In this study, the ability of CF groups to bind to the electron-rich side chains and backbone groups of proteins has been investigated by combining a Protein Data Bank (PDB) survey and quantum mechanics calculations. More precisely, an inspection of the PDB involving organic ligands containing a CF group and electron-rich atoms (A = N, O and S) in the vicinity revealed 419 X-ray structures exhibiting CF⋯A tetrel bonds (TtBs). In a posterior stage, those hits that exhibited the most relevant features in terms of directionality and intermolecular distance were selected for theoretical calculations at the RI-MP2/def2-TZVPD level of theory. Also, Hammett's regression plots of several TtB complexes involving - and -substituted benzene derivatives were computed to shed light on the substituent effects. Moreover, the TtBs were characterized through several state-of-the-art computational techniques, such as the Quantum Theory of Atoms in Molecules (QTAIM) and Noncovalent Interactions plot (NCIplot) methodologies. We believe that the results gathered from our study will be useful for rational drug design and biological communities as well as for further expanding the role of this interaction to biomedical applications.
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http://dx.doi.org/10.1039/d3cp00839h | DOI Listing |
J Phys Chem A
December 2024
Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław 50-370, Poland.
J Phys Chem A
December 2024
College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-Materials, Hebei Normal University, Shijiazhuang 050024, China.
Halogen, chalcogen, pnictogen, and tetrel bonds in organocatalysis have gained noticeable attention. In this work, carbon-bromide bond activation in the Ritter reaction by bidentate imidazole-type halogen, chalcogen, pnicogen, and tetrel bond donors was studied by density functional theory. All of the above four kinds of catalysts exhibited excellent catalytic performance.
View Article and Find Full Text PDFChempluschem
November 2024
Research Laboratory of Multiscale modelling of multicomponent materials, South Ural State University, 76, Lenin ave, Chelyabinsk, Russia, 454080.
Understanding and exploring the existence of a recognizable boundary between the noncovalent tetrel bond (TtB) and the coordination or weakened covalent bond are important for the bonding characterization. We have developed a simple methodology for analysing the type of bonds based on comparison of the electrostatic and total static potentials along the bond line. For the typical σ-hole noncovalent bond formed by a Tt atom in a tetrahedral molecule, we have found that the space gap between positions of the maxima of the total static potential and the negative quantity of electrostatic potential is much wider than that for the coordination bonds in a trigonal bipyramid molecular system for the Cl-Tt/Cl⋅⋅⋅Tt and N-Tt/N⋅⋅⋅Tt (Tt=C, Si, Ge) bonds in molecules and molecular complexes.
View Article and Find Full Text PDFOrg Biomol Chem
November 2024
Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka - 560012, India.
NMR spectral and theoretical analyses of homologous prolyl carbamates reveal subtle charge transfer tetrel bonding interactions (TBIs), selectively stabilizing their Pro rotamers. These TBIs involve C-terminal-amide to N-terminal carbamate carbonyl-carbonyl (n → π* type) followed by intra-carbamate (n → σ* type) charge transfer interactions exclusively in the Pro motif. The number of TBIs and hence the Pro stability increase with increasing number of C groups at the carbamate alcohol.
View Article and Find Full Text PDFPhys Chem Chem Phys
November 2024
Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
The existence of halogen, chalcogen, pnicogen, and tetrel bonds as variants of noncovalent σ and π-hole bonds is now widely accepted, and many of their properties have been elucidated. The ability of the d-block transition metals to potentially act as Lewis acids in a similar capacity is examined systematically by DFT calculations. Metals examined span the entire range of the d-block from Group 3 to 12, and are selected from several rows of the periodic table.
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