Replacement of the Cobalt Center of Vitamin B 12 by Nickel: Nibalamin and Nibyric Acid Prepared from Metal‐Free B 12 Ligands Hydrogenobalamin and Hydrogenobyric Acid

The (formal) replacement of Co in cobalamin (Cbl) by NiII generates nibalamin (Nibl), a new transition‐metal analogue of vitamin B12. Described here is Nibl, synthesized by incorporation of a NiII ion into the metal‐free B12 ligand hydrogenobalamin (Hbl), itself prepared from hydrogenobyric acid (Hby). The related NiII corrin nibyric acid (Niby) was similarly synthesized from Hby, the metal‐free cobyric acid ligand. The solution structures of Hbl, and Niby and Nibl, were characterized by spectroscopic studies. Hbl features two inner protons bound at N2 and N4 of the corrin ligand, as discovered in Hby. X‐ray analysis of Niby shows the structural adaptation of the corrin ligand to NiII ions and the coordination behavior of NiII. The diamagnetic Niby and Nibl, and corresponding isoelectronic CoI corrins, were deduced to be isostructural. Nibl is a structural mimic of four‐coordinate base‐off Cbls, as verified by its ability to act as a strong inhibitor of bacterial adenosyltransferase

Solution, Crystal and in Silico Structures of the Organometallic Vitamin B 12 ‐Derivative Acetylcobalamin and of its Novel Rhodium‐Analogue Acetylrhodibalamin

The natural vitamin B12‐derivatives are intriguing complexes of cobalt that entrap the metal within the strikingly skewed and ring‐contracted corrin ligand. Here, we describe the synthesis of the Rh(III)‐corrin acetylrhodibalamin (AcRhbl) from biotechnologically produced metal‐free hydrogenobyric acid and analyze the effect of the replacement of the cobalt‐center of the organometallic vitamin B12‐derivative acetylcobalamin (AcCbl) with its group‐IX homologue rhodium, to give AcRhbl. The structures of AcCbl and AcRhbl were thoroughly analyzed in aqueous solution, in crystals and by in silico methods, in order to gain detailed insights into the structural adaptations to the two homologous metals. Indeed, the common, nucleotide‐appended corrin‐ligand in these two metal corrins features extensive structural similarity. Thus, the rhodium‐corrin AcRhbl joins the small group of B12‐mimics classified as ‘antivitamins B12’, isostructural metal analogues of the natural cobalt‐corrins that hold significant potential in biological and biomedical applications as selective inhibitors of key cellular processes

Zinc Substitution of Cobalt in Vitamin B12: Zincobyric acid and Zincobalamin as Luminescent Structural B12-Mimics

Replacing the central cobalt ion of vitamin B12 by other metals has been a long‐held aspiration within the B12‐field. Herein, we describe the synthesis from hydrogenobyric acid of zincobyric acid (Znby) and zincobalamin (Znbl), the Zn‐analogues of the natural cobalt‐corrins cobyric acid and vitamin B12, respectively. The solution structures of Znby and Znbl were studied by NMR‐spectroscopy. Single crystals of Znby were produced, providing the first X‐ray crystallographic structure of a zinc corrin. The structures of Znby and of computationally generated Znbl were found to resemble the corresponding CoII‐corrins, making such Zn‐corrins potentially useful for investigations of B12‐dependent processes. The singlet excited state of Znby had a short life‐time, limited by rapid intersystem crossing to the triplet state. Znby allowed the unprecedented observation of a corrin triplet (ET=190 kJ mol−1) and was found to be an excellent photo‐sensitizer for 1O2 (ΦΔ=0.70)

The Hydrogenobyric Acid Structure Reveals the Corrin Ligand as an Entatic State Module Empowering B12‐Cofactors for Catalysis

The B12 cofactors instill a natural curiosity regarding the primordial selection and evolution of their corrin ligand. Surprisingly, this important natural macrocycle has evaded molecular scrutiny, and its specific role in predisposing the incarcerated cobalt-ion for organometallic catalysis has remained obscure. Herein, we report the biosynthesis of the cobalt-free B12 corrin moiety, hydrogenobyric acid (Hby), a compound crafted through pathway redesign. Detailed insights from single crystal X-ray and solution structures of Hby have revealed a distorted helical cavity, redefining the pattern for binding cobalt-ions. Consequently, the corrin ligand coordinates cobalt-ions in de-symmetrized ‘entatic’ states, thereby promoting the activation of B12-cofactors for their challenging chemical transitions. The availability of Hby also provides a route to the synthesis of transition metal analogs of B12

PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent

We introduce PyConSolv, a freely available python package that automates the generation of conformers of metal and non-metal containing complexes in explicit solvent, through classical molecular dynamics simulations. Using a streamlined workflow and interfacing with widely used computational chemistry software, PyConSolv is an all-in-one tool for the generation of conformers in any solvent. Input requirements are minimal, only the geometry of the structure and the desired solvent in xyz (XMOL) format are needed. The package can also account for charged systems, by including arbitrary counterions in the simulation. A bonded model parametrization is performed automatically, utilizing the AmberTools, ORCA, and Multiwfn software packages. PyConSolv provides a selection of pre-parametrized solvents and counterions for use in classical molecular dynamics simulations. We show the applicability of our package on a number of (transition-metal-containing) systems. The software is provided open-source and free of charge

Quantum Chemical Microsolvation by Automated Water Placement

We developed a quantitative approach to quantum chemical microsolvation. Key in our methodology is the automatic placement of individual solvent molecules based on the free energy solvation thermodynamics derived from molecular dynamics (MD) simulations and grid inhomogeneous solvation theory (GIST). This protocol enabled us to rigorously define the number, position, and orientation of individual solvent molecules and to determine their interaction with the solute based on physical quantities. The generated solute–solvent clusters served as an input for subsequent quantum chemical investigations. We showcased the applicability, scope, and limitations of this computational approach for a number of small molecules, including urea, 2-aminobenzothiazole, (+)-syn-benzotriborneol, benzoic acid, and helicene. Our results show excellent agreement with the available ab initio molecular dynamics data and experimental results.ISSN:1420-304

The intermolecular anthracene-transfer in a regiospecific antipodal C60 difunctionalization

We analyze the mechanism of the topochemically controlled difunctionalization of C60 and anthracene, where an anthracene molecule is transferred from one C60 monoadduct to another one under exclusive formation of equal amounts of C60 and the difficult to make antipodal C60 bisadduct. Our herein disclosed dispersion corrected DFT studies show the anthracene transfer to take place in a synchronous retro Diels-Alder/Diels-Alder reaction: an anthracene molecule dissociates from one fullerene under formation of an intermediate, while already undergoing stabilizing interactions with both neighboring fullerenes, facilitating the reaction kinetically. In the intermediate, a planar anthracene molecule is sandwiched between two neighboring fullerenes and forms equally strong "double-decker" type pi-pi stacking interactions with both of these fullerenes. Analysis with the distorsion interaction model shows that the anthracene unit of the intermediate is almost planar with minimal distorsions. This analysis sheds light on the existence of noncovalent interactions engaging both faces of a planar polyunsaturated ring and two convex fullerene surfaces in an unprecedented \u27inverted sandwich\u27 structure. Hence, it sheds light on new strategies to design functional fullerene based materials.<br /

Is Mn(I) more promising than Fe(II) – A comparison of Mn vs. Fe complexes for olefin metathesis

Olefin metathesis is one of the most significant transformations in organic chemistry and an excellent example for efficient homogeneous catalysis. Although most currently used catalysts are primarily based on 4d and 5d metals, cycloaddition and cycloreversion reactions can also be attributed to first-row transition metals, such as Fe. Surprisingly, the potential of Mn(I) based catalysts for olefin metathesis has been unexplored, despite its prominence in homogeneous catalysis and its diagonal relationship to Ru(II). In the present study, we have investigated the prospective capabilities of Mn complexes for cycloaddition and reversion reactions, using density functional theory. Therefore, we have initially compared literature known iron model systems and their isoelectronic Mn counterparts regarding reactivity and electronic structure. Next, we constructed potential Mn complexes derived from synthetically accessible species including carbonyl ligands and obeying octahedral geometry. Based on thermodynamic parameters and the calculation of electronic descriptors, we were able to validate the isodiagonal relationship. Our study serves as guidance for the experimental chemist