C–H Activation in Pyridoxal-5′-phosphate and Pyridoxamine-5′-phosphate Schiff Bases: Effect of Metal Chelation. A Computational Study

Intramolecular Hydrogen Bond in Pyridine Schiff Bases as Ancillary Ligands of Re(I) Complexes Is a Switcher between Visible and NIR Emissions: A Relativistic Quantum Chemistry Study

Rhenium(I) tricarbonyl complexes have been described as suitable fluorophores, particularly for biological applications. fac-[Re(CO)₃(N,N)L]^(0 or 1+) complexes, where N,N is a substituted dinitrogenated ligand (bipyridine or derivatives with relatively small substituents) and L the ancillary ligand [a pyridine Schiff base (PSB) harboring an intramolecular hydrogen bond (IHB)], have presented promissory results concerning their use as fluorophores, especially for walled cells (i.e., bacteria and fungi). In this work, we present a relativistic theoretical analysis of two series of fac-[Re(CO)₃(N,N)PSB]¹⁺ complexes to predict the role of the IHB in the ancillary ligand concerning their photophysical behavior. N,N corresponds to 2,2'-bipyridine (bpy) (series A) or 4,4'-bis(ethoxycarbonyl)-2,2'-bipyridine (deeb) (series B). We found that all the complexes present absorption in the visible light range. In addition, complexes presenting a PSB with an IHB exhibit luminescent emission suitable for biological purposes: large Stokes shift, emission in the range of 600-700 nm, and τ in the order of 10^-2 to 10^-3 s. By contrast, complexes with PSB lacking the IHB show a predicted emission with the lowest triplet excited-state energy entering the NIR region. These results suggest a role of the IHB as an important switcher between visible and NIR emissions in this kind of complexes. Since the PSB can be substituted to modulate the properties of the whole Re(I) complex, it will be interesting to explore whether other substitutions can also affect the photophysical properties, mainly the emission range.

Aldehyde catalysis - from simple aldehydes to artificial enzymes

Chemists have been learning and mimicking enzymatic catalysis in various aspects of organic synthesis. One of the major goals is to develop versatile catalysts that inherit the high catalytic efficiency of enzymatic processes, while being effective for a broad scope of substrates. In this field, the study of aldehyde catalysts has achieved significant progress. This review summarizes the application of aldehydes as sustainable and effective catalysts in different reactions. The fields, in which the aldehydes successfully mimic enzymatic systems, include light energy absorption/transfer, intramolecularity introduction through tether formation, metal binding for activation/orientation and substrate activation via aldimine formation. Enantioselective aldehyde catalysis has been achieved with the development of chiral aldehyde catalysts. Direct simplification of aldehyde-dependent enzymes has also been investigated for the synthesis of noncanonical chiral amino acids. Further development in aldehyde catalysis is expected, which might also promote exploration in fields related to prebiotic chemistry, early enzyme evolution, etc.

The l-Thr Kinase/l-Thr-Phosphate Decarboxylase (CobD) Enzyme from Methanosarcina mazei Gö1 Contains Metallocenters Needed for Optimal Activity

The MM2060 (cobD) gene from Methanosarcina mazei strain Gö1 encodes a protein (MmCobD) with l-threonine kinase (PduX) and l-threonine-O-3-phosphate decarboxylase (CobD) activities. In addition to the unexpected l-Thr kinase activity, MmCobD has an extended carboxy-terminal (C-terminal) region annotated as a putative metal-binding zinc finger-like domain. Here, we demonstrate that the C-terminus of MmCobD is a ferroprotein containing ∼25 non-heme iron atoms per monomer of protein. The absence of the C-terminus substantially reduces, but does not abolish, enzymatic activities in vitro and in vivo. Single-residue substitutions of C-terminal putative Fe-binding cysteinyl and histidinyl residues resulted in the loss of Fe and changes in enzyme activity levels. Salmonella enterica ΔpduX and ΔcobD strains were used as heterologous hosts to assess coenzyme B12 biosynthesis as a function of 17 MmCobD variants tested. Some of the latter displayed 5-fold higher enzymatic activity in vitro and enhanced the growth rate of the S. enterica strains that synthesized them. Most of the MmCobD variants tested were up to 6-fold less active in vitro and supported slow growth rates of the S. enterica strains that synthesized them; some substitutions abolished enzyme activity. MmCobD exhibited an ultraviolet-visible absorption spectrum consistent with [4Fe-4S] clusters that appeared to be susceptible to oxidation by H2O2 and reduction by sodium dithionite. The presence of FeS clusters in MmCobD was corroborated by electron paramagnetic resonance and magnetic circular dichroism studies. Collectively, our results suggest that MmCobD contains one or more diamagnetic [4Fe-4S]2+ center(s) that may play a structural or regulatory role.

Chiral Aldehyde Catalysis for the Catalytic Asymmetric Activation of Glycine Esters

Chiral aldehyde catalysis is uniquely suitable for the direct asymmetric α-functionalization of N-unprotected amino acids, because aldehydes can reversibly form imines. However, there have been few successful reports of these transformations. In fact, only chiral aldehyde catalyzed aldol reactions of amino acids and alkylation of 2-amino malonates have been reported with good chiral induction. Here, we report a novel type of chiral aldehyde catalyst based on face control of the enolate intermediates. The resulting chiral aldehyde is the first efficient nonpyridoxal-dependent catalyst that can promote the direct asymmetric α-functionalization of N-unprotected glycine esters. Possible transition states and the proton transfer process were investigated by density functional theory calculations.

Isodesmic reaction for accurate theoretical pKa calculations of amino acids and peptides

Theoretical and quantitative prediction of pKa values at low computational cost is a current challenge in computational chemistry. We report that the isodesmic reaction scheme provides semi-quantitative predictions (i.e. mean absolute errors of 0.5-1.0 pKa unit) for the pKa1 (α-carboxyl), pKa2 (α-amino) and pKa3 (sidechain groups) of a broad set of amino acids and peptides. This method fills the gaps of thermodynamic cycles for the computational pKa calculation of molecules that are unstable in the gas phase or undergo proton transfer reactions or large conformational changes from solution to the gas phase. We also report the key criteria to choose a reference species to make accurate predictions. This method is computationally inexpensive and makes use of standard density functional theory (DFT) and continuum solvent models. It is also conceptually simple and easy to use for researchers not specialized in theoretical chemistry methods.

Nonenzymatic Reactions above Phospholipid Surfaces of Biological Membranes: Reactivity of Phospholipids and Their Oxidation Derivatives

Phospholipids play multiple and essential roles in cells, as components of biological membranes. Although phospholipid bilayers provide the supporting matrix and surface for many enzymatic reactions, their inherent reactivity and possible catalytic role have not been highlighted. As other biomolecules, phospholipids are frequent targets of nonenzymatic modifications by reactive substances including oxidants and glycating agents which conduct to the formation of advanced lipoxidation end products (ALEs) and advanced glycation end products (AGEs). There are some theoretical studies about the mechanisms of reactions related to these processes on phosphatidylethanolamine surfaces, which hypothesize that cell membrane phospholipids surface environment could enhance some reactions through a catalyst effect. On the other hand, the phospholipid bilayers are susceptible to oxidative damage by oxidant agents as reactive oxygen species (ROS). Molecular dynamics simulations performed on phospholipid bilayers models, which include modified phospholipids by these reactions and subsequent reactions that conduct to formation of ALEs and AGEs, have revealed changes in the molecular interactions and biophysical properties of these bilayers as consequence of these reactions. Then, more studies are desirable which could correlate the biophysics of modified phospholipids with metabolism in processes such as aging and diseases such as diabetes, atherosclerosis, and Alzheimer's disease.