Vibrational Coupling Infrared Nanocrystallography

Coupling between molecular vibrations leads to collective vibrational states with spectral features sensitive to local molecular order. This provides spectroscopic access to the low-frequency intermolecular energy landscape. In its nanospectroscopic implementation, this technique of vibrational coupling nanocrystallography (VCNC) offers information on molecular disorder and domain formation with nanometer spatial resolution. However, deriving local molecular order relies on prior knowledge of the transition dipole magnitude and crystal structure of the underlying ordered phase. Here we develop a quantitative model for VCNC by relating nano-FTIR collective vibrational spectra to the molecular crystal structure from X-ray crystallography. We experimentally validate our approach at the example of a metal organic porphyrin complex with a carbonyl ligand as the probe vibration. This framework establishes VCNC as a powerful tool for measuring low-energy molecular interactions, wave function delocalization, nanoscale disorder, and domain formation in a wide range of molecular systems.

Interactions of arylhydroxylamines and alkylaldoximes with a rhodium porphyrin

Heme enzymes are involved in the binding and metabolism of hydroxylamine (RNHOH) and aldoxime (RCH=NOH) compounds (R = H, alkyl, aryl). We report the synthesis and X-ray crystal structure of a metalloporphyrin in complex with an arylhydroxylamine, namely that of (TPP)Rh(PhNHOH)(C6H4Cl) (TPP = tetraphenylpophryinato dianion). The crystal structure reveals, in addition to N-binding of PhNHOH to Rh, the presence of an intramolecular H-bond between the hydroxylamine -OH proton and a porphyrin N-atom. Results from density functional theory (DFT) calculations support the presence of this intramolecular H-bond in this global minimum structure, and a natural bond order (NBO) analysis reveals that this H-bond comprises a donor π N=C (porphyrin) to acceptor σ* O-H (hydroxylamine) interaction of 2.32 kcal/mol. While DFT calculations predict the presence of similar intramolecular H-bond interactions in the related aldoxime complexes (TPP)Rh(RCH=NOH)(C6H4Cl) in their global minima structures, the X-ray crystal structure obtained for the (TPP)Rh(CH3(CH2)2CH=NOH)(C6H4Cl) complex is consistent with the local (non-global) minima conformation that does not have this intramolecular H-bond interaction.

Crystal structural investigations of heme protein derivatives resulting from reactions of aryl- and alkylhydroxylamines with human hemoglobin

Phenylhydroxylamine (PhNHOH) and nitrosobenzene (PhNO) interact with human tetrameric hemoglobin (Hb) to form the nitrosobenzene adduct Hb(PhNO). These interactions also frequently lead to methemoglobin formation in red blood cells. We utilize UV-vis spectroscopy and X-ray crystallography to identify the primary and secondary products that form when PhNHOH and related alkylhydroxylamines (RNHOH; R = Me, t-Bu) react with human ferric Hb. We show that with MeNHOH, the primary product is Hb[α-FeIII(H2O)][β-FeII(MeNO)], in which nitrosomethane is bound to the β subunit but not the α subunit. Attempts to isolate a nitrosochloramphenicol (CAMNO) adduct resulted in our isolation of a Hb[α-FeII][β-FeII-cySOx]{CAMNO} product (cySOx = oxidized cysteine) in which CAMNO was located outside of the protein in the solvent region between the β2 and α2 subunits of the same tetramer. We also observed that the βcys93 residue had been oxidized. In the case of t-BuNHOH, we demonstrate that the isolated product is the β-hemichrome Hb[α-FeIII(H2O)][β-FeIII(His)2]{t-BuNHOH}, in which the β heme has slipped ∼4.4 Å towards the solvent exterior to accommodate the bis-His heme coordination. When PhNHOH is used, a similar β-hemichrome Hb[α-FeIII(H2O)][β-FeIII(His)2-cySOx]{PhNHOH} was obtained. Our results reveal, for the first time, the X-ray structural determination of a β-hemichrome in a human Hb derivative. Our UV-vis and X-ray crystal structural result reveal that although Hb(PhNO) and Hb(RNO) complexes may form as primary products, attempted isolation of these products by crystallization may result in the structural determination of their secondary products which may contain β-hemichromes en route to further protein degradation.

Interactions of metronidazole and chloramphenicol with myoglobin: Crystal structure of a Mb-acetamide product

Nitroorganics present a general concern for a safe environment due to their health hazards. However, some nitroorganics such as metronidazole (Mtz) and chloramphenicol (CAM) also possess medicinal value. Mtz and CAM can undergo reductive bioactivation presumably via their nitroso derivatives. We show, using UV-vis spectroscopy, that sperm whale myoglobin (swMb) and its distal pocket mutants retaining H-bonding capacity react with Mtz in the presence of dithionite to generate products with spectra suggestive of the Fe-bound nitroso (Fe-RNO; λmax ~420 nm) forms. We have crystallized and solved the X-ray crystal structure of an H64Q swMb-acetamide compound to 1.76 Å resolution; formation of this compound results from the serendipitous crystallographic trapping, by the heme center, of acetamide from the reductive decomposition of Mtz. Only one of the swMb proteins, namely H64Q swMb with a relatively flexible Gln64 residue, reacted with CAM presumably due to the bulky nature of CAM that generally may restrict its access to the heme site.

Insights into Nitrosoalkane Binding to Myoglobin Provided by Crystallography of Wild-Type and Distal Pocket Mutant Derivatives

Nitrosoalkanes (R-N═O; R = alkyl) are biological intermediates that form from the oxidative metabolism of various amine (RNH₂) drugs or from the reduction of nitroorganics (RNO₂). RNO compounds bind to and inhibit various heme proteins. However, structural information on the resulting Fe-RNO moieties remains limited. We report the preparation of ferrous wild-type and H64A sw Mb^II-RNO derivatives (λ_max 424 nm; R = Me, Et, Pr, iPr) from the reactions of Mb^III-H₂O with dithionite and nitroalkanes. The apparent extent of formation of the wt Mb derivatives followed the order MeNO > EtNO > PrNO > iPrNO, whereas the order was the opposite for the H64A derivatives. Ferricyanide oxidation of the Mb^II-RNO derivatives resulted in the formation of the ferric Mb^III-H₂O precursors with loss of the RNO ligands. X-ray crystal structures of the wt Mb^II-RNO derivatives at 1.76-2.0 Å resoln. revealed N-binding of RNO to Fe and the presence of H-bonding interactions between the nitroso O-atoms and distal pocket His64. The nitroso O-atoms pointed in the general direction of the protein exterior, and the hydrophobic R groups pointed toward the protein interior. X-ray crystal structures for the H64A mutant derivatives were determined at 1.74-1.80 Å resoln. An analysis of the distal pocket amino acid surface landscape provided an explanation for the differences in ligand orientations adopted by the EtNO and PrNO ligands in their wt and H64A structures. Our results provide a good baseline for the structural analysis of RNO binding to heme proteins possessing small distal pockets.

Insights into the Observed trans-Bond Length Variations upon NO Binding to Ferric and Ferrous Porphyrins with Neutral Axial Ligands

NO is well-known for its trans effect. NO binding to ferrous hemes of the form (por)Fe(L) (L = neutral N-based ligand) to give the {FeNO}⁷ (por)Fe(NO)(L) product results in a lengthening of the axial trans Fe-L bond. In contrast, NO binding to the ferric center in [(por)Fe(L)]⁺ to give the {FeNO}⁶ [(por)Fe(NO)(L)]⁺ product results in a shortening of the trans Fe-L bond. NO binding to both ferrous and ferric centers involves the lowering of their spin states. Density functional theory (DFT) calculations were used to probe the experimentally observed trans-bond shortening in some NO adducts of ferric porphyrins. We show that the strong σ antibonding interaction of d _{z ²} and the axial (L) ligand p orbitals present in the Fe(II) systems is absent in the Fe(III) systems, as it is now in an unoccupied orbital. This feature, combined with a lowering of spin state upon NO binding, provides a rationale for the observed net trans-bond shortening in the {FeNO}⁶ but not the {FeNO}⁷ derivatives.

Insight into the preferential N-binding versus O-binding of nitrosoarenes to ferrous and ferric heme centers

Nitrosoarenes (ArNOs) are toxic metabolic intermediates that bind to heme proteins to inhibit their functions. Although much of their biological functions involve coordination to the Fe centers of hemes, the factors that determine N-binding or O-binding of these ArNOs have not been determined. We utilize X-ray crystallography and density functional theory (DFT) analyses of new representative ferrous and ferric ArNO compounds to provide the first theoretical insight into preferential N-binding versus O-binding of ArNOs to hemes. Our X-ray structural results favored N-binding of ArNO to ferrous heme centers, and O-binding to ferric hemes. Results of the DFT calculations rationalize this preferential binding on the basis of the energies of associated spin-states, and reveal that the dominant stabilization forces in the observed ferrous N-coordination and ferric O-coordination are dπ-pπ* and dσ-pπ*, respectively. Our results provide, for the first time, an explanation why in situ oxidation of the ferrous-ArNO compound to its ferric state results in the observed subsequent dissociation of the ligand.

The nitrosoamphetamine metabolite is accommodated in the active site of human hemoglobin: Spectroscopy and crystal structure

Amphetamine-based (Amph) drugs are metabolized in humans to their hydroxylamine (AmphNHOH) and nitroso (AmphNO) derivatives. The latter metabolites are known to bind to the Fe centers of cytochrome P450 and other heme enzymes to inhibit their activities. Although these AmphNHOH/AmphNO metabolites are present in vivo, their interactions with the blood protein hemoglobin (Hb) and the muscle protein (Mb) have been largely discounted due to a perception that the relatively small heme active sites of Hb and Mb will not be able to accommodate the large AmphNO group. We report the 2.15 Å resolution X-ray crystal structure of the AmphNO adduct of adult human hemoglobin as the Hb [α-Fe^III(H₂O)][β-Fe^II(AmphNO)] derivative. We show that the binding of AmphNO to the β subunit is enabled by an E helix movement and stabilization of ligand binding by H-bonding with the distal His63 residue. We also observe an AmphNHOH group in the Xe2 pocket in close proximity to the α heme site in this derivative. Additionally, UV-vis spectroscopy was used to characterize this and related wt and mutant Mb adducts. Importantly, our X-ray crystal structure of this Hb-nitrosoamphetamine complex represents the first crystal structure of a wild-type heme protein adduct of any amphetamine metabolite. Our results provide a framework for further studies of AmphNHOH/AmphNO interactions with Hb and Mb as viable processes that potentially contribute to the overall biological inorganic chemistry of amphetamine drugs.

Not Limited to Iron: A Cobalt Heme-NO Model Facilitates N-N Coupling with External NO in the Presence of a Lewis Acid to Generate N2 O

Some bacterial heme proteins catalyze the coupling of two NO molecules to generate N₂ O. We previously reported that a heme Fe-NO model engages in this N-N bond-forming reaction with NO. We now demonstrate that (OEP)Co^II (NO) similarly reacts with 1 equiv of NO in the presence of the Lewis acids BX₃ (X=F, C₆ F₅ ) to generate N₂ O. DFT calculations support retention of the Co^II oxidation state for the experimentally observed adduct (OEP)Co^II (NO⋅BF₃ ), the presumed hyponitrite intermediate (P^.+ )Co^II (ONNO⋅BF₃ ), and the porphyrin π-radical cation by-product of this reaction, and that the π-radical cation formation likely occurs at the hyponitrite stage. In contrast, the Fe analogue undergoes a ferrous-to-ferric oxidation state conversion during this reaction. Our work shows that cobalt hemes are chemically competent to engage in the NO-to-N₂ O conversion reaction.

Interactions of acetamide and acrylamide with heme models: Synthesis, infrared spectra, and solid state molecular structures of five- and six-coordinate ferric porphyrin derivatives

The amide functional group is a fundamental building block of proteins, but is also present in several industrial chemicals such as acetamide and acrylamide. Some acetamide derivatives are known to deplete cytoplasmic heme, and some acrylamide derivatives are known to cause porphyria and may activate soluble guanylyl cyclase through a heme-dependent mechanism. We have prepared a representative set of six-coordinate acetamide and acrylamide (L) complexes of iron porphyrins of the form [(por)Fe(L)₂]ClO₄ (por = TPP (tetraphenylporphyrinato dianion), T(p-OMe)PP (tetrakis(p-methoxyphenyl)porphyrinato dianion)) in 76-83% yields. We have also prepared the five-coordinate derivatives [(OEP)Fe(L)]ClO₄ (OEP = octaethylporphyrinato dianion) in 68-75% yields. These compounds were characterized by IR spectroscopy and by single-crystal X-ray crystallography. The molecular structures reveal the monodentate O-binding of the acetamide and acrylamide ligands to the ferric centers, with variable H-bonding exhibited between the acetamide/acrylamide -NH₂ moieties and the perchlorate anions. The five-coordinate OEP derivatives exhibit a π-π stacking of their porphyrin macrocycles, with the acetamide complex in the Class I and the acrylamide complex in the Class S groups. These compounds represent the first structurally characterized acetamide and acrylamide adducts of iron porphyrins. Reactions of the six-coordinate derivatives with NO result in the nitrosyl [(por)Fe(NO)(L)]ClO₄ derivatives that have been characterized by IR spectroscopy.

Regulatory Targets of the Response Regulator RR_1586 from Clostridioides difficile Identified Using a Bacterial One-Hybrid Screen

The Clostridioides difficile R20291 genome encodes 57 response regulator proteins that, as part of two-component signaling pathways, regulate adaptation to environmental conditions. Genomic and transcriptomic studies in C. difficile have been limited, due to technical challenges, to the analysis of either high-throughput screens or high-priority targets, such as primary regulators of toxins or spore biology. We present the use of several technically accessible and generally applicable techniques to elucidate the putative regulatory targets of a response regulator, RR_1586, involved in sporulation of the hypervirulent C. difficile strain R20291. A DNA-binding specificity motif for RR_1586 was determined using a bacterial one-hybrid assay originally developed for Drosophila transcription factors. Comparative bioinformatics approaches identified and in vitro experiments confirmed RR_1586 binding sites upstream of putative target genes, including those that encode phosphate ion transporters, spermidine/putrescine biosynthesis and transport pathways, ABC type transport systems, known regulators of sporulation, and genes encoding spore structural proteins. Representative examples of these regulatory interactions have been tested and confirmed in Escherichia coli-based reporter assays. Finally, evidence of possible regulatory mechanisms is also presented. A working model includes self-regulation by RR_1586 and phosphorylation-dependent and -independent DNA binding at low- and high-fidelity binding sites, respectively. Broad application of this and similar approaches is anticipated to be an important catalyst for the study of gene regulation by two-component systems from pathogenic or technically challenging bacteria.IMPORTANCEClostridioides difficile spores survive under harsh conditions and can germinate into actively dividing cells capable of causing disease. An understanding of the regulatory networks controlling sporulation and germination in C. difficile could be exploited for therapeutic advantage. However, such studies are hindered by the challenges of working with an anaerobic pathogen recalcitrant to genetic manipulation. Although two-component response regulators can be identified from genetic sequences, identification of their downstream regulatory networks requires further development. This work integrates experimental and bioinformatic approaches, which provide practical advantages over traditional transcriptomic analyses, to identify the putative regulon of the C. difficile response regulator RR_1586 by first screening for protein-DNA interactions in E. coli and then predicting regulatory outputs in C. difficile.

Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets

The globular dioxygen binding heme protein myoglobin (Mb) is present in several species. Its interactions with the simple nitrogen oxides, namely, nitric oxide (NO) and nitrite, have been known for decades, but the physiological relevance has only recently become more fully appreciated. We previously reported the O-nitrito mode of binding of nitrite to ferric horse heart wild-type (wt) Mb^III and human hemoglobin. We have expanded on this work and report the interactions of nitrite with wt sperm whale (sw) Mb^III and its H64A, H64Q, and V68A/I107Y mutants whose dissociation constants increase in the following order: H64Q < wt < V68A/I107Y < H64A. We also report their X-ray crystal structures that reveal the O-nitrito mode of binding of nitrite to these derivatives. The Mb^II-mediated reductions of nitrite to NO and structural data for the wt and mutant Mb^II-NOs are described. We show that their FeNO orientations vary with distal pocket identity, with the FeNO moieties pointing toward the hydrophobic interiors when the His64 residue is present but toward the hydrophilic exterior when this His64 residue is absent in this set of mutants. This correlates with the nature of H-bonding to the bound NO ligand (nitrosyl O vs N atom). Quantum mechanics and hybrid quantum mechanics and molecular mechanics calculations help elucidate the origin of the experimentally preferred NO orientations. In a few cases, the calculations reproduce the experimentally observed orientations only when the whole protein is taken into consideration.

Bis(cobaltocenium) tetrachloridocobaltate(II) dichloromethane 1.2-solvate

The structure of bis(cobaltocenium) tetrachloridocobaltate(II) dichloromethane 1.2-solvate, [Co(C5H5)2]2[CoCl4]·1.2CH2Cl2, has been determined at 100 K. The title compound crystallizes in the space groupP-1 and is an example of an unusualZ′ = 5 structure. The asymmetric unit contains ten cobaltocenium ions, five tetrachloridocobaltate(II) ions and six molecules of dichloromethane,i.e.5{[Cp2Co]2[CoCl4]}·6CH2Cl2. All the cobaltocenium ions are determined to be in the eclipsed conformation with respect to the cyclopentadienyl rings.

Lewis Acid Activation of the Ferrous Heme-NO Fragment toward the N-N Coupling Reaction with NO To Generate N2O

Bacterial NO reductase (bacNOR) enzymes utilize a heme/non-heme active site to couple two NO molecules to N₂O. We show that BF₃ coordination to the nitrosyl O-atom in (OEP)Fe(NO) activates it toward N-N bond formation with NO to generate N₂O. ¹⁵N-isotopic labeling reveals a reversible nitrosyl exchange reaction and follow-up N-O bond cleavage in the N₂O formation step. Other Lewis acids (B(C₆F₅)₃ and K⁺) also promote the NO coupling reaction with (OEP)Fe(NO). These results, complemented by DFT calculations, provide experimental support for the cis: b₃ pathway in bacNOR.

Over or under: hydride attack at the metal versus the coordinated nitrosyl ligand in ferric nitrosyl porphyrins

Hydride attack at a ferric heme-NO to give an Fe-HNO intermediate is a key step in the global N-cycle. We demonstrate differential reactivity when six- and five-coordinate ferric heme-NO models react with hydride. Although Fe-HNO formation is thermodynamically favored from this reaction, Fe-H formation is kinetically favored for the 5C case.

Carbon-Nitrogen and Nitrogen-Nitrogen Bond Formation from Nucleophilic Attack at Coordinated Nitrosyls in Fe and Ru Heme Models

The conversion of inorganic NO_x species to organo-N compounds is an important component of the global N-cycle. Reaction of a C-based nucleophile, namely the phenyl anion, with the ferric heme nitrosyl [(OEP)Fe(NO)(5-MeIm)]⁺ generates a mixture of the C-nitroso derivative (OEP)Fe(PhNO)(5-MeIm) and (OEP)Fe(Ph). The related reaction with [(OEP)Ru(NO)(5-MeIm)]⁺ generates the (OEP)Ru(PhNO)(5-MeIm) product. Reactions with the N-based nucleophile diethylamide results in the formation of free diethylnitrosamine, whereas the reaction with azide results in N₂O formation; these products derive from attack of the nucleophiles on the bound NO groups. These results provide the first demonstrations of C-N and N-N bond formation from attack of C-based and N-based nucleophiles on synthetic ferric-NO hemes.

Nitrosoamphetamine binding to myoglobin and hemoglobin: Crystal structure of the H64A myoglobin-nitrosoamphetamine adduct

N-hydroxyamphetamine (AmphNHOH) is an oxidative metabolite of amphetamine and methamphetamine. It is known to form inhibitory complexes upon binding to heme proteins. However, its interactions with myoglobin (Mb) and hemoglobin (Hb) have not been reported. We demonstrate that the reactions of AmphNHOH with ferric Mb and Hb generate the respective heme-nitrosoamphetamine derivatives characterized by UV-vis spectroscopy. We have determined the X-ray crystal structure of the H64A Mb-nitrosoamphetamine complex to 1.73 Å resolution. The structure reveals the N-binding of the nitroso-d-amphetamine isomer, with no significant H-bonding interactions between the ligand and the distal pocket amino acid residues.

Crystal structures of two nitroreductases from hypervirulent Clostridium difficile and functionally related interactions with the antibiotic metronidazole

Nitroreductases (NRs) are flavin mononucleotide (FMN)-dependent enzymes that catalyze the biotransformation of organic nitro compounds (RNO2; R = alkyl, aryl) to the nitroso RN=O, hydroxylamino RNHOH, or amine RNH2 derivatives. Metronidazole (Mtz) is a nitro-containing antibiotic that is commonly prescribed for lower-gut infections caused by the anaerobic bacterium Clostridium difficile. C. difficile infections rank number one among hospital acquired infections, and can result in diarrhea, severe colitis, or even death. Although NRs have been implicated in Mtz resistance of C. difficile, no NRs have been characterized from the hypervirulent R20291 strain of C. difficile. We report the first expression, purification, and three-dimensional X-ray crystal structures of two NRs from the C. difficile R20291 strain. The X-ray crystal structures of the two NRs were solved to 2.1 Å resolution. Their homodimeric structures exhibit the classic NR α+β fold, with each protomer binding one FMN cofactor near the dimer interface. Functional assays demonstrate that these two NRs metabolize Mtz with associated re-oxidation of the proteins. Importantly, these results represent the first isolation and characterization of NRs from the hypervirulent R20291 strain of relevance to organic RNO2 (e.g., Mtz) metabolism.

Organometallic myoglobins: Formation of Fe-carbon bonds and distal pocket effects on aryl ligand conformations

Bioorganometallic Fe-C bonds are biologically relevant species that may result from the metabolism of natural or synthetic hydrazines. The molecular structures of four new sperm whale mutant myoglobin derivatives with Fe-aryl moieties, namely H64A-tolyl-m, H64A-chlorophenyl-p, H64Q-tolyl-m, and H64Q-chlorophenyl-p, have been determined at 1.7-1.9Å resolution. The structures reveal conformational preferences for the substituted aryls resulting from attachment of the aryl ligands to Fe at the site of net -NHNH2 release from the precursor hydrazines, and show distal pocket changes that readily accommodate these bulky ligands.

Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291

Background

Clostridium difficile is a spore-forming obligate anaerobe that can remain viable for extended periods, even in the presence of antibiotics, which contributes to the persistence of this bacterium as a human pathogen during host-to-host transmission and in hospital environments. We examined the structure and function of a gene product with the locus tag CDR20291_0991 (cdPadR1) as part of our broader goal aimed at elucidating transcription regulatory mechanisms involved in virulence and antibiotic resistance of the recently emergent hypervirulent C. difficile strain R20291. cdPadR1 is genomically positioned near genes that are involved in stress response and virulence. In addition, it was previously reported that cdPadR1 and a homologue from the historical C. difficile strain 630 (CD630_1154) were differentially expressed when exposed to stressors, including antibiotics.

Results

The crystal structure of cdPadR1 was determined to 1.9 Å resolution, which revealed that it belongs to the PadR-s2 subfamily of PadR transcriptional regulators. cdPadR1 binds its own promoter and other promoter regions from within the C. difficile R20291 genome. DNA binding experiments demonstrated that cdPadR1 binds a region comprised of inverted repeats and an AT-rich core with the predicted specific binding motif, GTACTAT(N₂)ATTATA(N)AGTA, within its own promoter that is also present in 200 other regions in the C. difficile R20291 genome. Mutation of the highly conserved W in α4 of the effector binding/oligomerization domain, which is predicted to be involved in multi-drug recognition and dimerization in other PadR-s2 proteins, resulted in alterations of cdPadR1 binding to the predicted binding motif, potentially due to loss of higher order oligomerization.

Conclusions

Our results indicate that cdPadR1 binds a region within its own promoter consisting of the binding motif GTACTAT(N₂)ATTATA(N)AGTA and seems to associate non-specifically with longer DNA fragments in vitro, which may facilitate promoter and motif searching. This suggests that cdPadR1 acts as a transcriptional auto-regulator, binding specific sites within its own promoter, and is part of a broad gene regulatory network involved, in part, with environmental stress response, antibiotic resistance and virulence.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0850-0) contains supplementary material, which is available to authorized users.

Nitric oxide coupling to generate N2O promoted by a single-heme system as examined by density functional theory

Bacteria utilize a heme/non-heme enzyme system to detoxify nitric oxide (NO) to N₂O. In order to probe the capacity of a single-heme system to mediate this NO-to-N₂O transformation, various scenarios for addition of electrons, protons, and a second NO molecule to a heme nitrosyl to generate N₂O were explored by density functional theory calculations. We describe, utilizing this single-heme system, several stepwise intermediates along pathways that enable the critical N-N bond formation step yielding the desired Fe-N₂O product. We also report a hitherto unreported directional second protonation that results in either productive N₂O formation with loss of water, or formation of a non-productive hyponitrous acid adduct Fe{HONNOH}.

Hydride Attack on a Coordinated Ferric Nitrosyl: Experimental and DFT Evidence for the Formation of a Heme Model-HNO Derivative

Heme-HNO species are crucial intermediates in several biological processes. To date, no well-defined Fe heme-HNO model compounds have been reported. Hydride attack on the cationic ferric [(OEP)Fe(NO)(5-MeIm)]OTf (OEP = octaethylporphyrinato dianion) generates an Fe-HNO product that has been characterized by IR and (1)H NMR spectroscopy. Results of DFT calculations reveal a direct attack of the hydride on the N atom of the coordinated ferric nitrosyl.

Six-coordinate ferric porphyrins containing bidentate N-t-butyl-N-nitrosohydroxylaminato ligands: structure, magnetism, IR spectroelectrochemisty, and reactivity

NONOates (diazeniumdiolates) containing the [X{N2O2}](-) functional group are frequently employed as nitric oxide (NO) donors in biology, and some NONOates have been shown to bind to metalloenzymes. We report the preparation, crystal structures, detailed magnetic behavior, redox properties, and reactivities of the first isolable alkyl C-NONOate complexes of heme models, namely (OEP)Fe(η(2)-ON(t-Bu)NO) (1) and (TPP)Fe(η(2)-ON(t-Bu)NO) (2) (OEP = octaethylporphyrinato dianion, TPP = tetraphenylporphyrinato dianion). The compounds display the unusual NONOate O,O-bidentate binding mode for porphyrins, resulting in significant apical Fe displacements (+0.60 Å for 1, and +0.69 Å for 2) towards the axial ligands. Magnetic susceptibility and magnetization measurements made from 1.8-300 K at magnetic fields from 0.02 to 5 T, yielded magnetic moments of 5.976 and 5.974 Bohr magnetons for 1 and 2, respectively, clearly identifying them as high-spin (S = 5/2) ferric compounds. Variable-frequency (9.4 GHz and 34.5 GHz) EPR measurements, coupled with computer simulations, confirmed the magnetization results and yielded more precise values for the spin Hamiltonian parameters: g(avg) = 2.00 ± 0.03, |D| = 3.89 ± 0.09 cm(-1), and E/D = 0.07 ± 0.01 for both compounds, where D and E are the axial and rhombic zero-field splittings. IR spectroelectrochemistry studies reveal that the first oxidations of these compounds occur at the porphyrin macrocycles and not at the Fe-NONOate moieties. Reactions of 1 and 2 with a histidine mimic (1-methylimidazole) generate RNO and NO, both of which may bind to the metal center if sterics allow, as shown by a comparative study with the Cupferron complex (T(p-OMe)PP)Fe(η(2)-ON(Ph)NO). Protonation of 1 and 2 yields N2O as a gaseous product, presumably from the initial generation of HNO that dimerizes to the observed N2O product.

A bridged di-iron porphyrin hyponitrite complex as a model for biological N2O production from hyponitrite

Heme-hyponitrites are intermediates that form at the bimetallic active sites of bacterial nitric oxide reductases. To probe a possible effect of the Fe-Fe distance on hyponitrite stability, we prepared a bridged bis-porphyrin Fe-hyponitrite compound, namely [(OEP-CH2)Fe]2(μ2,η(1),η(1)-ONNO). Its υNO of 992 cm(-1) (υ15NO of 976 cm(-1)) is close to the υNO of 983 cm(-1) reported previously by us for the crystallographically characterized [(OEP)Fe]2(μ2,η(1),η(1)-ONNO) compound. The bridged bis-porphyrin Fe-hyponitrite complex is unstable with respect to N2O production, supporting the role of the bis-Fe porphyrin system in hyponitrite conversion to N2O. The preparation and crystallographic determination of the bridging sulfato derivative is also reported.

Crystal structure of N-(2-{[2,6-bis-(2,2,2-tri-fluoro-acetamido)-phen-yl]disulfan-yl}-3-(2,2,2-tri-fluoro-acetamido)-phen-yl)-2,2,2-tri-fluoro-acetamide

The title compound, C20H10F12N4O4S2, is an organic diaryl di-sulfide compound with tri-fluoro-acetamide substituents at the ortho-positions of each benzene ring. There are two mol-ecules (labeled A and B) in the asymmetric unit. The F atoms of three of the -CF3 groups exhibit rotational disorder over two positions each. The S-S bond distances are 2.0914 (7) and 2.0827 (6) Å for mol-ecules A and B, respectively. The dihedral angle between the S-S-C and S-C-C planes is 103.05 (15)° for mol-ecule A and 104.09 (15)° for mol-ecule B. The three-dimensional supra-molecular architecture of the crystal is sustained by numerous N-H⋯O, N-H⋯S and C-H⋯O inter-actions.

Crystal structure of bis-(1-methyl-1H-imidazole-κN (3))(5,10,15,20-tetra-phenyl-porphyrinato-κ(4) N)iron(II)-1-methyl-1H-imidazole (1/2)

The title compound, [Fe(C44H28N4)(C4H6N2)2]·2C4H6N2, is a six-coordinate Fe(II)-porphyrinate complex with the metal located on a center of inversion and coordinated by two axial 1-methyl-imidazole ligands; the complex crystallizes as a 1-methyl-imidazole disolvate. The 1-methyl-imidazole group bonded to the Fe(II) atom [occupancy ratio 0.789 (4):0.211 (4)] and the unbound 1-methyl-imidazole mol-ecule [0.519 (4):0.481 (4)] were disordered. The average Fe-N(porphyrinate) bond length is 1.998 (3) Å and the axial Fe-N(imidazole) bond length is 1.9970 (12) Å. In the crystal, mol-ecules are linked into a three-mol-ecule aggregate by two weak C-H⋯N inter-actions.

Crystal structure of chlorido-{5,10,15,20-tetra-kis-[2-(2,2-di-methyl-propanamido)-phen-yl]porphyrinato-κ(4) N}iron(III)

The title compound, [Fe(C64H64N8O4)Cl], is a five-coordinate square-pyramidal porphyrin complex with a chloride ion in the axial position, being coordinated from the protected side of the porphyrin; the Fe(III) atom is displaced by 0.474 (5) Å from the 24-atom mean plane of the porphyrin core towards the chloride. The porphyrin moiety is a 'picket-fence' 5,10,15,20-tetra-kis-[2-(2,2-di-methyl-propanamido)-phen-yl]porph-yrinate (por) group. The Fe-Cl bond length is 2.221 (2) Å and the Fe-N(por) bond lengths are in the range 2.043 (5)-2.063 (5) Å. The supra-molecular architecture of the crystal is sustained by C-H⋯O inter-actions between the pyrrolic and phenyl H atoms of one mol-ecule and the carbonyl O atoms of the 2,2-di-methyl-propanamido groups of adjacent mol-ecules. The methyl groups of three of the four tert-butyl substituents exhibited rotational disorder over two positions. The investigated crystal was twinned by a twofold rotation about the (001) axis with a refined twin ratio of 0.4086 (16).

Crystallographic characterization of the nitric oxide derivative of R-state human hemoglobin

Nitric oxide (NO) is a signaling agent that is biosynthesized in vivo. NO binds to the heme center in human hemoglobin (Hb) to form the HbNO adduct. This reaction of NO with Hb has been studied for many decades. Of continued interest has been the effect that the bound NO ligand has on the geometrical parameters of the resulting heme-NO active site. Although the crystal structure of a T-state human HbNO complex has been published previously, that of the high affinity R-state HbNO derivative has not been reported to date. We have crystallized and solved the three-dimensional X-ray structure of R-state human HbNO to 1.90 Å resolution. The differences in the FeNO bond parameters and H-bonding patterns between the α and β subunits contribute to understanding of the observed enhanced stability of the α(FeNO) moieties relative to the β(FeNO) moieties in human R-state HbNO.

Synthesis, molecular structure, and spectroelectrochemistry of a nitrosyl iron porphyrin containing an unsymmetrical xanthene-linked porphyrin core

Synthetic nitrosyl porphyrins with meso-aryl substituents are potential models for the biologically-important NO-bound P460 heme cofactor. A five-coordinate iron nitrosyl tetraaryl-porphyrin (HTPPX-CO2H)Fe(NO) containing a xanthene-based meso substituent has been prepared. The crystal structure of this formally {FeNO}7 complex reveals an ordered axial and bent NO ligand (∠FeNO=142.5(6)Å) displaying an off-axis tilt of the nitrosyl N atom from the heme normal by 9.2°. Surprisingly, the porphyrin core does not display the expected asymmetry in FeN(por) distances frequently observed in iron nitrosyl porphyrins. The redox behavior as determined by cyclic voltammetry reveals, in contrast to most (por)Fe(NO) compounds, a fast NO dissociation after electrooxidation in CH2Cl2 to result in a net chemically-irreversible oxidation at Epa=+0.77V vs Ag/AgCl. IR spectroelectrochemistry reveals a recombination, on the spectroelectrochemistry time-scale, of the dissociated NO on oxidation with electrogenerated [(HTPPX-CO2H)Fe]+.

(1-Methyl-1H-imidazole-κN (3))(1-methyl-2-nitroso-benzene-κN)(5,10,15,20-tetra-phenyl-porphyrinato-κ(4) N)iron(II) di-chloro-methane monosolvate

The solvated title compound, [Fe(C₄₄H₂₈N₄)(C₄H₆N₂)(C₇H₇NO)]·CH₂Cl₂, is a porphyrin complex containing an octahedrally coordinated Fe^II atom with 1-methylimidazole [Fe—N = 2.0651 (17) Å] and o-nitro­sotoluene ligands at the axial positions. The o-nitro­sotoluene ligand is N-bound to iron(II) [Fe—N = 1.8406 (18)Å and Fe—N—O = 122.54 (14)°]. The axial N—Fe—N linkage is almost linear, with a bond angle of 177.15 (7)°. One phenyl group of the porphyrin ligand is disordered over two orientations in a 0.710 (3):0.290 (3) ratio. The di­chloro­methane solvent mol­ecule was severely disordered and its contribution to the scattering was removed with the SQUEEZE routine [van der Sluis & Spek (1990 ▶). Acta Cryst. A46, 194–201].

(2,3,5,6-Tetrafluorophenolato-κO)(5,10,15,20-tetraphenylporphyrinato)iron(III)

The title compound, [Fe(C₄₄H₂₈N₄)(C₆HF₄O)], is a porphyrin complex with iron(III) in fivefold coordination with a tetra­fluoro­phenolate group as the axial ligand. The Fe atom and the phenolate ligand are disordered across the porphyrin ring with the two phenolates appearing to be roughly related by a center of symmetry. The occupancies of the two phenolate groups refined to 0.788 (3) for the major component and 0.212 (3) for the minor component. The structure shows extraordinary Fe displacements of 0.488 (4) (major) and 0.673 (4) Å (minor) from the 24-atom mean plane of the porphyrin. The Fe—N_p distances range from 2.063 (4) to 2.187 (6) Å and the Fe—O distances are 1.903 (5) Å for major component and 1.87 (2) Å for minor component. The four phenyl groups attached to the porphyrin ring form dihedral angles of 63.4 (4), 49.6 (4), 62.4 (4), and 63.3 (4)° (in increasing numerical order) with the three nearest C atoms of the porphyrin ring. The major and minor component phenolate groups form dihedral angles of 24.9 (4)° and 24.8 (4)°, respectively, with the four porphyrin N atoms. The Fe⋯Fe distance between the two iron(III) atoms of adjacent porphyrin mol­ecules is 6.677 (3) Å. No close inter­molecular inter­action was observed. The crystal studied was twinned by inversion, with a major–minor component ratio of 0.53 (3):0.47 (3).

(2,3,5,6-Tetrafluorophenolato)[5,10,15,20-tetrakis(4-methoxyphenyl)porphyrinato]iron(III) cyclohexane monosolvate

The title compound, [Fe(C₆HF₄O)(C₄₈H₃₆N₄O₄)]·C₆H₁₂, represents a five-coordinate iron(III) porphyrin complex in a square-pyramidal geometry with a tetra­fluoro­phenolate anion as the axial ligand. The Fe^III atom is displaced by 0.364 (2) Å from the 24-atom mean plane of the porphyrinate ring towards the tetra­fluoro phenolate anion. The average Fe—N distance is 2.053 (2) Å and the Fe—O distance is 1.883 (2) Å. A porphyrin aryl H atom points in the general direction of the phenoxide ring. The mean plane separation between the 24-atom porphyrin planes of two adjacent porphyrin rings is ∼3.7 Å, and the lateral shift is ∼3.5 Å resu, ting in an Fe⋯Fe separation of 5.6167 (14) Å.

Nitric oxide coupling mediated by iron porphyrins: the N-N bond formation step is facilitated by electrons and a proton

The coupling of two NO molecules catalyzed by iron porphyrins is of biological importance. We use density functional theory calculations to examine the factors that control the fundamental N-N bond formation step mediated by a single iron porphyrin. The presence of an axial Im ligand, extra electrons, and most importantly a proton, enhance the N-N bond formation step in our model.