Computational and crystallographic study of hydrogen bonds in the second coordination sphere of chelated amino acids with a free water molecule: Influence of complex charge and metal ion
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Hydrogen bonds of glycine complexes were calculated using quantum chemistry calculations at M06L-GD3/def2-TZVPP level and by analyzing the crystal structures from the Cambridge Structural Database (CSD). One hydrogen bond where amino acid plays the role of the H-donor (NH/O), and two where it plays the role of the H-acceptor (O1/HO, O1 is a coordinated oxygen atom, and, O2/HO, O2 is a non-coordinated oxygen atom) were investigated. The calculations were done on octahedral nickel(II), square pyramidal copper(II), square planar copper(II), palladium(II), and platinum(II) glycine complexes with different charges adjusted using water(s) and/or chlorine ion(s) as the remaining ligands. For NH/O hydrogen bond, interaction energies of neutral complexes are the weakest, from -5.2 to -7.2 kcal/mol for neutral, stronger for singly positive, from -8.3 to -12.1 kcal/mol, and the strongest for doubly positive complex, -16.9 kcal/mol. For O1/HO and O2/HO interactions, neutral complexes have weaker i...nteraction energies (from -2.2 to -5.1 kcal/mol for O1/HO, and from -3.7 to -5.0 kcal/mol for O2/HO), than for singly negative complexes (from -6.9 to -8.2 kcal/mol for O1/HO, and from -8.0 to -9.0 kcal/mol for O2/HO). Additionally to the complex charge, metal oxidation number, coordination number, and metal atomic number also influence the hydrogen bond strength, however, the influence is smaller.
Кључне речи:
Hydrogen bonds / Amino acids / Metal complexes / crystal structures / Density functional theory (DFT) / Cambridge Structural Database (CSD)Извор:
Journal of Inorganic Biochemistry, 2024, 251, 112442-Издавач:
- Elsevier
Финансирање / пројекти:
- Нековалентне интеракције pi-система и њихова улога у молекулском препознавању (RS-MESTD-Basic Research (BR or ON)-172065)
Напомена:
- This is the peer-reviewed version of the article: Zrilić, S. S., Živković, J.,& Zarić, S.. (2023). Computational and crystallographic study of hydrogen bonds in the second coordination sphere of chelated amino acids with a free water molecule: Influence of complex charge and metal ion. in Journal of Inorganic Biochemistry Elsevier., 251. https://doi.org/10.1016/j.jinorgbio.2023.112442
Повезане информације:
- Верзија документа
https://doi.org/10.1016/j.jinorgbio.2023.112442 - Верзија документа
https://cherry.chem.bg.ac.rs/handle/123456789/6377
URI
http://cherry.chem.bg.ac.rs/handle/123456789/6377http://cherry.chem.bg.ac.rs/handle/123456789/6447
Институција/група
Hemijski fakultet / Faculty of ChemistryTY - JOUR AU - Zrilić, Sonja S. AU - Živković, Jelena AU - Zarić, Snežana D. PY - 2024 UR - http://cherry.chem.bg.ac.rs/handle/123456789/6377 UR - http://cherry.chem.bg.ac.rs/handle/123456789/6447 AB - Hydrogen bonds of glycine complexes were calculated using quantum chemistry calculations at M06L-GD3/def2-TZVPP level and by analyzing the crystal structures from the Cambridge Structural Database (CSD). One hydrogen bond where amino acid plays the role of the H-donor (NH/O), and two where it plays the role of the H-acceptor (O1/HO, O1 is a coordinated oxygen atom, and, O2/HO, O2 is a non-coordinated oxygen atom) were investigated. The calculations were done on octahedral nickel(II), square pyramidal copper(II), square planar copper(II), palladium(II), and platinum(II) glycine complexes with different charges adjusted using water(s) and/or chlorine ion(s) as the remaining ligands. For NH/O hydrogen bond, interaction energies of neutral complexes are the weakest, from -5.2 to -7.2 kcal/mol for neutral, stronger for singly positive, from -8.3 to -12.1 kcal/mol, and the strongest for doubly positive complex, -16.9 kcal/mol. For O1/HO and O2/HO interactions, neutral complexes have weaker interaction energies (from -2.2 to -5.1 kcal/mol for O1/HO, and from -3.7 to -5.0 kcal/mol for O2/HO), than for singly negative complexes (from -6.9 to -8.2 kcal/mol for O1/HO, and from -8.0 to -9.0 kcal/mol for O2/HO). Additionally to the complex charge, metal oxidation number, coordination number, and metal atomic number also influence the hydrogen bond strength, however, the influence is smaller. PB - Elsevier T2 - Journal of Inorganic Biochemistry T1 - Computational and crystallographic study of hydrogen bonds in the second coordination sphere of chelated amino acids with a free water molecule: Influence of complex charge and metal ion VL - 251 SP - 112442 DO - 10.1016/j.jinorgbio.2023.112442 ER -
@article{ author = "Zrilić, Sonja S. and Živković, Jelena and Zarić, Snežana D.", year = "2024", abstract = "Hydrogen bonds of glycine complexes were calculated using quantum chemistry calculations at M06L-GD3/def2-TZVPP level and by analyzing the crystal structures from the Cambridge Structural Database (CSD). One hydrogen bond where amino acid plays the role of the H-donor (NH/O), and two where it plays the role of the H-acceptor (O1/HO, O1 is a coordinated oxygen atom, and, O2/HO, O2 is a non-coordinated oxygen atom) were investigated. The calculations were done on octahedral nickel(II), square pyramidal copper(II), square planar copper(II), palladium(II), and platinum(II) glycine complexes with different charges adjusted using water(s) and/or chlorine ion(s) as the remaining ligands. For NH/O hydrogen bond, interaction energies of neutral complexes are the weakest, from -5.2 to -7.2 kcal/mol for neutral, stronger for singly positive, from -8.3 to -12.1 kcal/mol, and the strongest for doubly positive complex, -16.9 kcal/mol. For O1/HO and O2/HO interactions, neutral complexes have weaker interaction energies (from -2.2 to -5.1 kcal/mol for O1/HO, and from -3.7 to -5.0 kcal/mol for O2/HO), than for singly negative complexes (from -6.9 to -8.2 kcal/mol for O1/HO, and from -8.0 to -9.0 kcal/mol for O2/HO). Additionally to the complex charge, metal oxidation number, coordination number, and metal atomic number also influence the hydrogen bond strength, however, the influence is smaller.", publisher = "Elsevier", journal = "Journal of Inorganic Biochemistry", title = "Computational and crystallographic study of hydrogen bonds in the second coordination sphere of chelated amino acids with a free water molecule: Influence of complex charge and metal ion", volume = "251", pages = "112442", doi = "10.1016/j.jinorgbio.2023.112442" }
Zrilić, S. S., Živković, J.,& Zarić, S. D.. (2024). Computational and crystallographic study of hydrogen bonds in the second coordination sphere of chelated amino acids with a free water molecule: Influence of complex charge and metal ion. in Journal of Inorganic Biochemistry Elsevier., 251, 112442. https://doi.org/10.1016/j.jinorgbio.2023.112442
Zrilić SS, Živković J, Zarić SD. Computational and crystallographic study of hydrogen bonds in the second coordination sphere of chelated amino acids with a free water molecule: Influence of complex charge and metal ion. in Journal of Inorganic Biochemistry. 2024;251:112442. doi:10.1016/j.jinorgbio.2023.112442 .
Zrilić, Sonja S., Živković, Jelena, Zarić, Snežana D., "Computational and crystallographic study of hydrogen bonds in the second coordination sphere of chelated amino acids with a free water molecule: Influence of complex charge and metal ion" in Journal of Inorganic Biochemistry, 251 (2024):112442, https://doi.org/10.1016/j.jinorgbio.2023.112442 . .