Regiodivergent Biocatalytic Hydroxylation of L-Glutamine Facilitated by Characterization of Non-Heme Dioxygenases from Non-Ribosomal Peptide Biosyntheses.

We report the functional characterization of two iron- and α-ketoglutarate-dependent dioxygenases that are capable of hydroxylating free-standing glutamine at its C3 and C4 position respectively. In particular, the C4 hydroxylase, Q4Ox, catalyzes the reaction with approximately 4,300 total turnover numbers, facilitating synthesis of a solid-phase compatible building block and stereochemical elucidation at the C4 position of the hydroxylated product. This work will enable the development of novel synthetic strategies to prepare useful glutamine derivatives and stimulate further discoveries of new amino acid hydroxylases with distinct substrate specificities.

Modular Chemoenzymatic Synthesis of GE81112 B1 and Related Analogues Enables Elucidation of Its Key Pharmacophores.

The GE81112 complex has garnered much interest due to its broad antimicrobial properties and unique ability to inhibit bacterial translation initiation. Herein we report the use of a chemoenzymatic strategy to complete the first total synthesis of GE81112 B1. By pairing iron and α-ketoglutarate dependent hydroxylases found in GE81112 biosynthesis with traditional synthetic methodology, we were able to access the natural product in 11 steps (longest linear sequence). Following this strategy, 10 GE81112 B1 analogues were synthesized, allowing for identification of its key pharmacophores. A key feature of our medicinal chemistry effort is the incorporation of additional biocatalytic hydroxylations in modular analogue synthesis to rapidly enable exploration of relevant chemical space.

Harnessing the biocatalytic potential of iron- and α-ketoglutarate-dependent dioxygenases in natural product total synthesis.

Covering: up to the end of 2019Iron- and α-ketoglutarate-dependent dioxygenases (Fe/αKGs) represent a versatile and intriguing enzyme family by virtue of their ability to directly functionalize unactivated C-H bonds at the cost of αKG and O2. Fe/αKGs play an important role in the biosynthesis of natural products, valuable biologically active secondary metabolites frequently pursued as drug leads. The field of natural product total synthesis seeks to contruct these molecules as effeciently as possible, although natural products continue to challenge chemists due to their intricate structural complexity. Chemoenzymatic approaches seek to remedy the shortcomings of traditional synthetic methodology by combining Nature's biosynthetic machinery with traditional chemical methods to efficiently construct natural products. Although other oxygenase families have been widely employed for this purpose, Fe/αKGs remain underutilized. The following review will cover recent chemoenzymatic total syntheses involving Fe/αKG enzymes. Additionally, related information involving natural product biosynthesis, methods development, and non-chemoenzymatic total syntheses will be discussed to inform retrosynthetic logic and synthetic design.

Characterization of a Citrulline 4-Hydroxylase from Nonribosomal Peptide GE81112 Biosynthesis and Engineering of Its Substrate Specificity for the Chemoenzymatic Synthesis of Enduracididine.

The GE81112 tetrapeptides are a small family of unusual nonribosomal peptide congeners with potent inhibitory activity against prokaryotic translation initiation. With the exception of the 3-hydroxy-l-pipecolic acid unit, little is known about the biosynthetic origins of the non-proteinogenic amino acid monomers of the natural product family. Here, we elucidate the biogenesis of the 4-hydroxy-l-citrulline unit and establish the role of an iron- and α-ketoglutarate-dependent enzyme (Fe/αKG) in the pathway. Homology modelling and sequence alignment analysis further facilitate the rational engineering of this enzyme to become a specific 4-arginine hydroxylase. We subsequently demonstrate the utility of this engineered enzyme in the synthesis of a dipeptide fragment of the antibiotic enduracidin. This work highlights the value of applying a bioinformatics-guided approach in the discovery of novel enzymes and engineering of new catalytic activity into existing ones.

Fraternal twins: distinction between PbPc and SnPc by their switching behaviour in a scanning tunnelling microscope.

In this contribution, we compare the optical absorbance behaviour and the structural properties of lead(II)-phthalocyanine (PbPc) and tin(II)-phthalocyanine (SnPc) thin films. To this end, we employ a Ag(1 1 1) substrate terminated with a monolayer of 3,4,9,10-perylene tetracarboxylic dianhydride constituting an internal interface whose main effect is an electronic decoupling of the phthalocyanine adlayer from the metal surface. As deduced from low-energy electron diffraction and scanning tunnelling microscopy (STM) measurements, the epitaxial relations and unit cell compositions of the prevailing PbPc monolayer and multilayer domains are confusingly similar to those of SnPc on PTCDA/Ag(1 1 1). However, SnPc and PbPc can be readily distinguished by their STM-induced switching behaviours: while the former is capable of reversible configurational changes, no effect on the latter could be achieved by us under comparable conditions. This corroborates earlier theoretical predictions and even renders the chemical identification of individual shuttlecock-shaped metal-phthalocyanines feasible.

Oxidopyrylium-Alkene [5 + 2] Cycloaddition Conjugate Addition Cascade (C3) Sequences: Scope, Limitation, and Computational Investigations.

Oxidopyrylium-alkene [5 + 2] cycloaddition conjugate addition cascade (C3) sequences are described. Intramolecular cycloadditions involving terminal alkenes, enals, and enones were investigated. Substrates with tethers of varying lengths delivered five- and six-membered carbocycles and heterocycles thus demonstrating the scope and limitation of the cycloaddition-conjugate addition cascade. Several experiments and theoretical calculations provide evidence for the proposed mechanistic pathway.

Evolution of Biocatalytic and Chemocatalytic C-H Functionalization Strategy in the Synthesis of Manzacidin C.

Because of their unique molecular architecture, the manzacidins have been the subject of intense synthetic efforts in the past two decades. Here, we describe two synthetic approaches toward manzacidin C that center on the enzymatic hydroxylation of unprotected l-leucine. This study also resulted in the discovery of novel synthetic methodologies, including a photocatalytic C-H azidation of unprotected amino acids. Additionally, we describe the use of hydroxylated l-leucine in the preparation of various densely substituted pyrrolidines.

Remote C-H Hydroxylation by an α-Ketoglutarate-Dependent Dioxygenase Enables Efficient Chemoenzymatic Synthesis of Manzacidin C and Proline Analogs.

Selective C-H functionalization at distal positions remains a highly challenging problem in organic synthesis. Though Nature has evolved a myriad of enzymes capable of such feat, their synthetic utility has largely been overlooked. Here, we functionally characterize an α-ketoglutarate-dependent dioxygenase (Fe/αKG) that selectively hydroxylates the δ position of various aliphatic amino acids. Kinetic analysis and substrate profiling of the enzyme show superior catalytic efficiency and substrate promiscuity relative to other Fe/αKGs that catalyze similar reactions. We demonstrate the practical utility of this transformation in the concise syntheses of a rare alkaloid, manzacidin C, and densely substituted amino acid derivatives with remarkable step efficiency. This work provides a blueprint for future applications of Fe/αKG hydroxylation in complex molecule synthesis and the development of powerful synthetic paradigms centered on enzymatic C-H functionalization logic.

Applications of Oxygenases in the Chemoenzymatic Total Synthesis of Complex Natural Products.

Nature has produced a diverse range of oxygenases for the modification of secondary metabolites with selectivity profiles that are unmatched by conventional man-made catalysts. In the past two decades, organic chemists have begun to harness the synthetic potential of these biocatalysts to develop efficient chemoenzymatic synthesis of complex natural products. Judicious combination of synthetic and enzymatic transformations in multistep synthesis can often result in powerful disconnections that compare favorably with contemporary chemical strategies for accessing the target natural products, while at the same time presenting opportunities to innovate. This Perspective highlights strategic applications of enzymatic hydroxylation to simplify problems in natural product synthesis. Finally, newly discovered enzymes that would facilitate further developments in this field are discussed.

Fully Atomistic Understanding of the Electronic and Optical Properties of a Prototypical Doped Charge-Transfer Interface.

The current study generates profound atomistic insights into doping-induced changes of the optical and electronic properties of the prototypical PTCDA/Ag(111) interface. For doping K atoms are used, as KxPTCDA/Ag(111) has the distinct advantage of forming well-defined stoichiometric phases. To arrive at a conclusive, unambiguous, and fully atomistic understanding of the interface properties, we combine state-of-the-art density-functional theory calculations with optical differential reflectance data, photoelectron spectra, and X-ray standing wave measurements. In combination with the full structural characterization of the KxPTCDA/Ag(111) interface by low-energy electron diffraction and scanning tunneling microscopy experiments (ACS Nano 2016, 10, 2365-2374), the present comprehensive study provides access to a fully characterized reference system for a well-defined metal-organic interface in the presence of dopant atoms, which can serve as an ideal benchmark for future research and applications. The combination of the employed complementary techniques allows us to understand the peculiarities of the optical spectra of K2PTCDA/Ag(111) and their counterintuitive similarity to those of neutral PTCDA layers. They also clearly describe the transition from a metallic character of the (pristine) adsorbed PTCDA layer on Ag(111) to a semiconducting state upon doping, which is the opposite of the effect (degenerate) doping usually has on semiconducting materials. All experimental and theoretical efforts also unanimously reveal a reduced electronic coupling between the adsorbate and the substrate, which goes hand in hand with an increasing adsorption distance of the PTCDA molecules caused by a bending of their carboxylic oxygens away from the substrate and toward the potassium atoms.

Complex Stoichiometry-Dependent Reordering of 3,4,9,10-Perylenetetracarboxylic Dianhydride on Ag(111) upon K Intercalation.

Alkali metal atoms are frequently used for simple yet efficient n-type doping of organic semiconductors and as an ingredient of the recently discovered polycyclic aromatic hydrocarbon superconductors. However, the incorporation of dopants from the gas phase into molecular crystal structures needs to be controlled and well understood in order to optimize the electronic properties (charge carrier density and mobility) of the target material. Here, we report that potassium intercalation into the pristine 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) monolayer domains on a Ag(111) substrate induces distinct stoichiometry-dependent structural reordering processes, resulting in highly ordered and large KxPTCDA domains. The emerging structures are analyzed by low-temperature scanning tunneling microscopy, scanning tunneling hydrogen microscopy (ST[H]M), and low-energy electron diffraction as a function of the stoichiometry. The analysis of the measurements is corroborated by density functional theory calculations. These turn out to be essential for a correct interpretation of the experimental ST[H]M data. The epitaxy types for all intercalated stages are determined as point-on-line. The K atoms adsorb in the vicinity of the oxygen atoms of the PTCDA molecules, and their positions are determined with sub-Ångström precision. This is a crucial prerequisite for the prospective assessment of the electronic properties of such composite films, as they depend rather sensitively on the mutual alignment between donor atoms and acceptor molecules. Our results demonstrate that only the combination of experimental and theoretical approaches allows for an unambiguous explanation of the pronounced reordering of KxPTCDA/Ag(111) upon changing the K content.

To tilt or not to tilt: correction of the distortion caused by inclined sample surfaces in low-energy electron diffraction.

Low-energy electron diffraction (LEED) is a widely employed technique for the structural characterization of crystalline surfaces and epitaxial adsorbates. For technical reasons the accessible reciprocal space is limited at a given primary electron energy E. This limitation may be overcome by sweeping E to observe higher diffraction orders decisively enhancing the quantitative examination. Yet, in many cases, such as molecular films with rather large unit cells, the adsorbate reflexes become less pronounced at energies high enough to observe substrate reflexes. One possibility to overcome this problem is an intentional inclination of the sample surface during the measurement at the expense of the quantitative interpretability of then severely distorted diffraction patterns. Here, we introduce a correction method for the axially symmetric distortion in LEED images of tilted samples. We provide experimental confirmation for micro-channel plate LEED and spot-profile analysis LEED instruments using the (7×7) reconstructed surface of a Si(111) single crystal as a reference sample. Finally, we demonstrate that the correction of this distortion considerably improves the quantitative analysis of diffraction patterns of adsorbates since substrate and adsorbate reflexes can be evaluated simultaneously. As an illustrative example we have chosen an epitaxial monolayer of 3,4,9,10-perylenetetracarboxylic dianhydride on Ag(111) that is known to form a commensurate superstructure.

Determination and correction of distortions and systematic errors in low-energy electron diffraction.

We developed and implemented an algorithm to determine and correct systematic distortions in low-energy electron diffraction (LEED) images. The procedure is in principle independent of the design of the apparatus (spherical or planar phosphorescent screen vs. channeltron detector) and is therefore applicable to all device variants, known as conventional LEED, micro-channel plate LEED, and spot profile analysis LEED. The essential prerequisite is a calibration image of a sample with a well-known structure and a suitably high number of diffraction spots, e.g., a Si(111)-7×7 reconstructed surface. The algorithm provides a formalism which can be used to rectify all further measurements generated with the same device. In detail, one needs to distinguish between radial and asymmetric distortion. Additionally, it is necessary to know the primary energy of the electrons precisely to derive accurate lattice constants. Often, there will be a deviation between the true kinetic energy and the value set in the LEED control. Here, we introduce a method to determine this energy error more accurately than in previous studies. Following the correction of the systematic errors, a relative accuracy of better than 1% can be achieved for the determination of the lattice parameters of unknown samples.