Enzyme-substrate interactions play a crucial role in enzymatic catalysis. Quantum theory of atoms in molecules (QTAIM) calculations are extremely useful in computational studies of these interactions because they provide very detailed information about the strengths and types of molecular interactions. QTAIM also provides information about the intramolecular changes that occur in the catalytic reaction. Here, we analyze the enzyme-substrate interactions and the topological properties of the electron density in the enantioselective step of the acylation of (,)-propranolol, an aminoalcohol with therapeutic applications, catalyzed by lipase B. Eight reaction paths (four for each enantiomer) are investigated and the energies, atomic charges, hydrogen bonds, and n → π* interactions of propranolol, the catalytic triad (composed of D187, H224, and S105), and the oxyanion hole are analyzed. It is found that D187 acts as an electron density reservoir for H224, and H224 acts as an electron density reservoir for the active site of the protein. It releases electron density when the tetrahedral intermediate is formed from the Michaelis complex and receives it when the enzyme-product complex is formed. Hydrogen bonds can be grouped into noncovalent and covalent hydrogen bonds. The latter are stronger and more important for the reaction than the former. We also found weak n → π* interactions, which are characterized by QTAIM and the natural bond orbital (NBO) analysis.
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http://dx.doi.org/10.1021/acsomega.1c02559 | DOI Listing |
J Am Chem Soc
January 2025
Molecular Synthesis Center, Key Laboratory of Marine Drugs of Ministry of Education, Shandong Key Laboratory of Glycoscience and Glycotherapeutics, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
2-Deoxy-β-glycosides are essential components of natural products and pharmaceuticals; however, the corresponding 2-deoxy-β-glycosidic bonds are challenging to chemically construct. Herein, we describe an efficient catalytic protocol for synthesizing 2-deoxy-β-glycosides via either IPrAuNTf-catalyzed activation of a unique 1,2--positioned C2--propargyl xanthate (OSPX) leaving group or (PhO)PAuNTf-catalyzed activation of a 1,2--C2--alkynylbenzoate (OABz) substituent of the corresponding thioglycosides. These activation processes trigger 1,2-alkyl/arylthio-migration glycosylation, enabling the synthesis of structurally diverse 2-deoxy-β-glycosides under mild reaction conditions.
View Article and Find Full Text PDFAngew Chem Int Ed Engl
January 2025
University of Regensburg, Faculty of Chemistry and Pharmacy, Institute of Inorganic Chemistry, Universitätsstraße 31, D-93053, Regensburg, GERMANY.
Aminophosphates are the focus of research on prebiotic phosphorylation chemistry. Their bifunctional nature also makes them a powerful class of organocatalysts. However, the structural chemistry and dynamics of proton-binding in phosphorylation and organocatalytic mechanisms are still not fully understood.
View Article and Find Full Text PDFJ Phys Chem B
January 2025
Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.
Computationally designed 29-residue peptides yield tetra-α-helical bundles with symmetry. The "bundlemers" can be bifunctionally linked via thiol-maleimide cross-links at their N-termini, yielding supramolecular polymers with unusually large, micrometer-scale persistence lengths. To provide a molecularly resolved understanding of these systems, all-atom molecular modeling and simulations of linked bundlemers in explicit solvent are presented.
View Article and Find Full Text PDFDalton Trans
January 2025
Department of Inorganic Chemistry, Shahid Beheshti University, 1983969411, Tehran, Iran.
In a systematic study, six pseudopolymorphic coordination polymers containing the ditopic 1,3-di(pyridin-4-yl)urea ligand (4bpu) constructed with d metal cations, possessing the formula {[M(4bpu)I]S} [(M = Zn, Cd and Hg), (S = MeOH or EtOH)], namely Zn-MeOH, Zn-EtOH, Cd-MeOH, Cd-EtOH, Hg- and Hg-EtOH were obtained. The title compounds were characterized by single-crystal X-ray diffraction analysis (SC-XRD), elemental analysis (CHN), FT-IR spectroscopy, thermogravimetric analysis (TGA), and powder X-ray diffraction (PXRD). The diffraction studies show that these compounds are isostructural 1D zig-zag chain coordination polymers which is also confirmed using XPac 2.
View Article and Find Full Text PDFAcc Chem Res
January 2025
The Department of Chemistry, State University of New York at Binghamton, Binghamton, New York 13902, United States.
ConspectusIn the search for efficient and selective electrocatalysts capable of converting greenhouse gases to value-added products, enzymes found in naturally existing bacteria provide the basis for most approaches toward electrocatalyst design. Ni,Fe-carbon monoxide dehydrogenase (Ni,Fe-CODH) is one such enzyme, with a nickel-iron-sulfur cluster named the C-cluster, where CO binds and is converted to CO at high rates near the thermodynamic potential. In this Account, we divide the enzyme's catalytic contributions into three categories based on location and function.
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