Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment
Various types of σ-hole bond complexes were formed with FX, HFY, H<sub>2</sub>FZ, and H<sub>3</sub>FT (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) as Lewis acid. In order to examine their interactions with a protein, N-methylacetamide (NMA), a model...
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MDPI AG
2019-09-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/24/18/3329 |
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| author | Mariusz Michalczyk Wiktor Zierkiewicz Rafał Wysokiński Steve Scheiner |
| author_facet | Mariusz Michalczyk Wiktor Zierkiewicz Rafał Wysokiński Steve Scheiner |
| author_sort | Mariusz Michalczyk |
| collection | DOAJ |
| description | Various types of σ-hole bond complexes were formed with FX, HFY, H<sub>2</sub>FZ, and H<sub>3</sub>FT (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) as Lewis acid. In order to examine their interactions with a protein, N-methylacetamide (NMA), a model of the peptide linkage was used as the base. These noncovalent bonds were compared by computational means with H-bonds formed by NMA with XH molecules (X = F, Cl, Br, I). In all cases, the A−F bond, which lies opposite the base and is responsible for the σ-hole on the A atom (A refers to the bridging atom), elongates and its stretching frequency undergoes a shift to the red with a band intensification, much as what occurs for the X−H bond in a H-bond (HB). Unlike the NMR shielding decrease seen in the bridging proton of a H-bond, the shielding of the bridging A atom is increased. The spectroscopic changes within NMA are similar for H-bonds and the other noncovalent bonds. The C=O bond of the amide is lengthened and its stretching frequency red-shifted and intensified. The amide II band shifts to higher frequency and undergoes a small band weakening. The NMR shielding of the O atom directly involved in the bond rises, whereas the C and N atoms both undergo a shielding decrease. The frequency shifts of the amide I and II bands of the base as well as the shielding changes of the three pertinent NMA atoms correlate well with the strength of the noncovalent bond. |
| first_indexed | 2024-12-22T20:02:19Z |
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| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-12-22T20:02:19Z |
| publishDate | 2019-09-01 |
| publisher | MDPI AG |
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| series | Molecules |
| spelling | doaj.art-963fba6949864b6eb11e6921da2680682022-12-21T18:14:15ZengMDPI AGMolecules1420-30492019-09-012418332910.3390/molecules24183329molecules24183329Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein EnvironmentMariusz Michalczyk0Wiktor Zierkiewicz1Rafał Wysokiński2Steve Scheiner3Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, PolandFaculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, PolandFaculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, PolandDepartment of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USAVarious types of σ-hole bond complexes were formed with FX, HFY, H<sub>2</sub>FZ, and H<sub>3</sub>FT (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) as Lewis acid. In order to examine their interactions with a protein, N-methylacetamide (NMA), a model of the peptide linkage was used as the base. These noncovalent bonds were compared by computational means with H-bonds formed by NMA with XH molecules (X = F, Cl, Br, I). In all cases, the A−F bond, which lies opposite the base and is responsible for the σ-hole on the A atom (A refers to the bridging atom), elongates and its stretching frequency undergoes a shift to the red with a band intensification, much as what occurs for the X−H bond in a H-bond (HB). Unlike the NMR shielding decrease seen in the bridging proton of a H-bond, the shielding of the bridging A atom is increased. The spectroscopic changes within NMA are similar for H-bonds and the other noncovalent bonds. The C=O bond of the amide is lengthened and its stretching frequency red-shifted and intensified. The amide II band shifts to higher frequency and undergoes a small band weakening. The NMR shielding of the O atom directly involved in the bond rises, whereas the C and N atoms both undergo a shielding decrease. The frequency shifts of the amide I and II bands of the base as well as the shielding changes of the three pertinent NMA atoms correlate well with the strength of the noncovalent bond.https://www.mdpi.com/1420-3049/24/18/3329stretching frequencyNMR shieldingatomic chargeNBOenergy decomposition |
| spellingShingle | Mariusz Michalczyk Wiktor Zierkiewicz Rafał Wysokiński Steve Scheiner Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment Molecules stretching frequency NMR shielding atomic charge NBO energy decomposition |
| title | Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment |
| title_full | Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment |
| title_fullStr | Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment |
| title_full_unstemmed | Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment |
| title_short | Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment |
| title_sort | theoretical studies of ir and nmr spectral changes induced by sigma hole hydrogen halogen chalcogen pnicogen and tetrel bonds in a model protein environment |
| topic | stretching frequency NMR shielding atomic charge NBO energy decomposition |
| url | https://www.mdpi.com/1420-3049/24/18/3329 |
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