Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone.

Hemoproteins have recently emerged as promising biocatalysts for new-to-nature carbene transfer reactions. However, mechanistic understanding of the interplay between productive and unproductive pathways in these processes is limited. Using spectroscopic, structural, and computational methods, we investigate the mechanism of a myoglobin-catalyzed cyclopropanation reaction with diazoketones. These studies shed light on the nature and kinetics of key catalytic steps in this reaction, including the formation of an early heme-bound diazo complex intermediate, the rate-determining nature of carbene formation, and the cyclopropanation mechanism. Our analyses further reveal the existence of a complex mechanistic manifold for this reaction that includes a competing pathway resulting in the formation of an N-bound carbene adduct of the heme cofactor, which was isolated and characterized by X-ray crystallography, UV-Vis, and Mössbauer spectroscopy. This species can regenerate the active biocatalyst, constituting a non-productive, yet non-destructive detour from the main catalytic cycle. These findings offer a valuable framework for both mechanistic analysis and design of hemoprotein-catalyzed carbene transfer reactions.

Liposome-Templated Green Synthesis of Mesoporous Metal Nanostructures with Universal Composition for Biomedical Application.

Porous noble metal nanoparticles have received particular attention recently for their unique optical, thermal, and catalytic functions in biomedicine. However, limited progress has been made to synthesize such porous metallic nanostructures with large mesopores (≥25 nm). Here, a green yet facile synthesis strategy using biocompatible liposomes as templates to mediate the formation of mesoporous metallic nanostructures in a controllable fashion is reported. Various monodispersed nanostructures with well-defined mesoporous shape and large mesopores (≈ 40 nm) are successfully synthesized from mono- (Au, Pd, and Pt), bi- (AuPd, AuPt, AuRh, PtRh, and PdPt), and tri-noble metals (AuPdRh, AuPtRh, and AuPdPt). Along with a successful demonstration of its effectiveness in synthesis of various mesoporous nanostructures, the possible mechanism of liposome-guided formation of such nanostructures via time sectioning of the synthesis process (monitoring time-resolved growth of mesoporous structures) and computational quantum molecular modeling (analyzing chemical interaction energy between metallic cations and liposomes at the enthalpy level) is also revealed. These mesoporous metallic nanostructures exhibit a strong photothermal effect in the near-infrared region, effective catalytic activities in hydrogen peroxide decomposition reaction, and high drug loading capacity. Thus, the liposome-templated method provides an inspiring and robust avenue to synthesize mesoporous noble metal-based nanostructures for versatile biomedical applications.

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.

Stepwise nitrosylation of the nonheme iron site in an engineered azurin and a molecular basis for nitric oxide signaling mediated by nonheme iron proteins.

Mononitrosyl and dinitrosyl iron species, such as {FeNO}7, {FeNO}8 and {Fe(NO)2}9, have been proposed to play pivotal roles in the nitrosylation processes of nonheme iron centers in biological systems. Despite their importance, it has been difficult to capture and characterize them in the same scaffold of either native enzymes or their synthetic analogs due to the distinct structural requirements of the three species, using redox reagents compatible with biomolecules under physiological conditions. Here, we report the realization of stepwise nitrosylation of a mononuclear nonheme iron site in an engineered azurin under such conditions. Through tuning the number of nitric oxide equivalents and reaction time, controlled formation of {FeNO}7 and {Fe(NO)2}9 species was achieved, and the elusive {FeNO}8 species was inferred by EPR spectroscopy and observed by Mössbauer spectroscopy, with complemental evidence for the conversion of {FeNO}7 to {Fe(NO)2}9 species by UV-Vis, resonance Raman and FT-IR spectroscopies. The entire pathway of the nitrosylation process, Fe(ii) → {FeNO}7 → {FeNO}8 → {Fe(NO)2}9, has been elucidated within the same protein scaffold based on spectroscopic characterization and DFT calculations. These results not only enhance the understanding of the dinitrosyl iron complex formation process, but also shed light on the physiological roles of nitric oxide signaling mediated by nonheme iron proteins.

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.

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)CoII (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 CoII oxidation state for the experimentally observed adduct (OEP)CoII (NO⋅BF3 ), the presumed hyponitrite intermediate (P.+ )CoII (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.

Mechanistic Investigation of Biocatalytic Heme Carbenoid Si-H Insertions.

Recent studies reported the development of biocatalytic heme carbenoid Si-H insertions for the selective formation of carbon-silicon bonds, but many mechanistic questions remain unaddressed. To this end, a DFT mechanistic investigation was performed which reveals an FeII-based concerted hydride transfer mechanism with early transition state feature. The results from these computational analyses are consistent with experimental data of radical trapping, kinetic isotope effects, and structure-reactivity data using engineered variants of hemoproteins. Detailed geometric and electronic profiles along the heme catalyzed Si-H insertion pathways were provided to help understand the origin of experimental reactivity trends. Quantitative relationships between reaction barriers and some properties such as charge transfer from substrate to heme carbene and Si-H bond length change from reactant to transition state were found. Results suggest catalyst modifications to facilitate the charge transfer from the silane substrate to the carbene, which was determined to be a major electronic driving force of this reaction, should enable the development of improved biocatalysts for Si-H carbene insertion reactions.

Biocatalytic Strategy for Highly Diastereo- and Enantioselective Synthesis of 2,3-Dihydrobenzofuran-Based Tricyclic Scaffolds.

2,3-Dihydrobenzofurans are key pharmacophores in many natural and synthetic bioactive molecules. A biocatalytic strategy is reported here for the highly diastereo- and enantioselective construction of stereochemically rich 2,3-dihydrobenzofurans in high enantiopurity (>99.9% de and ee), high yields, and on a preparative scale via benzofuran cyclopropanation with engineered myoglobins. Computational and structure-reactivity studies provide insights into the mechanism of this reaction, enabling the elaboration of a stereochemical model that can rationalize the high stereoselectivity of the biocatalyst. This information was leveraged to implement a highly stereoselective route to a drug molecule and a tricyclic scaffold featuring five stereogenic centers via a single-enzyme transformation. This work expands the biocatalytic toolbox for asymmetric C-C bond transformations and should prove useful for further development of metalloprotein catalysts for abiotic carbene transfer reactions.

Catalytic Role of Conserved Asparagine, Glutamine, Serine, and Tyrosine Residues in Isoprenoid Biosynthesis Enzymes.

We report the results of an investigation into the catalytic role of highly conserved amide (asparagine, glutamine) and OH-containing (serine, tyrosine) residues in several prenyltransferases. We first obtained the X-ray structure of cyclolavandulyl diphosphate synthase containing two molecules of the substrate analog dimethylallyl (S)-thiolodiphosphate (DMASPP). The two molecules have similar diphosphate group orientations to those seen in other ζ-fold (cis- head-to-tail and head-to-middle) prenyltransferases with one diphosphate moiety forming a bidentate chelate with Mg2+ in the so-called S1 site (which is typically the allylic binding site in ζ-fold proteins) while the second diphosphate binds to Mg2+ in the so-called S2 site (which is typically the homoallylic binding site in ζ-fold proteins) via a single P1O1 oxygen. The latter interaction can facilitate direct phosphate-mediated proton abstraction via P1O2, or more likely by an indirect mechanism in which P1O2 stabilizes a basic asparagine species that removes H+, which is then eliminated via an Asn-Ser shuttle. The universal occurrence of Asn-Ser pairs in ζ-fold proteins leads to the idea that the highly conserved amide (Asn, Gln) and OH-containing (Tyr) residues seen in many "head-to-head" prenyltransferases such as squalene and dehydrosqualene synthase might play similar roles, in H+ elimination. Structural, bioinformatics and mutagenesis investigations indeed indicate an important role of these residues in catalysis, with the results of density functional theory calculations showing that Asn bound to Mg2+ can act as a general (imine-like) base, while Gln, Tyr and H2O form a proton channel that is adjacent to the conventional (Asp-rich) "active site". Taken together, our results lead to mechanisms of proton-elimination from carbocations in numerous prenyltransferases in which neutral species (Asn, Gln, Ser, Tyr, H2O) act as proton shuttles, complementing the more familiar roles of acidic groups (in Asp and Glu) that bind to Mg2+, and basic groups (primarily Arg) that bind to diphosphates, in isoprenoid biosynthesis.

Bisphosphonate-Generated ATP-Analogs Inhibit Cell Signaling Pathways.

Bisphosphonates are a major class of drugs used to treat osteoporosis, Paget's disease, and cancer. They have been proposed to act by inhibiting one or more targets including protein prenylation, the epidermal growth factor receptor, or the adenine nucleotide translocase. Inhibition of the latter is due to formation in cells of analogs of ATP: the isopentenyl ester of ATP (ApppI) or an AppXp-type analog of ATP, such as AMP-clodronate (AppCCl2p). We screened both ApppI as well as AppCCl2p against a panel of 369 kinases finding potent inhibition of some tyrosine kinases by AppCCl2p, attributable to formation of a strong hydrogen bond between tyrosine and the terminal phosphonate. We then synthesized bisphosphonate preprodrugs that are converted in cells to other ATP-analogs, finding low nM kinase inhibitors that inhibited cell signaling pathways. These results help clarify our understanding of the mechanisms of action of bisphosphonates, potentially opening up new routes to the development of bone resorption, anticancer, and anti-inflammatory drug leads.

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.

C-H Insertions by Iron Porphyrin Carbene: Basic Mechanism and Origin of Substrate Selectivity.

Recent experimental reports of heme carbene C-H insertions show promising results for sustainable chemistry due to good yield and selectivity, low cost of iron, and low/no toxicity of hemes. But mechanistic details are mostly unknown. Despite structural similarity and isoelectronic nature between heme carbene and the FeIV =O intermediate, our quantum chemical studies with detailed geometric and electronic information for the first time reveal an FeII -based, concerted, hydride-transfer mechanism, which is different from the FeIV -based stepwise hydrogen atom transfer mechanism for C-H functionalization by native heme enzymes. A trend of broad range experimental C-H insertion yields (0-88 %) of five different C-H bonds, including mostly non-functionalized moieties, was well reproduced. Results suggest that the substrate selectivity originates from the hydride formation capability. The predicted kinetic isotope effects were also in excellent agreement with experiment. Useful geometry, charge, and energy parameters well correlated with barriers were reported. These results provide the first theoretical evidence that carbene formation is the overall rate-limiting step, and suggest a key role of the formation of strong electrophilic heme carbene in developing heme-based C-H insertion catalysts and biocatalysts.

HNO-Binding in Heme Proteins: Effects of Iron Oxidation State, Axial Ligand, and Protein Environment.

HNO plays significant roles in many biological processes. Numerous heme proteins bind HNO, an important step for its biological functions. A systematic computational study was performed to provide the first detailed trends and origins of the effects of iron oxidation state, axial ligand, and protein environment on HNO binding. The results show that HNO binds much weaker with ferric porphyrins than corresponding ferrous systems, offering strong thermodynamic driving force for experimentally observed reductive nitrosylation. The axial ligand was found to influence HNO binding through its trans effect and charge donation effect. The protein environment significantly affects the HNO hydrogen bonding structures and properties. The predicted NMR and vibrational data are in excellent agreement with experiment. This broad range of results shall facilitate studies of HNO binding in many heme proteins, models, and related metalloproteins.

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.

Catalytic and Biocatalytic Iron Porphyrin Carbene Formation: Effects of Binding Mode, Carbene Substituent, Porphyrin Substituent, and Protein Axial Ligand.

Iron porphyrin carbenes (IPCs) are important intermediates in various chemical reactions catalyzed by iron porphyrins and engineered heme proteins, as well as in the metabolism of various xenobiotics by cytochrome P450. However, there are no prior theoretical reports to help understand their formation mechanisms and identify key information governing the binding mode, formation feasibility, and stability/reactivity. A systematic quantum chemical study was performed to investigate the effects of carbene substituent, porphyrin substituent, and axial ligand on IPC formation pathways. Results not only are consistent with available experimental data but also provide a number of unprecedented insights into electronic, steric, and H-bonding effects of various structural factors on IPC formation mechanisms. These results shall facilitate research on IPC and related systems for sustainable chemical catalysis and biocatalysis.

Solid-state ¹7O NMR spectroscopy of paramagnetic coordination compounds.

High-quality solid-state (17)O (I=5/2) NMR spectra can be successfully obtained for paramagnetic coordination compounds in which oxygen atoms are directly bonded to the paramagnetic metal centers. For complexes containing V(III) (S=1), Cu(II) (S=1/2), and Mn(III) (S=2) metal centers, the (17)O isotropic paramagnetic shifts were found to span a range of more than 10,000 ppm. In several cases, high-resolution (17)O NMR spectra were recorded under very fast magic-angle spinning (MAS) conditions at 21.1 T. Quantum-chemical computations using density functional theory (DFT) qualitatively reproduced the experimental (17)O hyperfine shift tensors.

A distonic radical-ion for detection of traces of adventitious molecular oxygen (O2) in collision gases used in tandem mass spectrometers.

We describe a diagnostic ion that enables rapid semiquantitative evaluation of the degree of oxygen contamination in the collision gases used in tandem mass spectrometers. Upon collision-induced dissociation (CID), the m/z 359 positive ion generated from the analgesic etoricoxib undergoes a facile loss of a methyl sulfone radical [(•)SO(2)(CH(3)); 79-Da] to produce a distonic radical cation of m/z 280. The product-ion spectrum of this m/z 280 ion, recorded under low-energy activation on tandem-in-space QqQ or QqTof mass spectrometers using nitrogen from a generator as the collision gas, or tandem-in-time ion-trap (LCQ, LTQ) mass spectrometers using purified helium as the buffer gas, showed two unexpected peaks at m/z 312 and 295. This enigmatic m/z 312 ion, which bears a mass-to-charge ratio higher than that of the precursor ion, represented an addition of molecular oxygen (O(2)) to the precursor ion. The exceptional affinity of the m/z 280 radical cation towards oxygen was deployed to develop a method to determine the oxygen content in collision gases.

Iron porphyrin carbenes as catalytic intermediates: structures, Mössbauer and NMR spectroscopic properties, and bonding.

Iron porphyrin carbenes (IPCs) are thought to be intermediates involved in the metabolism of various xenobiotics by cytochrome P450, as well as in chemical reactions catalyzed by metalloporphyrins and engineered P450s. While early work proposed IPCs to contain Fe(II), more recent work invokes a double-bond description of the iron-carbon bond, similar to that found in Fe(IV) porphyrin oxenes. Reported herein is the first quantum chemical investigation of IPC Mössbauer and NMR spectroscopic properties, as well as their electronic structures, together with comparisons to ferrous heme proteins and an Fe(IV) oxene model. The results provide the first accurate predictions of the experimental spectroscopic observables as well as the first theoretical explanation of their electrophilic nature, as deduced from experiment. The preferred resonance structure is Fe(II)←{:C(X)Y}(0) and not Fe(IV)={C(X)Y}(2-), a result that will facilitate research on IPC reactivities in various chemical and biochemical systems.

Structural, EPR superhyperfine, and NMR hyperfine properties of the Cu-octarepeat binding site in the prion protein.

Previous experimental and computational investigations show that the copper binding in the prion protein that is involved in a number of neurodegenerative diseases is complicated and the exact binding structures remain to be determined. To facilitate structural investigation in this field, we report a quantum chemical investigation of structural, EPR superhyperfine, and NMR hyperfine properties of various copper complexes of the octarepeat domain, which has several copies of highly conserved amino acid sequence of PHGGGWGQ. The predicted metal-ligand bond lengths of the X-ray structure of CuHGGGW, involving the central five residues in this domain, from the best method examined here, have a mean absolute deviation (MAD) of 0.030 Å, basically the same as found with experimental errors of various metal complexes. Prior controversial results regarding water coordination were resolved here with a more extensive computational investigation on 10 models with various water molecules and sequences (both HGGGW and PHGGGWGQ), which are consistent with the experimental reports. Experimental EPR superhyperfine constants are accurately reproduced with a MAD of 0.95 MHz. Results here suggest that the NMR hyperfine shifts which can be readily measured in NMR experiments and accurately predicted in quantum chemical calculations can provide more extensive and more sensitive structural probes than those from the current EPR studies. These results will be helpful for future experimental and computational investigations of the copper binding structures of the prion protein as well as other related systems.