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Abstract Computational methods for predicting product ratios in dynamically controlled reactions with shallow intermediates or bifurcating pathways after an ambimodal transition state are reviewed and benchmarked. The range of methods includes molecular dynamics simulations, machine learning-based models and recent advancements in correlational methods, all of which rely on quantum mechanical computations. Together, these approaches form a computational toolbox that enhances the efficiency and effectiveness of exploring reaction selectivity influenced by dynamic effects. 

Manipulation of polar functional groups to extend the druggability and developability space is an important approach in the current field of drug discovery. Here, we report an editing method that enables the direct insertion of anthranilyl units into inert amides to form versatile oligoamides and cyclic peptides under exceptionally mild reaction conditions. We showcase a diverse array of pharmaceuticals, natural products, and bioactive molecules involving the mentioned scaffold insertion. The synthesis of the secondary metabolites from marine-derived fungi, the expedited construction of bioactive molecules, and the assembly of functionalized peptide macrocycles through iterative insertions highlight the synthetic utility of this method. Computational tools and experimental measurements indicate that a hydrogen bond network formed by reacting and catalytic amide enables the insertion of the anthranilyl unit into a C─N bond. 

ABSTRACT Reaction mechanism studies typically involve the characterization of products, and intermediates are often characterized by (sub)millisecond techniques, such as nuclear magnetic resonance, while femto/attosecond spectroscopies are used to elucidate the evolution of transition states and electron dynamics. However, due to the lack of detection techniques in the microsecond to nanosecond range, as well as the emergent complexity with increasing scale, most of the proposed intermediates have not yet been detected, which significantly hinders reaction optimization. Here, we present such a nanosecond-scale real-time single-molecule electrical monitoring technique. Using this technique, a series of hidden intermediates in an example Morita-Baylis-Hillman reaction were directly observed, allowing the visualization of the reaction pathways, clarification of the two proposed proton transfer pathways, and quantitative description of their contributions to the turnover. Moreover, the emergent complexity of the catalysis, including the catalysis oscillation effect and the proton quantum tunneling effect, is further unveiled. Finally, this useful yet low-yield reaction was successfully catalyzed by the application of an electric field, leading to a high turnover frequency (∼5000 s−1 at a 1 V bias voltage). This new paradigm of mechanistic study and reaction optimization shows potential application in scalable synthesis by integrated single-molecule electronic devices on chip. 

Crystals undergoing tandem reactions where the first transformation enables the second one are rare. Using photoreactive Dewar benzene 3,4,5,6-tetramethyl-1,2-dicarboxylic diacid (DB) as a hydrogen-bonding template for the [2π+2π] photodimerization of trans-4,4′-bipyridyl-ethenes (BPE), we obtained crystals DB-BPE-NT with a DB:BPE = 2:1 stoichiometry with double bonds at a nonreactive distance of 5.957 Å. Exposure to UV light resulted in valence bond isomerization to Hückel benzene 3,4,5,6-tetramethyl-1,2-dicarboxylic acid (HB) by a quantum chain reaction that triggered the sought-after topochemical [2π+2π] photodimerization reaction. Notably, crystals HB:BPE-T with the Hückel benzene isomer and BPE adopted a 2:2 stoichiometry and displayed an efficient topochemically templated photodimerization reaction. 

Abstract The chemiluminescent light‐emission pathway of phenoxy‐1,2‐dioxetane luminophores attracts growing interest within the scientific community. Dioxetane probes undergoing rapid flash‐type chemiexcitation exhibit higher detection sensitivity than those with a slow glow‐type chemiexcitation rate. We discovered that dioxetanes fused to non‐strained six‐member rings, with hetero atoms or inductive electron‐withdrawing groups, present both accelerated chemiexcitation rates and elevated chemical stability compared to dioxetanes fused to four‐member strained rings. DFT computational simulations supported the chemiexcitation acceleration observed by spiro‐fused six‐member rings with inductive electron‐withdrawing groups of dioxetanes. Specifically, a spiro‐dioxetane with a six‐member sulfone ring exhibited a chemiexcitation rate 293‐fold faster than that of spiro‐adamantyl‐dioxetane. A turn‐ON dioxetane probe for the detection of the enzyme β‐galactosidase, containing the six‐member sulfone unit, exhibited a S/N value of 108 in LB cell growth medium. This probe demonstrated a substantial increase in detection sensitivity towardsE. colibacterial cells expressing β‐galactosidase, with an LOD value that is 44‐fold more sensitive than that obtained by the adamantyl counterpart. The accelerated chemiexcitation and the elevated chemical stability presented by dioxetane containing a spiro‐fused six‐member ring with a sulfone inductive electron‐withdrawing group, make it an ideal candidate for designing efficient turn‐on chemiluminescent probes with exceptionally high detection sensitivity. 

Doxorubicin, a widely used chemotherapy drug, is produced byStreptomyces peucetiusATCC27952. The biosynthesis relies on the cytochrome P450 monooxygenase DoxA, which catalyzes three consecutive late-stage oxidation steps. However, conversion from daunorubicin to doxorubicin is inefficient, necessitating semi-synthetic industrial manufacturing. Here, we address key limitations in DoxA catalysis. We identify the natural redox partners ferredoxin Fdx4 and ferredoxin reductase FdR3 by transcriptomic analysis. We discovered the vicinal oxygen chelate family protein DnrV to prevent product inhibition by binding doxorubicin. Structural analysis of DoxA and density functional theory (DFT) calculations reveal that inefficient C14 hydroxylation results from the unfavorable anti-conformation of the methyl ketone side chain of daunorubicin. We harness these advances for rational strain engineering, leading to an 180% increase in doxorubicin yields and an improved production profile. This study provides singular insights into enzymatic constraints in anthracycline biosynthesis and facilitates cost-effective manufacturing to meet the growing global demand for doxorubicin.