DFT studies of the substituent effects of dimethylamino on non-heme active oxidizing species: iron(V)-oxo species or iron(IV)-oxo acetate aminopyridine cation radical species?

Nonheme Manganese-Catalyzed Oxidative N-Dealkylation of Tertiary Amides: Manganese(IV)-Oxo Aminopyridine Cation Radical Species and Hydride Transfer Mechanism

The development of efficient and practical N-dealkylation reactions stands as a longstanding objective in synthetic chemistry. Inspired by the oxidative N-dealkylation reactions mediated by heme and nonheme metalloenzymes, we disclose a biomimetic oxidative N-dealkylation catalysis that utilizes a nonheme manganese complex bearing anthryl-appended aminopyridine ligand and hydrogen peroxide (H2O2) as the terminal oxidant. A variety of Weinreb amides and cyclic aliphatic amines are efficiently transformed into valuable methyl hydroxamates and ω-amino acids through oxidative C-N bond cleavage. Mechanistic studies, including density functional theory (DFT) calculations, reveal that a manganese(IV)-oxo aminopyridine cation radical species, which is formed via the bromoacetic acid-assisted heterolytic O-O bond cleavage of a presumed manganese(III)-hydroperoxo aminopyridine species and the subsequent intramolecular electron transfer (ET) from the anthryl group of the aminopyridine ligand to the manganese center, is the active intermediate that initiates the oxidative N-dealkylation reactions; this process is reminiscent to the heterolytic O-O bond cleavage of iron(III)-hydroperoxo porphyrin intermediates (Cpd 0) to form iron(IV)-oxo porphyrin π-cation radicals (Cpd I) that are responsible for diverse selective oxidation reactions. Moreover, it is revealed that the oxidative activation of the C-H bond adjacent to the nitrogen atom proceeds via a hydride transfer (HT) mechanism, which involves a concerted asynchronous proton-coupled electron transfer (PCET), followed by an ET process. Thus, this study reports the first instance of catalytic oxidative N-dealkylation of a variety of tertiary amides, such as Weinreb amides and cyclic aliphatic amines, mediated by a Cpd I-like nonheme manganese(IV)-oxo aminopyridine cation radical species via an initial HT pathway.

Comparing the reactivity of an oxoiron(IV) cation radical and its oxoiron(V) tautomer towards C-H bonds

An oxoiron(IV) cation radical is generated upon two-electron oxidation of an iron(III) complex bearing an electron-rich methoxy substituted bTAML framework and thoroughly characterized via multiple spectroscopic techniques and density functional theory (DFT). Reactivity studies demonstrate faster rates for oxidation of strong aliphatic sp³ C-H bonds than for its corresponding oxoiron(V) valence tautomer.

A direct approach toward investigating DNA-ligand interactions via surface-enhanced Raman spectroscopy combined with molecular dynamics simulations

Small molecules that interfere with DNA replication can trigger genomic instability, which makes these molecules valuable in the search for anticancer drugs. Thus, interactions between DNA and its ligands at the molecular level are of great significance. In the present study, a new method based on surface-enhanced Raman spectroscopy (SERS) combined with molecular dynamics simulations has been proposed for analyzing the interactions between DNA and its ligands. The SERS signals of DNA hairpins (ST: d(CGACCAACGTGTCGCCTGGTCG), AP1: d(CGCACAACGTGTCGCCTGTGCG)), pure argininamide, and their complexes, were obtained, and the characteristic peak sites of the DNA secondary structure and argininamide ligand-binding region were analyzed. Molecular dynamics calculations predicted that argininamide binds to the 8C and 9G bases of AP1 via hydrogen bonding. Our method successfully detected the changes of SERS fingerprint peaks of hydrogen bonds and bases between argininamide and DNA hairpin bases, and their binding sites and action modes were consistent with the predicted results of the molecular dynamics simulations. This SERS technology combined with the molecular dynamics simulation detection platform provides a general analysis tool, with the advantage of effective, rapid, and sensitive detection. This platform can obtain sufficient molecular level conformational information to provide avenues for rapid drug screening and promote progress in several fields, including targeted drug design.

Molecular Basis of the Recognition of Cholesterol by Cytochrome P450 46A1 along the Major Access Tunnel

CYP46A1 is an important potential target for the treatment of Alzheimer's disease (AD), which is the most common neurodegenerative disease among older individuals. However, the binding mechanism between CYP46A1 and substrate cholesterol (CH) has not been clarified and will not be conducive to the research of relevant drug molecules. In this study, we integrated molecular docking, molecular dynamics (MD) simulations, and adaptive steered MD simulations to explore the recognition and binding mechanism of CYP46A1 with CH. Two key factors affecting the interaction between CH and CYP46A1 are determined: one is a hydrophobic cavity formed by seven hydrophobic residues (F80, Y109, L112, I222, W368, F371, and T475), which provides nonpolar interactions to stabilize CH, and the other is a hydrogen bond formed by H81 and CH, which ensures the binding direction of CH. In addition, the tunnel analysis results show that tunnel 2a is identified as the primary pathway of CH. The entry of CH induces tunnel 2e to close and tunnel w to open. Our results may provide effective clues for the design of drugs based on the substrate for AD and improve our understanding of the structure-function of CYP46A1.

Can the isonitrile biosynthesis enzyme ScoE assist with the biosynthesis of isonitrile groups in drug molecules? A computational study

Computational studies show that the isonitrile synthesizing enzyme ScoE can catalyse the conversion of γ-Gly substituents in substrates to isonitrile. This enables efficient isonitrile substitution into target molecules such as axisonitrile-1.

Effect of the Ligand Backbone on the Reactivity and Mechanistic Paradigm of Non-Heme Iron(IV)-Oxo during Olefin Epoxidation

The oxygen atom transfer (OAT) reactivity of the non-heme [Fe^IV (2PyN2Q)(O)]²⁺ (2) containing the sterically bulky quinoline-pyridine pentadentate ligand (2PyN2Q) has been thoroughly studied with different olefins. The ferryl-oxo complex 2 shows excellent OAT reactivity during epoxidations. The steric encumbrance and electronic effect of the ligand influence the mechanistic shuttle between OAT pathway I and isomerization pathway II (during the reaction stereo pure olefins), resulting in a mixture of cis-trans epoxide products. In contrast, the sterically less hindered and electronically different [Fe^IV (N4Py)(O)]²⁺ (1) provides only cis-stilbene epoxide. A Hammett study suggests the role of dominant inductive electronic along with minor resonance effect during electron transfer from olefin to 2 in the rate-limiting step. Additionally, a computational study supports the involvement of stepwise pathways during olefin epoxidation. The ferryl bend due to the bulkier ligand incorporation leads to destabilization of both d z 2 and d x 2 - y 2 orbitals, leading to a very small quintet-triplet gap and enhanced reactivity for 2 compared to 1. Thus, the present study unveils the role of steric and electronic effects of the ligand towards mechanistic modification during olefin epoxidation.

Acid-Triggered O-O Bond Heterolysis of a Nonheme FeIII (OOH) Species for the Stereospecific Hydroxylation of Strong C-H Bonds

A novel hydroperoxoiron(III) species [Fe^III (OOH)(MeCN)(PyNMe₃ )]²⁺ (3) has been generated by reaction of its ferrous precursor [Fe^II (CF₃ SO₃ )₂ (PyNMe₃ )] (1) with hydrogen peroxide at low temperatures. This species has been characterized by several spectroscopic techniques and cryospray mass spectrometry. Similar to most of the previously described low-spin hydroperoxoiron(III) compounds, 3 behaves as a sluggish oxidant and it is not kinetically competent for breaking weak C-H bonds. However, triflic acid addition to 3 causes its transformation into a much more reactive compound towards organic substrates that is capable of oxidizing unactivated C-H bonds with high stereospecificity. Stopped-flow kinetic analyses and theoretical studies provide a rationale for the observed chemistry, a triflic-acid-assisted heterolytic cleavage of the O-O bond to form a putative strongly oxidizing oxoiron(V) species. This mechanism is reminiscent to that observed in heme systems, where protonation of the hydroperoxo intermediate leads to the formation of the high-valent [(Porph^. )Fe^IV (O)] (Compound I).

Dramatic rate-enhancement of oxygen atom transfer by an iron(iv)-oxo species by equatorial ligand field perturbations

The reactivity and characterization of a novel iron(iv)-oxo species is reported that gives enhanced reactivity as a result of second-coordination sphere perturbations of the ligand system.