­(CO)₂L′] (pdt = propane-1,3-dithiolate; L = L′ = CO (<b>1</b>); L = PPh₃, L′ = CO (<b>2</b>); L = PMe₃, L′ = CO (<b>3</b>); L = L′ = PMe₃ (<b>4</b>). Although the enzyme may have a variety of possible sites for oxygenation, the model complexes would necessarily be oxygenated at either the diiron bridging site (<i><b>μ</b></i>-<b>O</b>) or at a sulfur (<b>SO</b>). Previous DFT studies with both B3LYP and TPSS functionals predicted a more stable <i><b>μ</b></i>-<b>O</b> isomer, whereas only the <b>SO</b> isomer was observed experimentally (<i>J. Am. Chem. Soc</i>. <b>2009</b>, 131, 8296–8307). Here, further calculations reveal that the relative stabilities of the <b>SO</b> and <i><b>μ</b></i>-<b>O</b> isomers are extremely sensitive to the choice of the functional, moderately sensitive to the S basis set, but not to the Fe basis set. The relative free energies [<i>G</i>_solv(<i><b>μ</b></i>-<b>O</b>) – <i>G</i>_solv(<b>SO</b>)] range from +10 to −60 kcal/mol, a range much larger than what would have been expected on the basis of the previous DFT results. Benchmarking of these results against coupled cluster with single and double excitation calculations, which predict that the <b>SO</b> isomer is favored, shows that the best performing functionals are BP86 and PBE0, while B97-D, M05, and SVWN overestimate and B2PLYP, BH&HLYP, BMK, M06-HF, and M06-2X underestimate the energy differences. Most of the variation occurs with the <i><b>μ</b></i>-<b>O</b> isomer and appears to be associated with a functional’s ability to predict the strength of the Fe–Fe bond in the reactant. With respect to the S basis set, it appears that the SO bond is sensitive to the nature of the d polarization functions available on the S atom. The S seems to need a d function more diffuse than the d orbital optimized to provide polarization for the S atom alone; that is, S seems to need a d orbital that has strong overlap with the O atom’s valence 2p. Other basis functions and the relative position of the PR₃ (R = Ph and Me) substituent groups have smaller influences on the free energy differences

The Distinctive Electronic Structures of Rhenium Tris(thiolate) Complexes, an Unexpected Contrast to the Valence Isoelectronic Ruthenium Tris(thiolate) Complexes

The noninnocent 2-diphenylphosphino-benzenethiolate (DPPBT) ligand containing both phosphorus and sulfur donors delocalizes the electron density in a manner reminiscent of dithiolenes. The electronic structure of the <b>[ReL</b>_<b>3</b><b>]</b>^{<b><i>n</i></b>} (L = DPPBT, <i>n</i> = 0, 1+, 2+) complexes was probed with density-functional theory (DFT) and high-level ab initio methods including complete active space self-consistent field (CASSCF and CASPT2) and coupled cluster (CCSD and CCSD­(T)). DFT predicts a slight preference for a closed-shell (CS) singlet ground state for the neutral <b>[ReL</b>_<b>3</b><b>]</b>^<b>0</b> and stronger preferences for low-spin ground states for the oxidized <b>[ReL</b>_<b>3</b><b>]</b>^<b>+</b> and <b>[ReL</b>_<b>3</b><b>]</b>^<b>2+</b>. High-level ab initio methods confirm a CS singlet with a Re­(III) (d⁴, <i>S</i> = 0) center as the ground state of <b>[ReL</b>_<b>3</b><b>]</b>^<b>0</b>. Thus, this neutral Re species has considerably less thiyl radical character than the valence isoelectronic <b>[RuL</b>_<b>3</b><b>]</b>^<b>+</b>, which is mainly a Ru­(III) (d⁵, <i>S</i> = 1/2) anti-ferromagnetically (AF) coupled to a thiyl radical (<i>S</i> = 1/2). However, the oxidized derivatives <b>[ReL</b>_<b>3</b><b>]</b>^<b>+</b> and <b>[ReL</b>_<b>3</b><b>]</b>^<b>2+</b> show significant metal-stabilized thiyl radical character like <b>[RuL</b>_<b>3</b><b>]</b>^<b>+</b>. Both <b>[ReL</b>_<b>3</b><b>]</b>^<b>+</b> and <b>[ReL</b>_<b>3</b><b>]</b>^<b>2+</b> have major contributions from Re­(III) (d⁴, <i>S</i> = 1) centers AF coupled to thiyl and dithiyl DPPBT ligands. These findings are consistent with the experimental chemistry as <b>[RuL</b>_<b>3</b><b>]</b>^<b>+</b>, <b>[ReL</b>_<b>3</b><b>]</b>^<b>+</b>, and <b>[ReL</b>_<b>3</b><b>]</b>^<b>2+</b> can add ethylene to form the new C–S bonds, but <b>[ReL</b>_<b>3</b><b>]</b>^<b>0</b> cannot. The thiyl radicals on the S2 position (the S trans to a P donor) serve as the intrinsic electron acceptors in the actual ethylene addition reactions with Ru and Re tris­(thiolate) complexes