Expanding and Testing a Computational Method for Predicting the Ground State Reduction Potentials of Organic Molecules on the Basis of Empirical Correlation to Experiment

A method for predicting the ground state reduction potentials of organic molecules on the basis of the correlation of computed energy differences between the starting S₀ and one-electron-reduced D₀ species with experimental reduction potentials in acetonitrile has been expanded to cover 3.5 V of potential range and 74 compounds across 6 broad families of molecules. Utilizing the conductor-like polarizable continuum model of implicit solvent allows a global correlation that is computationally efficient and has improved accuracy, with <i>r</i>² > 0.98 in all cases and root mean square deviation errors of <90 mV (mean absolute deviations <70 mV) for either B3LYP/6-311+G­(d,p) or B3LYP//6-31G­(d) with an appropriate choice of radii (UAKS or UA0). The correlations are proven to be robust across a wide range of structures and potentials, including four larger (27–28 heavy atoms) and more conformationally flexible photochromic molecules not used in calibrating the correlation. The method is also proven to be robust to a number of minor student “mistakes” or methodological inconsistencies

The Functional Model Complex [Fe₂(BPMP)(OPr)(NO)₂](BPh₄)₂ Provides Insight into the Mechanism of Flavodiiron NO Reductases

Flavodiiron nitric oxide reductases (FNORs), found in many pathogenic bacteria, are able to detoxify NO by reducing it to N₂O. In this way, FNORs equip these pathogens with immunity to NO, which is a central immune defense agent in humans. Hence, FNORs are thought to promote infection of the human body, leading to chronic diseases. Despite this importance of FNORs for bacterial pathogenesis, the mechanism of NO reduction by these enzymes is not well understood. Here we present the synthesis and spectroscopic characterization of the diiron dinitrosyl model complex [Fe₂­(BPMP)­(OPr)­(NO)₂]­(BPh₄)₂. The crystal structure of this complex shows two end-on-coordinated {FeNO}⁷ units that, based on spectroscopic and electrochemical results, are only weakly electronically coupled. Importantly, reduction of this complex by two electrons leads to the clean formation of N₂O in quantitative yield. This complex therefore represents the first example of a functional model system for FNORs. The results provide key mechanistic insight into the mechanism of FNORs and, in particular, represent strong support for the proposed “super-reduced” mechanism for these enzymes

The Functional Model Complex [Fe₂(BPMP)(OPr)(NO)₂](BPh₄)₂ Provides Insight into the Mechanism of Flavodiiron NO Reductases

Flavodiiron nitric oxide reductases (FNORs), found in many pathogenic bacteria, are able to detoxify NO by reducing it to N₂O. In this way, FNORs equip these pathogens with immunity to NO, which is a central immune defense agent in humans. Hence, FNORs are thought to promote infection of the human body, leading to chronic diseases. Despite this importance of FNORs for bacterial pathogenesis, the mechanism of NO reduction by these enzymes is not well understood. Here we present the synthesis and spectroscopic characterization of the diiron dinitrosyl model complex [Fe₂­(BPMP)­(OPr)­(NO)₂]­(BPh₄)₂. The crystal structure of this complex shows two end-on-coordinated {FeNO}⁷ units that, based on spectroscopic and electrochemical results, are only weakly electronically coupled. Importantly, reduction of this complex by two electrons leads to the clean formation of N₂O in quantitative yield. This complex therefore represents the first example of a functional model system for FNORs. The results provide key mechanistic insight into the mechanism of FNORs and, in particular, represent strong support for the proposed “super-reduced” mechanism for these enzymes

The Semireduced Mechanism for Nitric Oxide Reduction by Non-Heme Diiron Complexes: Modeling Flavodiiron Nitric Oxide Reductases

Flavodiiron nitric oxide reductases (FNORs) are a subclass of flavodiiron proteins (FDPs) capable of preferential binding and subsequent reduction of NO to N₂O. FNORs are found in certain pathogenic bacteria, equipping them with resistance to nitrosative stress, generated as a part of the immune defense in humans, and allowing them to proliferate. Here, we report the spectroscopic characterization and detailed reactivity studies of the diiron dinitrosyl model complex [Fe₂(BPMP)­(OPr)­(NO)₂]­(OTf)₂ for the FNOR active site that is capable of reducing NO to N₂O [Zheng et al., <i>J. Am. Chem. Soc.</i> <b>2013</b>, <i>135</i>, 4902–4905]. Using UV–vis spectroscopy, cyclic voltammetry, and spectro-electrochemistry, we show that one reductive equivalent is in fact sufficient for the quantitative generation of N₂O, following a semireduced reaction mechanism. This reaction is very efficient and produces N₂O with a first-order rate constant <i>k</i> > 10² s^–1. Further isotope labeling studies confirm an intramolecular N–N coupling mechanism, consistent with the rapid time scale of the reduction and a very low barrier for N–N bond formation. Accordingly, the reaction proceeds at −80 °C, allowing for the direct observation of the mixed-valent product of the reaction. At higher temperatures, the initial reaction product is unstable and decays, ultimately generating the diferrous complex [Fe₂(BPMP)­(OPr)₂]­(OTf) and an unidentified ferric product. These results combined offer deep insight into the mechanism of NO reduction by the relevant model complex [Fe₂(BPMP)­(OPr)­(NO)₂]²⁺ and provide direct evidence that the semireduced mechanism would constitute a highly efficient pathway to accomplish NO reduction to N₂O in FNORs and in synthetic catalysts

Unusual Synthetic Pathway for an {Fe(NO)₂}⁹ Dinitrosyl Iron Complex (DNIC) and Insight into DNIC Electronic Structure via Nuclear Resonance Vibrational Spectroscopy

Dinitrosyl iron complexes (DNICs) are among the most abundant NO-derived cellular species. Monomeric DNICs can exist in the {Fe­(NO)₂}⁹ or {Fe­(NO)₂}¹⁰ oxidation state (in the Enemark–Feltham notation). However, experimental studies of analogous DNICs in both oxidation states are rare, which prevents a thorough understanding of the differences in the electronic structures of these species. Here, the {Fe­(NO)₂}⁹ DNIC [Fe­(dmp)­(NO)₂]­(OTf) (<b>1</b>; dmp = 2,9-dimethyl-1,10-phenanthroline) is synthesized from a ferrous precursor via an unusual pathway, involving disproportionation of an {FeNO}⁷ complex to yield the {Fe­(NO)₂}⁹ DNIC and a ferric species, which is subsequently reduced by NO gas to generate a ferrous complex that re-enters the reaction cycle. In contrast to most {Fe­(NO)₂}⁹ DNICs with neutral N-donor ligands, <b>1</b> exhibits high solution stability and can be characterized structurally and spectroscopically. Reduction of <b>1</b> yields the corresponding {Fe­(NO)₂}¹⁰ DNIC [Fe­(dmp)­(NO)₂] (<b>2</b>). The Mössbauer isomer shift of <b>2</b> is 0.08 mm/s smaller than that of <b>1</b>, which indicates that the iron center is slightly more oxidized in the reduced complex. The nuclear resonance vibrational spectra (NRVS) of <b>1</b> and <b>2</b> are distinct and provide direct experimental insight into differences in bonding in these complexes. In particular, the symmetric out-of-plane Fe–N–O bending mode is shifted to higher energy by 188 cm^–1 in <b>2</b> in comparison to <b>1</b>. Using quantum chemistry centered normal coordinate analysis (QCC-NCA), this is shown to arise from an increase in Fe–NO bond order and a stiffening of the Fe­(NO)₂ unit upon reduction of <b>1</b> to <b>2</b>. DFT calculations demonstrate that the changes in bonding arise from an iron-centered reduction which leads to a distinct increase in Fe–NO π-back-bonding in {Fe­(NO)₂}¹⁰ DNICs in comparison to the corresponding {Fe­(NO)₂}⁹ complexes, in agreement with all experimental findings. Finally, the implications of the electronic structure of DNICs for their reactivity are discussed, especially with respect to N–N bond formation in NO reductases

The Semireduced Mechanism for Nitric Oxide Reduction by Non-Heme Diiron Complexes: Modeling Flavodiiron Nitric Oxide Reductases

Flavodiiron nitric oxide reductases (FNORs) are a subclass of flavodiiron proteins (FDPs) capable of preferential binding and subsequent reduction of NO to N₂O. FNORs are found in certain pathogenic bacteria, equipping them with resistance to nitrosative stress, generated as a part of the immune defense in humans, and allowing them to proliferate. Here, we report the spectroscopic characterization and detailed reactivity studies of the diiron dinitrosyl model complex [Fe₂(BPMP)­(OPr)­(NO)₂]­(OTf)₂ for the FNOR active site that is capable of reducing NO to N₂O [Zheng et al., <i>J. Am. Chem. Soc.</i> <b>2013</b>, <i>135</i>, 4902–4905]. Using UV–vis spectroscopy, cyclic voltammetry, and spectro-electrochemistry, we show that one reductive equivalent is in fact sufficient for the quantitative generation of N₂O, following a semireduced reaction mechanism. This reaction is very efficient and produces N₂O with a first-order rate constant <i>k</i> > 10² s^–1. Further isotope labeling studies confirm an intramolecular N–N coupling mechanism, consistent with the rapid time scale of the reduction and a very low barrier for N–N bond formation. Accordingly, the reaction proceeds at −80 °C, allowing for the direct observation of the mixed-valent product of the reaction. At higher temperatures, the initial reaction product is unstable and decays, ultimately generating the diferrous complex [Fe₂(BPMP)­(OPr)₂]­(OTf) and an unidentified ferric product. These results combined offer deep insight into the mechanism of NO reduction by the relevant model complex [Fe₂(BPMP)­(OPr)­(NO)₂]²⁺ and provide direct evidence that the semireduced mechanism would constitute a highly efficient pathway to accomplish NO reduction to N₂O in FNORs and in synthetic catalysts

Synthesis and Structural Investigation of an “Oxazinoquinolinespirohexadienone” That Only Exists as Its Long-Wavelength Ring-Opened Quinonimine Isomer

The spirocyclic oxazinoquinolinespirohexadienone (OSHD) “photochromes” are computationally predicted to be an attractive target as electron deficient analogues of the perimidinespirohexadienone (PSHD) photochromes, for eventual application as photochromic photooxidants. We have found the literature method for their preparation unsuitable and present an alternative synthesis. Unfortunately the product of this synthesis is the long wavelength (LW) ring-opened quinonimine isomer of the OSHD. We have found this isomer does not close to the spirocyclic short wavelength isomer (SW) upon prolonged standing in the dark, unlike other PSHD photochromes. The structure of this long wavelength isomer was found by NMR and X-ray crystallography to be exclusively the quinolinone (keto) tautomer, though experimental cyclic voltammetry supported by our computational methodology indicates that the quinolinol (enol) tautomer (not detected by other means) may be accessible through a fast equilibrium lying far toward the keto tautomer. Computations also support the relative stability order of keto LW over enol LW over SW

Synthesis and Structural Investigation of an “Oxazinoquinolinespirohexadienone” That Only Exists as Its Long-Wavelength Ring-Opened Quinonimine Isomer

The spirocyclic oxazinoquinolinespirohexadienone (OSHD) “photochromes” are computationally predicted to be an attractive target as electron deficient analogues of the perimidinespirohexadienone (PSHD) photochromes, for eventual application as photochromic photooxidants. We have found the literature method for their preparation unsuitable and present an alternative synthesis. Unfortunately the product of this synthesis is the long wavelength (LW) ring-opened quinonimine isomer of the OSHD. We have found this isomer does not close to the spirocyclic short wavelength isomer (SW) upon prolonged standing in the dark, unlike other PSHD photochromes. The structure of this long wavelength isomer was found by NMR and X-ray crystallography to be exclusively the quinolinone (keto) tautomer, though experimental cyclic voltammetry supported by our computational methodology indicates that the quinolinol (enol) tautomer (not detected by other means) may be accessible through a fast equilibrium lying far toward the keto tautomer. Computations also support the relative stability order of keto LW over enol LW over SW

Synthesis and Structural Investigation of an “Oxazinoquinolinespirohexadienone” That Only Exists as Its Long-Wavelength Ring-Opened Quinonimine Isomer

The spirocyclic oxazinoquinolinespirohexadienone (OSHD) “photochromes” are computationally predicted to be an attractive target as electron deficient analogues of the perimidinespirohexadienone (PSHD) photochromes, for eventual application as photochromic photooxidants. We have found the literature method for their preparation unsuitable and present an alternative synthesis. Unfortunately the product of this synthesis is the long wavelength (LW) ring-opened quinonimine isomer of the OSHD. We have found this isomer does not close to the spirocyclic short wavelength isomer (SW) upon prolonged standing in the dark, unlike other PSHD photochromes. The structure of this long wavelength isomer was found by NMR and X-ray crystallography to be exclusively the quinolinone (keto) tautomer, though experimental cyclic voltammetry supported by our computational methodology indicates that the quinolinol (enol) tautomer (not detected by other means) may be accessible through a fast equilibrium lying far toward the keto tautomer. Computations also support the relative stability order of keto LW over enol LW over SW

Development of a Rubredoxin-Type Center Embedded in a <i>de Dovo</i>-Designed Three-Helix Bundle

Protein design is a powerful tool for interrogating the basic requirements for the function of a metal site in a way that allows for the selective incorporation of elements that are important for function. Rubredoxins are small electron transfer proteins with a reduction potential centered near 0 mV (vs normal hydrogen electrode). All previous attempts to design a rubredoxin site have focused on incorporating the canonical CXXC motifs in addition to reproducing the peptide fold or using flexible loop regions to define the morphology of the site. We have produced a rubredoxin site in an utterly different fold, a three-helix bundle. The spectra of this construct mimic the ultraviolet–visible, Mössbauer, electron paramagnetic resonance, and magnetic circular dichroism spectra of native rubredoxin. Furthermore, the measured reduction potential suggests that this rubredoxin analogue could function similarly. Thus, we have shown that an α-helical scaffold sustains a rubredoxin site that can cycle with the desired potential between the Fe­(II) and Fe­(III) states and reproduces the spectroscopic characteristics of this electron transport protein without requiring the classic rubredoxin protein fold