Reversible dioxygen uptake at [Cu4] clusters.

Dioxygen binding solely through non-covalent interactions is rare. In living systems, dioxygen transport takes place via iron or copper-containing biological cofactors. Specifically, a reversible covalent interaction is established when O2 binds to the mono or polynuclear metal center. However, O2 stabilization in the absence of covalent bond formation is challenging and rarely observed. Here, we demonstrate a unique example of reversible non-covalent binding of dioxygen within the cavity of a well-defined synthetic all-Cu(i) tetracopper cluster.

Formation of (Aza)fulvenallene, Cyanocyclopentadiene, and (Aza)fluorenes in the Thermal Rearrangements of Indazoles, Azaindazoles, and Homoquinolinic Anhydride.

Flash vacuum pyrolysis (FVP) of pyrazoles and indazoles constitutes a valuable route to carbenes and nitrenes. In this study, we employed M062X and CCSD(T) calculations to provide a mechanistic rationale for the formation of fulvenallene and fluorenes from indazoles and the corresponding formation of azafulvenallene 15, cyanocyclopentadiene 19, and azafluorenes, e.g. 45, from azaindazoles, e.g. 12, and from homoquinolinic anhydride. The results reveal the importance of initial tautomerization in the pyrazole moiety of 7-azaindazole 12, which drives the mechanism toward 2-diazo-3-methylene-2,3-dihydropyridine 29 and hence 3-methylene-2,3-dihydropyridin-2-ylidene 26, followed by Wolff-type ring contraction to 1-azafulvenallene 15. This path has a calculated activation energy ∼10 kcal/mol lower than that for an alternate route involving ring opening to 3-diazomethylpyridine, dediazotization, and rearrangement of 3-pyridylcarbene to azacycloheptatetraene and phenylnitrene 24. FVP of 2,5-diphenyltetrazoles and phenyl(pyridyl)tetrazoles leads to nitrile imines, which cyclize to 3-phenylindazoles and -azaindazoles. Nitrogen elimination from these (aza) indazoles results in the formation of (aza) fluorenes, for which two alternate mechanisms are described: route A by rearrangement of (aza) indazoles to diazo(aza)cyclohexadienes and (aza)cyclohexadienylidenes and route B by rearrangement to diaryldiazomethanes and diarylcarbenes. Both paths are energetically feasible, but path A is preferred and corresponds to the azafluorenes obtained experimentally.

Azulene-Naphthalene, Naphthalene-Naphthalene, and Azulene-Azulene Rearrangements.

The mechanism(s) of thermal rearrangement of azulenes have been enigmatic for several decades. Herein, we have employed density functional theory (DFT) calculations at the M06-2X/6-311+G(d,p) level together with single-point calculations at the CCSD(T) level to assess possible mechanisms of the experimentally observed azulene and naphthalene automerizations. Of the two mechanisms proposed for naphthalene automerization, it is found that the benzofulvene (BF) route is favored over the naphthvalene mechanism by ∼6 kcal/mol and is energetically lower than the norcaradiene-vinylidene mechanism (NVM) for the azulene-naphthalene rearrangement (Ea ∼ 76.5 (74.6) kcal/mol). Moreover, contrary to older reports, we observe that a pathway involving indenylcarbene intermediates is a viable, alternate mechanism. Therefore, the naphthalene automerization is expected to take place during azulene pyrolysis, especially under conditions of low-pressure FVP, where it will be aided by chemical activation. Furthermore, thermal azulene-azulene isomerization is feasible through vinylidene-acetylene-vinylidene (VAV), dehydrotriquinacene (DTQ), and azulvalene (AV) pathways with activation energies lying below that required for the azulene-naphthalene conversion, i.e., the NVM. These results, together with the previously published NVM, provide reasonable explanations for most of the products of the thermal azulene-naphthalene rearrangement.

Thermal Rearrangement of Azulenes to Naphthalenes: A Deeper Insight into the Mechanisms.

The thermal rearrangement of azulene to naphthalene has been the subject of several experimental and computational studies. Here, we reexamine the proposed mechanisms at the DFT level. The use of different functionals showed that the HF-exchange contribution significantly affects reaction energies and barrier heights. Accordingly, all proposed pathways were investigated with the optimal method, M06-2X/6-311+G(d,p), which confirms the norcaradiene-vinylidene mechanism (A) as the dominant unimolecular route (Ea ≈ 76 kcal/mol) able to account for the major products of pyrolyses using 13C- or substituent-labeled azulenes. Moreover, a facile vinylidene-acetylene interconversion will scramble the terminal carbon atoms in the vinylidene. Several other potential intramolecular reaction mechanisms (B-E) are ruled out because of higher activation energies (>84 kcal/mol) and failure to reproduce the results obtained with substituted and 13C-labeled azulenes and benzazulenes. These experimental results also demonstrate that the proposed free radical or H atom-induced intermolecular methylene walk and spiran mechanisms cannot be major contributors, especially under flash vacuum pyrolysis conditions.

When a "Dimroth Rearrangement" Is Not a Dimroth Rearrangement.

In the Dimroth rearrangement of heterocycles, often pyrimidines, an exocyclic and a ring substituent are interchanged. However, the term Dimroth rearrangement is frequently used even when there is no knowledge of the reaction mechanism and alternatives are likely. Here, we have employed density functional theory (DFT) calculations at the M06-2X/6-311+G(d,p) level to determine the most plausible rearrangement pathways of 3-aminothiocarbonylquinazoline 5, tetrahydrofuranylpyrimidine 21, and 5-allyltriazocine 30. For the rearrangement of quinazoline 5 to 9, the [1,3]-sigmatropic shift of the thioamido group with an activation barrier of 26.7 kcal/mol is much preferred over the Dimroth rearrangement (∼46 kcal/mol). An even lower barrier of 21.6 kcal/mol applies to a stepwise [1,3]-shift. The migration of the tetrahydrofuranyl unit in pyrimidines like 21 → 23 can take place by means of a [1,3]-sigmatropic shift with a low barrier (≤17.5 kcal/mol) rather than a Dimroth rearrangement under acidic conditions and most likely also under neutral conditions (∼30 kcal/mol). In the rearrangement of 5-allyl-6-iminotriazocine 30 to 32, the [3,3]-sigmatropic shift (aza-Cope rearrangement) is preferred over the Dimroth mechanism under neutral conditions, but in the presence of acid, the azonia-Cope rearrangement of an allyl group and the true Dimroth rearrangement have comparable activation energies.

Mechanism-Based Inactivation of Cytochrome P450 Enzymes: Computational Insights.

Mechanism-based inactivation (MBI) refers to the metabolic bioactivation of a xenobiotic by cytochrome P450s to a highly reactive intermediate which subsequently binds to the enzyme and leads to the quasi-irreversible or irreversible inhibition. Xenobiotics, mainly drugs with specific functional units, are the major sources of MBI. Two possible consequences of MBI by medicinal compounds are drug-drug interaction and severe toxicity that are observed and highlighted by clinical experiments. Today almost all of these latent functional groups (e.g., thiophene, furan, alkylamines, etc.) are known, and their features and mechanisms of action, owing to the vast experimental and theoretical studies, are determined. In the past decade, molecular modeling techniques, mostly density functional theory, have revealed the most feasible mechanism that a drug undergoes by P450 enzymes to generate a highly reactive intermediate. In this review, we provide a comprehensive and detailed picture of computational advances toward the elucidation of the activation mechanisms of various known groups with MBI activity. To this aim, we briefly describe the computational concepts to carry out and analyze the mechanistic investigations, and then, we summarize the studies on compounds with known inhibition activity including thiophene, furan, alkylamines, terminal acetylene, etc. This study can be reference literature for both theoretical and experimental (bio)chemists in several different fields including rational drug design, the process of toxicity prevention, and the discovery of novel inhibitors and catalysts.

Angular ladder-type meta-phenylenes: synthesis and electronic structural analysis.

Herein, we report the synthesis of two new series of angular (all-syn) ladder-type meta-[n]phenylenes (LMP, n = 3-8). One series contains keto groups at the termini bridges, denoted angular keto (AKn), the second contains alkyl groups at all bridge sp3 carbons, denoted angular alkyl (AAn). Their electronic and structural properties were delineated by a combination of electrochemistry and spectroscopic (UV-Vis and emission) methods and further supported by DFT calculations. Interestingly, experimental and DFT data show that changing the bridging group at the termini from alkyl (AAn) to keto (AKn) gives an increase in the first reduction potentials and LUMO energies, as the π-system is extended. Also, the charge (de)localization behavior is different for these two species; while the AAn compounds stablize charge with Robin-Day class III, the AKn compounds show a clear switch from class III to class II. In comparison with the linear analogues (LKn and LAn), DFT results reveal a shape independency of the charge (de)localization mechanism in acceptor-π-acceptor series (AKn/LKn).