The interaction between aromatic rings and sulfur atoms in the side chains of amino acids is a factor in the formation and stabilization of alpha-helices in proteins. We studied the H(2)S-benzene dimer as the simplest possible prototype of sulfur-pi interactions. High-quality potential energy curves were obtained using coupled-cluster theory with single, double, and perturbative triple substitutions (CCSD(T)) and a large, augmented quadruple-zeta basis set (aug-cc-pVQZ). The equilibrium intermonomer distance for the hydrogens-down C(2)(v) configuration is 3.8 A with an interaction energy of -2.74 kcal mol(-1). Extrapolating the binding energy to the complete basis set limit gives -2.81 kcal mol(-1). This binding energy is comparable to that of H(2)O-benzene or of the benzene dimer, and the equilibrium distance is in close agreement with experiment. Other orientations of the dimer were also considered at less complete levels of theory. A considerable reduction in binding for the sulfur-down configuration, together with an energy decomposition analysis, indicates that the attraction in H(2)S-benzene is best thought of as arising from a favorable electrostatic interaction between partially positive hydrogens in H(2)S with the negatively charged pi-cloud of the benzene.
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Carbohydr Res
January 2025
Department of Chemistry, University of Georgia, 302 East Campus Road, Athens, GA, 30602, United States; Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, GA, 30602, United States; Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, United States. Electronic address:
Methyl 5-thio-α-d-galactopyranoside was synthesized and found to have a more favorable enthalpy of binding to Jacalin than methyl α-d-galactopyranoside, which is attributed to the greater magnitude of sulfur-π over oxygen-π interactions. This increase in enthalpy, however, was offset by a less favorable entropy of binding, arising from the need to constrain the more flexible thiosugar, thereby highlighting the complexities inherent in the design of effective sugar mimetics.
View Article and Find Full Text PDFProtein Sci
March 2024
Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.
Outer membrane proteins perform essential functions in uptake and secretion processes in bacteria. MspA is an octameric channel protein in the outer membrane of Mycobacterium smegmatis and is structurally distinct from any other known outer membrane protein. MspA is the founding member of a family with more than 3000 homologs and is one of the most widely used proteins in nanotechnological applications due to its advantageous pore structure and extraordinary stability.
View Article and Find Full Text PDFJ Biomol Struct Dyn
December 2024
Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.
Substituted ethoxy phthalimide pyrazole derivatives () have been produced using a one-pot synthesis technique. Spectral analysis was used to establish the molecular structure of the synthesized compounds, and they were examined and for their ability to bind to and inhibit replication of the AD-169 strain, the Davis strain of CMV, the OKA strain and the 07/1 strain of Varicella-Zoster virus (VZV). Molecular Docking was used to estimate the binding mechanism and energy of compounds to their respective target proteins, thymidine kinase (TK), Varicella-Zoster protease (VZP) of VZV and tegument protein pp71 (TPpp71) of Cytomegalovirus (CMV).
View Article and Find Full Text PDFJ Phys Chem B
April 2023
Laboratorio de Química Supramolecular y Fotobiología, Departamento de Química Física, Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile.
Supramolecular control of singlet oxygen generation is incredibly valuable for several fields with broad applications and thus still challenging. However, macrocyclic inclusion complexes inherently restrict the interaction of photosensitizers with surrounding oxygen in the media. To circumvent this issue, we turned our attention in this work to acyclic cucurbituril-like containers and uncover their properties as supramolecular hosts for photosensitizers with extraordinary control of their photophysics, including singlet oxygen generation.
View Article and Find Full Text PDFJ Phys Chem A
March 2023
Department of Chemistry, University of California─Davis, Davis, California 95616, United States.
Noncovalent interactions involving sulfur atoms play essential roles in protein structure and function by significantly contributing to protein stability, folding, and biological activity. Sulfur is a highly polarizable atom that can participate in many types of noncovalent interactions including hydrogen bonding, sulfur-π interactions, and S-lone pair interactions, but the impact of these sulfur-based interactions on molecular recognition and drug design is still often underappreciated. Here, we examine, using quantum chemical calculations, the roles of sulfur-based noncovalent interactions in complex naturally occurring molecules representative of thiopeptide antibiotics: glycothiohexide α and its close structural analogue nocathiacin I.
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