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. 2025 Feb 28;147(10):8444–8454. doi: 10.1021/jacs.4c16585

Selective Stepwise Reduction of Nitrate and Nitrite to Dinitrogen or Ammonia

Jewelianna M Moore †, Tabitha J Miller ‡, Manting Mu §, Marconi N Peñas-Defrutos §,∥, Kelly L Gullett ‡, Lindsey S Elford †, Sebastian Quintero †, Max García-Melchor §,⊥,#,*, Alison R Fout †,*
PMCID: PMC11912340  PMID: 40019004

Abstract

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This study reports a method for the selective reduction of NO3– and NO2– to N2 or NH3, extending prior work in our lab where NO3– was reduced to NO by [N(afaCy)3Fe]OTf2 (N(afaCy)3 = tris(5-cyclohexyl-amineazafulvene-2-methyl)amine, OTf = triflate). The first pathway involves the reduction of NO2– to N2, where the NO generated in the initial step is transformed to N2O by PPh3 and further reduced to N2 by the [N(afaCy)3Fe]OTf2 complex. An alternative pathway showcases the reduction of the bound NO complex, [N(afaCy)3Fe(NO)]2+, to NH3 using chemical reductants, albeit with a modest yield of 29%. Confirmation of the nitrogen source as NO is established through 15N labeling studies. Hydroxylamine (NH2OH) is proposed as a plausible intermediate in the reduction of bound NO, supported by independent NH2OH reduction experiments and computational studies. Nature employs a well-orchestrated, stepwise process involving several enzymes to reduce N-containing oxyanions, and this approach provides valuable insights into the stepwise reduction mechanisms of nitrate and nitrite, yielding NH3 or N2 as the product.

Introduction

Nitrate (NO3–) and nitrite (NO2–), common water pollutants,1,2 play pivotal roles in the global nitrogen cycle, acting as terminal electron acceptors in various biochemical processes. To reduce these N-containing compounds, Nature has evolved finely tuned, stepwise enzymatic processes. Two primary pathways exist for nitrate reduction, leading to the formation of either ammonium (NH4+) or dinitrogen (N2), but not both.3,4 In the denitrification pathway (Scheme 1, right) NO3– is reduced to N2 through a multistep process carried out by a series of enzymes. Nitrate is initially reduced to nitrite by the molybdenum-dependent nitrate reductase (NaR),4,5 followed by nitrite reduction to nitric oxide (NO) via heme-based nitrite reductase (cd1NiR)3,6 or copper-based nitrite reductase (CuNiR).3,6,7 The critical formation of the N–N bond occurs when NO is reduced to nitrous oxide (N2O) by either heme or nonheme nitric oxide reductase (NOR).8,9 The final step, catalyzed by iron/copper-containing nitrous oxide reductase (N2OR), reduces N2O to N2.10

Scheme 1. Stepwise Reduction of NO3– to NH3 (Left) or N2 (Right) by Nature and by our Synthetic Complex [N(afaCy)3Fe]OTf2 (1). The Arrows Representing the Natural Pathways are Color-coded to Correspond to the Appropriate Enzymes: Nitrate Reductase (NaR), Cytochrome cd1 Nitrite Reductase (cd1NiR), Nitric Oxide Reductase (NOR), Nitrous Oxide Reductase (N2OR), and Cytochrome c Ntrite Rductase (ccNiR). The Bottom Panel shows the Structure of Compound 1 Along with the Isolated Reaction Intermediates (3 and 4) Formed During the Sepwise Reduction Process.

Scheme 1

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On the other hand, in the dissimilatory nitrate reduction (DNRA) pathway (Scheme 1, left), NO3– is first deoxygenated to NO2– by NaR.4 Subsequently, the heme-containing cytochrome c nitrite reductase (ccNiR) reduces NO2– directly to NH4+,3,11 which is then incorporated into the organic nitrogen pool, contributing to the production of amino acids such as glutamate and glutamine.12 This intricate interplay of enzymes highlights the sophistication of Nature’s nitrogen cycling mechanisms.

Human activities, particularly the persistent use of fertilizers, have disrupted the natural nitrogen cycle, leading to adverse effects such as eutrophication and contamination of groundwater and drinking water.2,13,14 To address these environmental challenges, the conversion of NOx– compounds has become crucial in remediation efforts and has driven the exploration of synthetic systems capable of reducing N-containing oxyanions. While biological systems efficiently and selectively reduce NO3– to specific N-containing products, synthetic systems typically struggle to achieve high selectivity. Most synthetic systems involve solely deoxygenation events, reducing nitrate or nitrite to nitric oxide, resembling the incomplete reduction of nitrate observed in Nature (Scheme 1).15−44 This underscores the ongoing challenge of developing synthetic systems that can achieve the selectivity and efficiency of the natural nitrogen reduction processes.

The electrochemical reduction of nitrate45−49 and nitrite45,48,50−56 to ammonia or ammonium has been extensively studied.57−60 However, synthetic systems have been lesser explored, with only a few synthetic systems capable of one of the two reduction pathways observed in Nature. Specifically, two synthetic systems have demonstrated the ability to reduce NO2– to NH3 but remain incapable of reducing NO3– as seen in the DNRA pathway.61,62 In contrast, denitrification pathways have been more successfully modeled by synthetic systems. In 2019, Lee and co-workers demonstrated complete denitrification using a single metal site.63 Their (PNP)nickel(II) pincer complex efficiently reduced NO3– to N2 gas, employing carbon monoxide as the oxygen atom acceptor to produce carbon dioxide. A year later, Gilbertson and co-workers developed a system using Samarium(II) iodide that could stoichiometrically reduce NO3– to N2.64 Despite these advances, to the best of our knowledge, there is currently no known molecular system capable of selectively reducing NO3– to either NH3 or N2 gas depending on the conditions of the system. Drawing inspiration from Nature, we propose the production of a synthetic system which models the stepwise reductions like those observed in the DNRA and denitrification pathways, following the N-containing intermediates identified or hypothesized in each pathway.

Herein we report a distinctive and selective process for the stepwise reduction of NO3– and NO2– to either N2 or NH3. This is achieved using a tripodal iron complex in conjunction with a sacrificial reductant, effectively emulating the denitrification and dissimilatory nitrate reduction pathways observed in Nature. The tripodal ligand framework, tris(5-cycloimminopyrrol-2-ylmethyl)amine ([N(piCy)3]), previously reported, is capable of tautomerization and features H-bond donating and accepting moieties in the secondary coordination sphere.65 Our prior research utilizing this framework highlighted the catalytic reduction of NO3– or NO2– to NO using the metalated iron complex [N(afaCy)3Fe]OTf2 (1).15,16 During the catalytic reduction, the formation of a terminal Fe(III)-oxo species, [N(afaCy)FeIII(O)]+ (3), and NO gas were observed (Scheme 2, top). Compound 3 was then turned over with 1,2-diphenylhydrazine to reform 1, producing an equivalent of water and azobenzene, thereby making the reduction catalytic. Unlike ccNiR, 1 is unable to further deoxygenate or reduce NO, which binds to 1 forming a stable iron-nitrosyl complex, [N(afaCy)Fe(NO)]2+ (2) (Scheme 2, bottom).15,16 Given the environmental significance of NO, which contributes to acid rain and reacts with ozone to produce N2O, a potent greenhouse gas,66 the focus of this work is on the selective reduction of NO to either N2 or NH3. This approach mimics the NOx– (x = 2, 3) reduction pathways observed in Nature and aims to inform the development of synthetic systems for sustainable N2 and NH3 production from NOx–.

Scheme 2. Reduction of [TBA]NO3 by Complex1 to Complex3 and NO Gas (top) or Complexes 3 and 2 (Bottom) Dependent on the Number of Equivalents of [TBA]NO3 Used.

Scheme 2

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Results and Discussion

Nitrate/Nitrite Reduction to Dinitrogen

To model the denitrification pathway, a one-pot reduction of NO3– or NO2– to N2O was carried out, followed by the reduction of N2O to N2 (Scheme 3). In the former reaction, compound 1 reduced NO3– or NO2– (2 or 1 equiv of compound 1 was used respectively), yielding compound 3 (2 or 1 equiv) and releasing one equivalent of NO gas. To further reduce the NO gas produced during this process, triphenylphosphine (PPh3) was utilized as a mild external reductant, known to convert NO to N2O, while forming triphenylphosphine oxide (O=PPh3).67

Scheme 3. Stepwise Reduction of Nitrite to N2 by Complex1 and PPh3. The Top Pathway Shows a Summary of the Overall Reaction. The Bottom Pathway Shows the Stepwise Reactions.

Scheme 3

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In the one-pot reduction of nitrite to nitrous oxide, a reaction mixture containing one equivalent of compound 1 and tetrabutylammonium nitrite ([TBA]NO2), along with an excess of PPh3, was stirred overnight (Scheme 3). After extracting the phosphine product(s) with ether, 31P NMR spectroscopy confirmed the clean formation of triphenylphosphine oxide. Using triphenylphosphine sulfide as an internal standard, the yield of O=PPh3 was quantified by 31P NMR spectroscopy, achieving quantitative yield based on integration. To rule out the possibility of deoxygenation of the iron-oxo species, compound 3 was stirred with PPh3 in acetonitrile overnight. After workup, no O=PPh3 was detected by 31P NMR spectroscopy. Additionally, no reaction was observed between compound 2 and PPh3, indicating that nitric oxide must remain unbound to the iron center for effective reduction. Therefore, this reaction must take place in two steps to preclude the formation of complex 2 prior to reduction of NO by PPh3.

In this reduction of nitrite to nitrous oxide, compound 3 was identified as the sole Fe-containing product by 1H NMR spectroscopy and was isolated in quantitative yield. Gas chromatography head space analysis confirmed nitrous oxide was the only gas produced, with no detectable nitric oxide, demonstrating the role of PPh3 as a sacrificial reductant in the reduction of NO generated in situ from nitrite.

Although the reduction of N2O to N2 is thermodynamically favorable, nitrous oxide is typically kinetically inert, requiring high temperatures and pressures to oxidize most organic compounds.68−70 However, there are precedents for the reduction of nitrous oxide to dinitrogen by metal complexes under ambient or low-temperature conditions.68,69,71−76 Given the success of 1 in reducing kinetically inert oxyanions such as perchlorate, and forming a stable iron-oxo species 3,77,78 we proposed the reduction of the generated N2O by compound 1 (Scheme 3). The reaction of 1 with N2O under inert atmosphere led to the formation of 3, as confirmed by 1H NMR spectroscopy. Initial experiments produced proto-demetalated ligand (N(piCy)3·3OTf) along with 3, similar to the reactivity of 1 with dioxygen.79 To suppress proto-demetalated ligand formation, triethylamine was added to the reaction mixture, successfully leading to the exclusive formation of 3, as confirmed via 1H NMR spectroscopy. Based on similar metal-based systems where N2O serves as an oxygen atom transfer reagent,69,71−76 we propose the formation of dinitrogen gas as the N-containing product, thus illustrating the stepwise reduction of nitrate or nitrite to nitric oxide to nitrous oxide in situ, followed by the reduction of nitrous oxide to dinitrogen.

Nitrate Reduction to Ammonia

To model the dissimilatory nitrate reduction pathway, we investigated the reduction of the bound nitrosyl in 2 formed in nitrate reduction to ammonia, focusing on the novel reduction step. Initial trials with mild to moderate reductants, such as 1,2-diphenylhydrazine (DPH), sodium naphthalenide, and cobaltocene, showed no reaction with 2. However, introducing potent chemical reductants, such as potassium graphite (KC8) or sodium potassium alloy (NaK), led to the disappearance of the nitrosyl complex 2 and the concomitant formation of the previously reported hydroxide complex, N(afaCy)2(piCy)FeOH (4),65 as confirmed by 1H NMR spectroscopy. Based on these findings, we envisioned a mechanism where NO is reduced to form NH3 and H2O, analogous to the process observed in ccNiR, with the resulting water binding to the iron center, forming the metal-bound OH compound 4.53

To optimize the system for the 5e–/5H+ reduction of NO to NH3 and 4, five electron equivalents of the reductant (5 equiv KC8 or 2.5 equiv NaK) and three equivalents of 2,6-lutidinium triflate (LuHOTf) were added to a THF solution of complex 2 at room temperature (Figure 1, top), with the ligand providing two additional proton equivalents during the process, facilitating its completion.

Figure 1.

Figure 1

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Top: reduction of complex 2 or15N-2 to complex 4 and ammonia. Bottom: selected region of the 1H NMR spectra of the acid traps, displaying signals for the formation of 14NH4Cl (blue, 1JN–H = 51 Hz) and 15NH4Cl (red, 1JN–H = 71 Hz) in DMSO-d6.

While the addition of KC8 and LuHOTf to previously published nitrate reduction conditions (Scheme 2, bottom) resulted in the formation of ammonia, we focus on the direct reduction of complex 2 to gain insight into the novel reaction steps. The addition of KC8 (5 equiv) or NaK (2.5 equiv) and LuHOTf (3 equiv) to 2 resulted in the formation of 4 in moderate crystalline yield (56.7%). To confirm the formation of NH3, an acid trap was employed to convert the generated NH3 to NH4Cl, which was identified by 1H NMR spectroscopy. The NH4+ proton peak exhibited the expected 1:1:1 triplet due to the coupling with the 14N nucleus (Figure 1, blue trace). The yield of ammonia, quantified by the indophenol method,80 was low to moderate depending on the reductant used (9.5% for KC8 and 28.7% for NaK). Initially, the low ammonia yield was attributed to poor selectivity toward any N-containing product. However, gas chromatography head space analysis confirmed ammonia as the sole N-containing gas, demonstrating the selectivity of the system. Nevertheless, a substantial amount of H2 gas was also produced due to the use of a strong reductant in conjunction with acid which likely is limiting the overall yield of ammonia produced.

To confirm that NH3 formation arises from the reduction of the bound nitrosyl rather than from ligand-based nitrogen atoms, control reductions of ligand (N(piCy)3) and complex 1 were conducted under the same conditions described above using NaK. The ammonia yields, as determined by the indophenol method, were significantly lower at 4.1 and 1.8%, respectively, compared to the reduction of 2 (28.7%). To further support this finding, 15N-labeled 15NO2– was used to ascertain that the ammonia produced originated from the reduction of the coordinated nitrosyl, rather than from the decomposition of metal complex 2 or the free ligand.

The 15N-labeled nitrosyl complex, [N(afaCy)3Fe15NO]OTf2 (15N-2), was generated by the reduction of Na15NO2 by 1 (2 equiv), followed by separation of 15N-2 from the equivalent amount of 3 produced (see SI for details). 15N-2 exhibited an identical 1H NMR spectrum to the unlabeled complex 2 and displayed the expected shift of the N = O stretching frequency from νNO = 1717 cm–1 to ν15NO = 1744 cm–1 for the 15N isotopologue in the infrared spectrum.15 Subsequently, the reduction of 15N-2 was carried out under the same conditions as 2 with an acid trap. The trapped NH4Cl salt was identified as 15NH4Cl by 1H NMR spectroscopy, showcasing the expected splitting pattern of a doublet and an N–H coupling value of 71 Hz (Figure 1, red trace). Notably, the triplet of 14NH4Cl was absent in the 1H NMR spectrum, provides clear confirmation that the generated ammonia results from the reduction of the bound nitrosyl in 2.

Hydroxylamine Reduction to Ammonia

Given that the reduction of 2 to ammonia requires strong heterogeneous chemical reductants, conventional methods for mechanistic studies, such as UV–visible, NMR, and react infrared spectroscopies are not applicable to this system. Therefore, to gain mechanistic insight, we explored the reduction of hydroxylamine to ammonia by 1, as hydroxylamine is a commonly proposed intermediate in the reduction of nitrite to ammonia in ccNiR and related inorganic systems.81,82 Specifically, ccNiR is known to reduce NO2–, NO, and NH2OH to NH3 without the release of detectable intermediates. Additionally, NH2OH has been crystallized in the active site of ccNiR, suggesting its viability as an intermediate in nitrite reduction.82

In contrast to the reduction of 2, the reduction of hydroxylamine to ammonia by 1 proceeds without the need for external reductant (Scheme 4). When [(NH2OH)2]H2SO4 is subjected to 1 (2 equiv), 3 is observed via 1H NMR spectroscopy and is isolated in high yield (70.6% crystalline yield). In the absence of a proton source or external reducing agents, the anticipated product of the 2e–/2H+ reduction of NH2OH would be an iron(IV)-oxo if the generated H2O were to bind to the metal center. However, we propose that high valent iron species are unstable in this tripodal ligand framework and instead hypothesize that an H atom is abstracted, forming an iron(III)-hydroxide, [N(afaCy)3FeOH]OTf2. Our prior work demonstrates that this complex can be cleanly deprotonated to form 3.79 The formation of ammonia was confirmed using an acid trap, and the yield, though moderate, of 29.8%, as assayed by the indophenol method, aligns well with the ammonia yield obtained in the reduction of 2 using NaK. While the system’s ability to reduce hydroxylamine suggests that it could be a viable intermediate in the reduction of nitrate to ammonia, we turned to computational methods to gain additional mechanistic insight.

Scheme 4. Reduction of Hydroxylamine by Complex1 to Form Complex3 and Ammonia.

Scheme 4

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Mechanistic Insights on NO to NH3 Reduction

To shed light on the mechanism of NO reduction to NH3, we performed density functional theory (DFT) calculations on the NO-bound iron complex 2 in THF under experimental conditions (see Figure 1). The calculations were carried out using Gaussian 16 software at the ωB97XD level of theory, considering key ligand conformers and high-spin states of iron metal (ferro- and antiferromagnetically coupled spin states), focusing on those with the lowest energy. The proton-coupled electron transfer (PCET) steps involved in the reaction mechanism were modeled using the method reported by Van Voorhis et al.,83 and considering the redox potential of the KC8 reductant (see SI for details). Additionally, the effect of solvent THF, including its H-bond acceptor capability, was accounted for through the continuum solvation model (SMD), adding a correction factor derived from our previous work.84

In our mechanistic investigation we propose that the NO in complex 2 is reduced through a series of PCET steps, which are commonly accepted in literature for similar electrocatalytic processes.85 In our work, the proton source for these steps could originate externally from the added acid (LuHOTf) or sourced internally from the N–H bond within the ligand, similar to the mechanism proposed for ccNiR, where amino acids serve as proton donors.82,86 The sequence in which protons are transferred onto the bound NO, either through the external acid or internal transfers, can vary, offering a broad range of possibilities. Herein we focused on two extreme scenarios to gain an overall understanding of the system’s reactivity. The first scenario assumes that all three initial protons are transferred from LuHOTf, followed by intramolecular transfers (pathway A, Figure 2, black trace), while the second assumes that all initial protons are supplied by intramolecular transfers within the ligand, followed by the addition of three external protons from LuHOTf (pathway B, Figure 2, blue trace). While alternative mechanisms for paths A and B were also considered (see Schemes S2 and S3), we focus here on describing the most energetically favorable pathways from the two extremes, shown in Figure 2.

Figure 2.

Figure 2

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Gibbs energy profile calculated in THF at 298 K and 1 atm for the reduction of complex 2 to 4 and NH3 with KC8 serving as the sacrificial reducing agent (e–), providing electrons, while LuHOTf acts as the external proton source (HA+), the tripodal ligand offers the internal proton source (HL+). The two lowest-energy pathways in eV (1 eV = 23.06 kcal/mol) are shown, initiated by either intramolecular (pathway A, black) or intermolecular (pathway B, blue) proton transfer steps. The N(afaCy) and N(piCy) ligand arms are shaded in blue and red, respectively to demonstrate the different ligand tautomeric forms. Spin densities (in a.u.) are shown in brackets for key radical species. The DFT-optimized structure of 2 is shown as an inset, with relevant bond distances provided in Å.

We began our theoretical studies by modeling the NO-bound complex 2, considering all possible conformers resulting from the rotation of the N(afaCy) ligand arms, as shown in Scheme S1. The most favorable conformer features two arms with both nitrogen atoms in the same ligand arm in cis position. Notably, these cis-positioned arms do not orient their NH units toward the Fe-bound NO. This behavior is due to the Fe–N–O bond angle being 170°, and the lone pair of the NNO which is primarily involved in bonding with Fe, making it unavailable for further interaction (see Figure 2, inset).

The DFT-optimized structure of complex 2 in the quartet spin state exhibits Mulliken spin densities of +3.68, −0.57, and −0.54 au on the Fe, N, and O atoms, respectively. We also examined the ferromagnetic sextet spin state, which yielded spin densities of +3.72, +0.65, and +0.31 au on the same atoms. Notably, the Fe–N bond length in the sextet (2.340 Å) is noticeably longer than in the quartet (1.787 Å), with the latter closely aligning with the values observed in similar Fe–NO complexes bearing tripodal ligand scaffolds.87 The X-ray crystallographic structure of complex 2 clearly reveals a [N(afaCy)3FeNO]OTf2 unit featuring a nonlinear NO group; however, the data’s limited resolution restricts detailed assessment of bond lengths, including the Fe–N distance (Figure S17). Overall, the quartet spin state is more stable than the sextet by +0.33 eV, consistent with our previously reported 4K EPR spectrum, which indicate an S = 3/2 system.15

The EPR spectrum also suggests an Fe(III)–NO– species with a triplet NO–, consistent with descriptions by Borovik et al.87 and proposed by Wieghardt and co-workers for Tp*M(NO) complexes (Tp* = hydro-tris(3,5-Me2-pyrazolyl)borate; M = Co, Ni).88 Our calculated Mulliken spin density on NO (−1.11 au) in the lowest-energy quartet spin state, more negative than −1.00, suggests that this moiety is best described as an NO– with diradical character, antiferromagnetically coupled to the unpaired electrons on the Fe center. To further examine the Fe oxidation state and electronic structure, we performed CASSCF(7,7) calculations and CASCI(7,7) analysis on localized molecular orbitals derived from CASSCF wave functions for complex 2 (see SI for details).89 The CASCI analysis reveals a dominant configuration, with a 23.09% weight, corresponding to a singly antiferromagnetically coupled Fe(III)(S = 3/2)–NO–(S = 1) ground state configuration. Multireference analysis indicates that an Fe(III) oxidation state contributes approximately 90.15% to the ground state, with 82.75% in the intermediate-spin state (S = 3/2) and 7.58% in the high-spin state (S = 5/2). The Fe(III) spins show variable coupling with NO–, either singly, doubly, or uncoupled. Among these, NO– exhibits 55.56% diradical character (S = 1) and 34.59% closed-shell singlet (S = 0) character. In summary, the electronic structure of compound 2 is complex, involving multiple spin coupling configurations, and is most accurately described as an Fe(III)(S = 3/2)–NO–(S = 1) system based on CASCI analysis.

Similar to the behavior of ccNiR, complex 2 undergoes a 1 e– reduction to form the Fe(II)-bound {NO}− intermediate (I1). Unlike complex 2, in intermediate I1, the Fe–N–O bond angle decreases from 170 to 155°, suggesting that the lone pair on the NNO is available for interaction. Indeed, in this intermediate, the NH units of the two cis-positioned ligand arms are oriented toward the Fe-bound NO, forming two hydrogen-bonding interactions with r(NNO–Hafacy) = 1.880 and 1.944 Å. This step, common to both pathways A and B, is exergonic by −2.36 eV and is characterized by the quenching of the NO radical, accompanied by a tilting and elongation of the Fe–NNO bond from 1.787 Å (Fe2+) to 1.965 Å (Fe2+). Once I1 is formed, a proton transfer step yields an intermediate with a {NHO} moiety bound to Fe. When the proton is sourced from the ligand (pathway A), it leads to the endergonic formation of intermediate I2′ with a Gibbs energy of −1.52 eV and an overall charge +1. Conversely, if the proton is transferred from LuHOTf (pathway B), it results in the exergonic formation of intermediate I2 with a Gibbs energy of −2.52 eV and an overall charge of +2. The significant energy difference between intermediates I2′ and I2 (i.e., 1.00 eV) makes pathway B energetically more favorable.

In subsequent steps, I2 and I2′ each undergo another PCET step to form I3 and I3′, respectively. This H atom transfer is significantly exergonic, rendering the process irreversible and leading to a divergence in pathways. Notably, intermediate I3, resulting from the external proton transfer (pathway B), exhibits an interesting structure characterized by a 3-membered {Fe–N–O} metallocycle, resembling the side-on coordination of TEMPO, which is isoelectronic to H2NO radical, previously observed to nickel.90 Conversely, intermediate I3′, obtained via intramolecular proton transfer and outer-sphere electron transfer (pathway A), maintains a linear configuration with an NH2O radical bound to Fe through the N atom.

While I3 is considerably more stable than I3′ by −1.50 eV, the stability of these species relative to their respective structural conformers varies. Specifically, the linear I3′ with two deprotonated ligand arms (pathway A) is more stable by −0.30 eV compared to its cyclic counterpart I3′a. Conversely, the cyclic intermediate I3 (pathway B) with fully protonated ligand arms is less stable by 0.07 eV than its linear analogue, denoted as I3a.

To better understand the origin of the energy difference between I3 and I3a, formed along the most favorable pathway B, we performed noncovalent interaction (NCI) analysis. This analysis uses electron density distributions to provide semiquantitative insights into both the nature and strength of NCIs between defined fragments in a molecule (see SI for further details). Specifically, we aimed to investigate the interactions between the secondary coordination sphere of the ligand and the bound NH2O radical. For this purpose, the molecules were partitioned into two fragments: the {NH2O} moiety and the {FeL} component (where L = N(afaCy)3). The generated NCI plot and the corresponding three-dimensional isosurfaces representing the NCIs are illustrated in Figure 3.

Figure 3.

Figure 3

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NCI analysis of complexes I3 (top) and I3a (bottom), showing the reduced density gradient (RDG) plotted against the product of the sign of the second eigenvalue of the Hessian matrix, sign(λ2)ρ, and the electron density, (ρ). Additional details on this analysis are provided in the SI. In the NCI plot, attractive (repulsive) interactions are indicated by blue (red) shades, with darker (lighter) shades denoting stronger (weaker) interactions. The inset highlights the most relevant attractive NCIs as isosurfaces (isovalue = 0.6 au), along with their associated ρ values (in a.u.).

The O···H electrostatic interactions are notably stronger in the 3-membered {Fe–N–O} metallocycle I3 (shifted to more negative values of sign(λ2)ρ) with ρ values of 0.0171 and 0.0172 au, compared to those in linear {Fe–N–O} I3a, which are 0.0137 and 0.0158 au This enhanced stabilization in I3 arises from the favorable orientation of the NH2O group within the cyclic structure, optimally aligning the oxygen’s lone pairs for effective electrostatic interactions with the C–H moieties of the ligand. Additionally, I3 exhibits a relatively weak electrostatic interaction between the N and H atoms, characterized by a ρ = 0.0137 au In contrast, the corresponding H···H interactions in I3a are even weaker (ρ = 0.0066 au), typical for van der Waals interactions.91 Altogether, the NCI interactions depicted in the inset of Figure 3 illustrate the greater stabilization in I3 compared to I3a.

While the NCI analysis provides valuable insight, it does not fully account for the higher stability of the linear intermediate I3′ relative to its cyclic counterpart I3′a. We attribute this apparent discrepancy to the instability of the NH2O radical in the cyclic intermediate I3′a, likely due to increased electron donation from the two deprotonated ligand arms. In contrast, this electronic repulsion is minimized in the linear analogue I3′ by increasing the radical character on the O atom of the {NH2O} moiety, away from the deprotonated ligand arms. This is further supported by the presence of a weak Fe–N bond in I3a with significant noncovalent character in the region below −0.030 au (Figure 3), a feature not presented in I3.

The subsequent PCET process from I3 leads to the formation of the NH2OH-bound intermediate I4 (Figure 2), consistent with our independent NH2OH reduction experiments. Calculations show that the N–Fe bound isomer (I4) is favored over the O–Fe counterpart (I4a, Scheme S2a) by −0.28 eV. Considering the stoichiometry of the external acid added (3 equiv), which is fully consumed in the prior reaction steps through the pathway B, sequential PCET steps will source the protons from the ligand. Progressive intramolecular proton transfer and outer-sphere electron transfer to I4 lead to the release of a water molecule, forming I5, a species featuring an NH2 radical bound to a high-spin Fe(II) center. The analogous structure with an NH2 anion attached to a low-spin Fe(III) center was also computed (I 5s, Scheme S2b), but it is higher in energy by +0.18 eV, suggesting a stabilization preference for the Fe(II) oxidation state and the nitrogen-based radical.

The next PCET step from I5 is highly exergonic by −2.60 eV, resulting in the formation of I6 with the generated NH3 still bound to the Fe(II) center. From I6, the eventual release of NH3 occurs (I7), followed by the binding of a water molecule, which transfers one of its protons to the ligand arm, generating complex 4, as evidenced by 1H NMR spectroscopy.

For pathway A, calculations revealed an intriguing switch in binding preferences, where the O–Fe bound isomer (I4′) is favored over the N–Fe variant by −0.33 eV (I4′a, Scheme S3). This reversal in affinity leads first to the elimination of NH3, while the OH group remains bound to Fe, yielding the intermediate I6′. A series of PCET steps then follow, and ultimately, both pathways A and B converge to form the same final products: 4 and NH3.

Overall, this computational study emphasizes the significant influence of the ligand’s secondary coordination sphere and the preferential sourcing of protons from the external acid LuHOTf (pathway B) in these two extreme scenarios. While the PCET is likely extremely complicated, these insights will likely inform the design and optimization of analogous systems in future developments.

Conclusions

This work demonstrates a selective, stepwise reduction of nitrate or nitrite to either dinitrogen or ammonia, with the outcome controlled by the choice of sacrificial reductant used in the nitric oxide reduction step.15,78 While complex 1 is incredibly successful in deoxygenation reactions, the addition of external reagents in the crucial nitric oxide reduction step allows for novel reactivity in this system, such as N–N coupling to form nitrous oxide. In the first pathway, selective nitrite reduction to dinitrogen was achieved without requiring strong reductants. When using PPh3 as a sacrificial reductant in the nitric oxide reduction step, quantitative O=PPh3 production was observed, with nitrous oxide as the sole N-containing product. In the second step, the oxidation of complex 1 by nitrous oxide yielded an iron-oxo complex (3) alongside dinitrogen, closely mimicking the N-containing intermediates in the biological denitrification processes.

In the nitrate-to-ammonia pathway, strong reductants are required to reduce the iron nitrosyl species 2, formed in the reduction of nitrate or nitrite by 1, leading to relatively low yields of ammonia (28.7%). The electronic structure and iron oxidation state of complex 2 were examined through CASSCF and CASCI calculations, identifying the species as primarily Fe(III)(S = 3/2)–NO–(S = 1), in agreement with previous reported EPR spectroscopy.15

Analogous to ccNiR-mediated nitrate reduction, our results suggest a hydroxylamine intermediate in the ammonia production pathway, as supported by complex 1’s ability to directly reduce hydroxylamine to ammonia. This hypothesis is further reinforced by computational studies, which identify a bound hydroxylamine intermediate along the lowest-energy pathway in the reduction of 2. Additionally, NCI analysis highlights the crucial role of the ligand’s secondary coordination sphere in stabilizing an N-bound hydroxylamine radical, favoring it over a cyclic intermediate. This system is a rare example of a molecular catalyst selectively producing either ammonia or dinitrogen from nitrate or nitrite, with product selectivity governed by the choice of reductant at the crucial NO reduction step. These findings provide valuable insights for the rational design of related catalytic systems, showcasing methods to overcome difficult reaction steps and paving the way for future advancements in selective nitrate reduction.

Acknowledgments

This work was supported by the U.S. Department of Energy, Office of Sciences, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division under award number DOE DE-SC002102529. J.M.M. thanks Texas A&M for a graduate student HEEP fellowship. The authors thank R.L.W. for designing the TOC graphic. The DJEI/DES/SFI/HEA Irish Centre for High-End Computing (ICHEC) is also acknowledged for the generous provision of computational facilities and support. M.N.P.-D. thanks the University of Valladolid (award CONVREC-2021-221) and the JCyL (project VA016G24) for funding. M.M. and M.G.-M. also thank the Irish Research Council (GOIPG/2021/88) for a postgraduate scholarship.

Data Availability Statement

All the DFT data underlying this work, including the Cartesian coordinates and energies of all the modelled structures, is free and openly accessible via the following ioChem-BD online dataset: DOI: 10.19061/iochem-bd-6-402.

Supporting Information Available

The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.4c16585.

  • Experimental, spectral, and computational details (PDF).

The authors declare no competing financial interest.

Supplementary Material

ja4c16585_si_001.pdf (4.1MB, pdf)

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

ja4c16585_si_001.pdf (4.1MB, pdf)

Data Availability Statement

All the DFT data underlying this work, including the Cartesian coordinates and energies of all the modelled structures, is free and openly accessible via the following ioChem-BD online dataset: DOI: 10.19061/iochem-bd-6-402.

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