Applying 3D ED/MicroED workflows toward the next frontiers.

We report on the latest advancements in Microcrystal Electron Diffraction (3D ED/MicroED), as discussed during a symposium at the National Center for CryoEM Access and Training housed at the New York Structural Biology Center. This snapshot describes cutting-edge developments in various facets of the field and identifies potential avenues for continued progress. Key sections discuss instrumentation access, research applications for small molecules and biomacromolecules, data collection hardware and software, data reduction software, and finally reporting and validation. 3D ED/MicroED is still early in its wide adoption by the structural science community with ample opportunities for expansion, growth, and innovation.

Regulating Access to Active Sites via Hydrogen Bonding and Cation-Dipole Interactions: A Dual Cofactor Approach to Switchable Catalysis.

Hydrogen bonding networks are ubiquitous in biological systems and play a key role in controlling the conformational dynamics and allosteric interactions of enzymes. Yet in small organometallic catalysts, hydrogen bonding rarely controls ligand binding to the metal center. In this work, a hydrogen bonding network within a well-defined organometallic catalyst works in concert with cation-dipole interactions to gate substrate access to the active site. An ammine ligand acts as one cofactor, templating a hydrogen bonding network within a pendent crown ether and preventing the binding of strong donor ligands, such as nitriles, to the nickel center. Sodium ions are the second cofactor, disrupting hydrogen bonding to enable switchable ligand substitution reactions. Thermodynamic analyses provide insight into the energetic requirements of the different supramolecular interactions that enable substrate gating. The dual cofactor approach enables switchable catalytic hydroamination of crotononitrile. Systematic comparisons of catalysts with varying structural features provide support for the critical role of the dual cofactors in achieving on/off catalysis with substrates containing strongly donating functional groups that might otherwise interfere with switchable catalysts.

Mechanism-Guided Kinetic Analysis of Electrocatalytic Proton Reduction Mediated by a Cobalt Catalyst Bearing a Pendant Basic Site.

Cobalt polypyridyl complexes stand out as efficient catalysts for electrochemical proton reduction, but investigations into their operating mechanisms, with broad-reaching implications in catalyst design, have been limited. Herein, we investigate the catalytic activity of a cobalt(II) polypyridyl complex bearing a pendant pyridyl base with a series of organic acids spanning 20 pKa units in acetonitrile. Structural analysis, as well as electrochemical studies, reveals that the Co(III) hydride intermediate is formed through reduction of the Co(II) catalyst followed by direct metal protonation in the initial EC step despite the presence of the pendant base, which is commonly thought of as a more kinetically accessible protonation site. Protonation of the pendant base occurs after the Co(III) hydride intermediate is further reduced in the overall ECEC pathway. Additionally, when the acid used is sufficiently strong, the Co(II) catalyst can be protonated, and the Co(III) hydride can react directly with acid to release H2. With thorough mechanistic understanding, the appropriate electroanalytical methods were identified to extract rate constants for the elementary steps over a range of conditions. Thermodynamic square schemes relating catalytic intermediates proposed in the three electrocatalytic HER mechanisms were constructed. These findings reveal a full description of the HER electrocatalysis mediated by this molecular system and provide insights into strategies to improve synthetic fuel-forming catalysts operative through metal hydride intermediates.

Synthesis and bonding analysis of pentagonal bipyramidal rhenium carboxamide oxo complexes.

Seven-coordinate rhenium oxo complexes supported by a tetradentate bipyridine carboxamide/carboxamidate ligand are reported. The neutral dicarboxamide H2Phbpy-da ligand initially coordinates in an L4 (ONNO) fashion to an octahedral rhenium oxo precursor, yielding a seven-coordinate rhenium oxo complex. Subsequent deprotonation generates a new oxo complex featuring the dianionic (L2X2) carboxamidate (NNNN) form of the ligand. Computational studies provide insight into the relative stability of possible linkage isomers upon deprotonation. Structural studies and molecular orbital theory are employed to rationalize the relative isomer stability and provide insight into the rhenium-oxo bond order.

Visible light induced formation of a tungsten hydride complex.

When irradiated with blue light in the presence of a Lewis base (L), [CpW(CO)3]2 undergoes metal-metal bond cleavage followed by a disproportionation reaction to form [CpW(CO)3L]+ and [CpW(CO)3]-. Here, we show that in the presence of pyridinium tetrafluoroborate, [CpW(CO)3]- reacts further to form a metal hydride complex CpW(CO)3H. The rection was monitored through in situ photo 1H NMR spectroscopy experiments and the mechanism of light-driven hydride formation was investigated by determining quantum yields of formation. Quantum yields of formation of CpW(CO)3H correlate with I-1/2 (I = photon flux on our sample tube), indicating that the net disproportionation of [CpW(CO)3]2 to form the hydride precursor [CpW(CO)3]- occurs primarily through a radical chain mechanism.

Isocyanide Ligands Promote Ligand-to-Metal Charge Transfer Excited States in a Rhenium(II) Complex.

A metal-to-ligand charge transfer with mixed intraligand character is observed for the rhenium hexakisarylisocyanide complex [Re(CNAr)6]PF6 (CNAr = 2,6-dimethylphenylisocyanide, λmax = 300 nm). Upon oxidation to [Re(CNAr)6](PF6)2, the dominant low energy optical transition is a ligand-to-metal charge transfer (LMCT) mixed with intraligand transitions (λmax = 650 nm). TD-DFT was used to identify the participating ligand-based orbitals in the LMCT transition, revealing that the majority of the donor orbital is based on the aryl ring (85%) as opposed to the CN bond (14%). For both [Re(CNAr)6]+ and [Re(CNAr)6]2+, structural characterization by X-ray diffraction reveals deviations from Oh geometry at the central Re ion, with larger reduction in symmetry observed for Re(II). For [Re(CNAr)6]+, these structural changes lead to a broadening of the strong ν(C≡N) stretch (2065 cm-1), as the degeneracy of the T1u IR-active mode is broken. Furthermore, a shoulder is observed for this ν(C≡N) stretch, resulting from deviation of the C-N-Ar bond from linearity. By contrast, [Re(CNAr)6]2+ has two weak bands in the ν(C≡N) region (2065 and 2121 cm-1). DFT calculations indicate that reduction of symmetry at the central rhenium ion manifests in the decrease in intensity and the observed split of the ν(C≡N) band. Stability of both complexes are limited by light-induced decomposition where Re(I) dissociates a isocyanide ligand upon irradiation and Re(II) absorbance decays under ambient light. These data provide new insights to the electronic structure of [Re(CNAr)6]2+, enhancing our understanding of LMCT excited states and the versatility of isocyanide ligands.

Oxidative Addition of a Phosphinite P-O Bond at Nickel.

Oxidative addition is an essential elementary reaction in organometallic chemistry and catalysis. While a diverse array of oxidative addition reactions has been reported to date, examples of P-O bond activation are surprisingly rare. Herein, we report the ligand-templated oxidative addition of a phosphinite P-O bond in the diphosphinito aniline compound HN(2-OPiPr2-3,5-tBu-C6H2)2 [H(P2ONO)] at Ni0 to form (PONO)Ni(HPiPr2) after proton rearrangement. Notably, the P-O cleavage occurs selectively over an amine N-H bond activation. Additionally, the ligand cannibalization is reversible, as addition of XPR2 (X = Cl, Br; R = iPr, Cy) to (PONO)Ni(HPiPr2) readily produces either symmetric or unsymmetric (P2ONO)NiX species and free HPiPr2. Finally, the mechanisms of both the initial P-O bond cleavage and its subsequent reconstruction are investigated to provide further insight into how to target P-O bond activation.

Doubly stereoconvergent crystallization enabled by asymmetric catalysis.

Synthetic methods that enable simultaneous control over multiple stereogenic centers are desirable for the efficient preparation of pharmaceutical compounds. Herein, we report the discovery and development of a catalyst-mediated asymmetric Michael addition/crystallization-induced diastereomer transformation of broad scope. The sequence controls three stereogenic centers, two of which are stereochemically labile. The configurational instability of 1,3-dicarbonyls and nitroalkanes, typically considered a liability in stereoselective synthesis, is productively leveraged by merging enantioselective Brønsted base organocatalysis and thermodynamic stereocontrol using a single convergent crystallization. The synthesis of useful γ-nitro ß-keto amides containing three contiguous stereogenic centers is thus achieved from Michael acceptors containing two prochiral centers.

A Redox-Active Tetrazine-Based Pincer Ligand for the Reduction of N-Oxyanions Using a Redox-Inert Metal.

The reaction chemistry of the bis-tetrazinyl pyridine ligand (btzp) towards nitrogen oxyanions coordinated to zinc is studied in order to explore the reduction of the NOx - substrates with a redox-active ligand in the absence of redox activity at the metal. Following syntheses and characterization of (btzp)ZnX2 for X=Cl, NO3 and NO2 , featuring O-Zn linkage of both nitrogen oxyanions, it is shown that a silylating agent selectively delivers silyl substituents to tetrazine nitrogens, without reductive deoxygenation of NOx -1 . A new synthesis of the highly hydrogenated H4 btzp, containing two dihydrotetrazine reductants is described as is the synthesis and characterization of (H4 btzp)ZnX2 for X=Cl and NO3 , both of which show considerable hydrogen bonding potential of the dihydrotetrazine ring NH groups. The (H4 btzp)ZnCl2 complex does not bind zinc in the pincer pocket, but instead H4 btzp becomes a bridge between neighboring atoms through tetrazine nitrogen atoms, forming a polymeric chain. The reaction of AgNO2 with (H4 btzp)ZnCl2 is shown to proceed with fast nitrite deoxygenation, yielding water and free NO. Half of the H4 btzp reducing equivalents form Ag0 and thus the chloride ligand remains coordinated to the zinc metal center to yield (btzp)ZnCl2 . To compare with AgNO2 , experiments of (H4 btzp)ZnCl2 with NaNO2 result in salt metathesis between chloride and nitrite, highlighting the importance of a redox-active cation in the reduction of nitrite to NO.

Redox-Induced Structural Reorganization Dictates Kinetics of Cobalt(III) Hydride Formation via Proton-Coupled Electron Transfer.

Two-electron, one-proton reactions of a family of [CoCp(dxpe)(NCCH3)]2+ complexes (Cp = cyclopentadienyl, dxpe = 1,2-bis(di(aryl/alkyl)phosphino)ethane) form the corresponding hydride species [HCoCp(dxpe)]+ (dxpe = dppe (1,2-bis(diphenylphosphino)ethane), depe (1,2-bis(diethylphosphino)ethane), and dcpe (1,2-bis(dicyclohexylphosphino)ethane)) through a stepwise proton-coupled electron transfer process. For three [CoCp(dxpe)(NCCH3)]2+ complexes, peak shift analysis was employed to quantify apparent proton transfer rate constants from cyclic voltammograms recorded with acids ranging 22 pKa units. The apparent proton transfer rate constants correlate with the strength of the proton source for weak acids, but these apparent proton transfer rate constants curiously plateau (kpl) as the reaction becomes increasingly exergonic. The absolute apparent proton transfer rate constants across both these regions correlate with the steric bulk of the chelating diphosphine ligand, with bulkier ligands leading to slower kinetics (kplateau,depe = 3.5 × 107 M-1 s-1, kplateau,dppe = 1.7 × 107 M-1 s-1, kplateau,dcpe = 7.1 × 104 M-1 s-1). Mechanistic studies were conducted to identify the cause of the aberrant kPTapp-ΔpKa trends. When deuterated acids are employed, deuterium incorporation in the Cp ring is observed, indicating protonation of the CoCp(dxpe) species to form the corresponding hydride proceeds via initial ligand protonation. Digital simulations of cyclic voltammograms show ligand loss accompanying initial reduction gates subsequent PCET activity at higher driving forces. Together, these experiments reveal the details of the reaction mechanism: reduction of the Co(III) species is followed by dissociation of the bound acetonitrile ligand, subsequent reduction of the unligated Co(II) species to form a Co(I) species is followed by protonation, which occurs at the Cp ring, followed by tautomerization to generate the stable Co(III)-hydride product [HCoCp(dxpe)]+. Analysis as a function of chelating disphosphine ligand, solvent, and acid strength reveals that the ligand dissociation equilibrium is directly influenced by the steric bulk of the phosphine ligands and gates protonation, giving rise to the plateau of the apparent proton transfer rate constant with strong acids. The complexity of the reaction mechanism underpinning hydride formation, encompassing dynamic behavior of the entire ligand set, highlights the critical need to understand elementary reaction steps in proton-coupled electron transfer reactions.

Polarity-Tolerant Chloride Binding in Foldamer Capsules by Programmed Solvent-Exclusion.

Persistent anion binding in a wide range of solution environments is a key challenge that continues to motivate and demand new strategies in synthetic receptor design. Though strong binding in low-polarity solvents has become routine, our ability to maintain high affinities in high-polarity solvents has not yet reached the standard set by nature. Anions are bound and transported regularly in aqueous environments by proteins that use secondary and tertiary structure to isolate anion binding sites from water. Inspired by this principle of solvent exclusion, we created a sequence-defined foldameric capsule whose global minimum conformation displays a helical folded state and is preorganized for 1:1 anion complexation. The high stability of the folded geometry and its ability to exclude solvent were supported by solid-state and solution phase studies. This capsule then withstood a 4-fold increase in solvent dielectric constant (εr) from dichloromethane (9) to acetonitrile (36) while maintaining a high and solvent-independent affinity of 105 M-1; ΔG ∼ 28 kJ mol-1. This behavior is unusual. More typical of solvent-dependent behavior, Cl- affinities were seen to plummet in control compounds, such as aryl-triazole macrocycles and pentads, with their solvent-exposed binding cavities susceptible to dielectric screening. Finally, dimethyl sulfoxide denatures the foldamer by putative solvent binding, which then lowers the foldamer's Cl- affinity to normal levels. The design of this capsule demonstrates a new prototype for the development of potent receptors that can operate in polar solvents and has the potential to help manage hydrophilic anions present in the hydrosphere and biosphere.

Selecting Double Bond Positions with a Single Cation-Responsive Iridium Olefin Isomerization Catalyst.

The catalytic transposition of double bonds holds promise as an ideal route to alkenes of value as fragrances, commodity chemicals, and pharmaceuticals; yet, selective access to specific isomers is a challenge, normally requiring independent development of different catalysts for different products. In this work, a single cation-responsive iridium catalyst selectively produces either of two different internal alkene isomers. In the absence of salts, a single positional isomerization of 1-butene derivatives furnishes 2-alkenes with exceptional regioselectivity and stereoselectivity. The same catalyst, in the presence of Na+, mediates two positional isomerizations to produce 3-alkenes. The synthesis of new iridium pincer-crown ether catalysts based on an aza-18-crown-6 ether proved instrumental in achieving cation-controlled selectivity. Experimental and computational studies guided the development of a mechanistic model that explains the observed selectivity for various functionalized 1-butenes, providing insight into strategies for catalyst development based on noncovalent modifications.

Stabilization of the Dinitrogen Analogue, Phosphorus Nitride.

The N2 analogue phosphorus nitride (PN) was the first phosphorus-containing compound to be detected in the interstellar medium; however, this thermodynamically unstable compound has a fleeting existence on Earth. Here, we show that reductive coupling of iron(IV) nitride and molybdenum(VI) phosphide complexes assembles PN as a bridging ligand in a structurally characterized bimetallic complex. Reaction with C≡N t Bu releases the mononuclear complex [(N3N)Mo-PN]-, N3N = [(Me3SiNCH2CH2)3N]3-), which undergoes light-induced linkage isomerization to provide [(N3N)Mo-NP]-, as revealed by photocrystallography. While structural and spectroscopic characterization, supported by electronic structure calculations, reveals the PN multiple bond character, coordination to molybdenum induces a nucleophilic character at the terminal atom of the PN/NP ligands. Indeed, the linkage isomers can be trapped in solution by reaction with a Rh(I) electrophile.

Two-State Reactivity in Iron-Catalyzed Alkene Isomerization Confers σ-Base Resistance.

A low-coordinate, high spin (S = 3/2) organometallic iron(I) complex is a catalyst for the isomerization of alkenes. A combination of experimental and computational mechanistic studies supports a mechanism in which alkene isomerization occurs by the allyl mechanism. Importantly, while substrate binding occurs on the S = 3/2 surface, oxidative addition to an η1-allyl intermediate only occurs on the S = 1/2 surface. Since this spin state change is only possible when the alkene substrate is bound, the catalyst has high immunity to typical σ-base poisons due to the antibonding interactions of the high spin state.

Nitrogen oxyanion reduction by Co(ii) augmented by a proton responsive ligand: recruiting multiple metals.

Deoxygenation of nitrite oxygen with divalent cobalt was achieved using (PNNH)CoCl2, carrying a pyridyl pincer ligand with one P(t-Bu)2 arm and one pyrazole arm. Reaction of (PNNH)CoCl2 with NaNO2 at a 2 : 5 mole ratio promptly forms equimolar (PNNH)Co(NO2)3 and (PNN)Co(NO2)(NO), {CoNO}8 with the lost ligand proton combined with removed oxo as hydroxide. These two CoIII products are characterized, showing a bent CoNO unit as the fate of the reduced nitrogen. DFT calculations are consistent with two one-electron CoII reductants binding to one NO2- bridge, then proton transfer being needed for facile N/O bond scission. A species detected by low temperature execution of this reaction contains cobalt in two oxidation states with an N,O bridging nitro group and pincer ligands that have been deprotonated, showing the active participation of the proton responsive ligand.

Unusual Dinitrogen Binding and Electron Storage in Dinuclear Iron Complexes.

A rare example of a dinuclear iron core with a non-linearly bridged dinitrogen ligand is reported in this work. One-electron reduction of [(tBupyrr2py)Fe(OEt2)] (1) (tBupyrr2py2- = 2,6-bis((3,5-di-tert-butyl)pyrrol-2-yl)pyridine) with KC8 yields the complex [K]2[(tBupyrr2py)Fe]2(µ2-η1:η1-N2) (2), where the unusual cis-divacant octahedral coordination geometry about each iron and the η5-cation-π coordination of two potassium ions with four pyrrolyl units of the ligand cause distortion of the bridging end-on µ-N2 about the FeN2Fe core. Attempts to generate a Et2O-free version of 1 resulted instead in a dinuclear helical dimer, [(tBupyrr2py)Fe]2 (3), via bridging of the pyridine moieties of the ligand. Reduction of 3 by two electrons under N2 does not break up the dimer, nor does it result in formation of 2 but instead formation of the ate-complex [K(OEt2)]2[(tBupyrr2py)Fe]2 (4). Reduction of 1 by two electrons and in the presence of crown-ether forms the tetraanionic N2 complex [K2][K(18-crown-6)]2(tBupyrr2py)Fe]2(µ2-η1:η1-N2) (5), also having a distorted FeN2Fe moiety akin to 2. Complex 2 is thermally unstable and loses N2, disproportionating to Fe nanoparticles among other products. A combination of single-crystal X-ray diffraction studies, solution and solid-state magnetic studies, and 57Fe Mössbauer spectroscopy has been applied to characterize complexes 2-5, whereas DFT studies have been used to help explain the bonding and electronic structure in these unique diiron-N2 complexes 2 and 5.

Hydrosilylation of an Iron(IV) Nitride Complex.

The nitride ligand in iron(IV) complex PhB(MesIm)3Fe≡N reacts with excess H3SiPh to afford PhB(MesIm)3Fe(µ-H)3(SiHPh) as the major product, which has been structurally and spectroscopically characterized. Bulkier silane HaSiPh2 provides iron(II) amido complex PhB(MesIm)3FeN(H)(SiHPh2) as the initial product of the reaction, with excess H2SiPh2 affording diamagnetic PhB(MesIm)3Fe(µ-H)3(SiPh2) as the major product. Unobserved iron(II) hydride PhB(MesIm)3Fe-H is implicated as an intermediate in this reaction, as suggested by the results of the reaction between iron(II) amido PhB(MesIm)3FeN(H)tBu and H3SiPh, which provides PhB(MesIm)3Fe(H)(µ-H)2(Si(NHtBu)Ph) as the sole product.

Dinitrogen Reduction to Ammonium at Rhenium Utilizing Light and Proton-Coupled Electron Transfer.

The direct scission of the triple bond of dinitrogen (N2) by a metal complex is an alluring entry point into the transformation of N2 to ammonia (NH3) in molecular catalysis. Reported herein is a pincer-ligated rhenium system that reduces N2 to NH3 via a well-defined reaction sequence involving reductive formation of a bridging N2 complex, photolytic N2 splitting, and proton-coupled electron transfer (PCET) reduction of the metal-nitride bond. The new complex (PONOP)ReCl3 (PONOP = 2,6-bis(diisopropylphosphinito)pyridine) is reduced under N2 to afford the trans,trans-isomer of the bimetallic complex [(PONOP)ReCl2]2(µ-N2) as an isolable kinetic product that isomerizes sequentially upon heating into the trans,cis and cis,cis isomers. All isomers are inert to thermal N2 scission, and the trans,trans-isomer is also inert to photolytic N2 cleavage. In striking contrast, illumination of the trans,cis and cis,cis-isomers with blue light (405 nm) affords the octahedral nitride complex cis-(PONOP)Re(N)Cl2 in 47% spectroscopic yield and 11% quantum yield. The photon energy drives an N2 splitting reaction that is thermodynamically unfavorable under standard conditions, producing a nitrido complex that reacts with SmI2/H2O to produce a rhenium tetrahydride complex (38% yield) and furnish ammonia in 74% yield.

Strong π-Backbonding Enables Record Magnetic Exchange Coupling Through Cyanide.

The paramagnetic cyano-bridged complex PhB(tBuIm)3Fe-NC-Mo(NtBuAr)3 (Ar = 3,5-Me2C6H3) is readily assembled from a new four-coordinate, high-spin (S = 2) iron(II) monocyanide complex and the three-coordinate molybdenum(III) complex Mo(NtBuAr)3. X-ray diffraction and IR spectroscopy reveal that delocalization of unpaired electron density into the cyanide π* orbitals leads to a reduction of the C-N bond order. Direct current (dc) magnetic susceptibility measurements, supported by electronic structure calculations, demonstrate the presence of strong antiferromagnetic exchange between spin centers, with a coupling constant of J = -122(2) cm-1. To our knowledge, this value represents the strongest magnetic exchange coupling ever to be observed through cyanide. These results demonstrate the ability of low-coordinate metal fragments to engender extremely strong magnetic exchange coupling through cyanide by virtue of significant π-backbonding into the cyanide ligand.

Intramolecular Hydrogen Bonding Facilitates Electrocatalytic Reduction of Nitrite in Aqueous Solutions.

This work reports a combined experimental and computational mechanistic investigation into the electrocatalytic reduction of nitrite to ammonia by a cobalt macrocycle in an aqueous solution. In the presence of a nitrite substrate, the Co(III) precatalyst, [Co(DIM)(NO2)2]+ (DIM = 2,3-dimethyl-1,4,8,11-tetraazacyclotetradeca-1,3-diene), is formed in situ. Cyclic voltammetry and density functional theory (DFT) calculations show that this complex is reduced by two electrons, the first of which is coupled with nitrite ligand loss, to provide the active catalyst. Experimental observations suggest that the key N-O bond cleavage step is facilitated by intramolecular proton transfer from an amine group of the macrocycle to a nitro ligand, as supported by modeling several potential reaction pathways with DFT. These results provide insights into how the combination of a redox active ligand and first-row transition metal can facilitate the multiproton/electron process of nitrite reduction.