Diffusion and Spectroscopy of H$_2$ in Myoglobin
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arXiv
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| Natura: | Preprint |
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2024
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| _version_ | 1866912026709721088 |
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| author | Käser, Jiri Töpfer, Kai Meuwly, Markus |
| author_facet | Käser, Jiri Töpfer, Kai Meuwly, Markus |
| contents | The diffusional dynamics and vibrational spectroscopy of molecular hydrogen (H$_2$) in myoglobin (Mb) is characterized. Hydrogen has been implicated in a number of physiologically relevant processes, including cellular aging or inflammation. Here, the internal diffusion through the protein matrix was characterized and the vibrational spectroscopy was investigated using conventional empirical energy functions and improved models able to describe higher-order electrostatic moments of the ligand. H$_2$ can occupy the same internal defects as already found for Xe or CO (Xe1 to Xe4 and B-state). Furthermore, 4 additional sites were found, some of which had been discovered in earlier simulation studies. The vibrational spectra using the most refined energy function indicate that depending on the docking site the spectroscopy of H$_2$ differs. The maxima of the absorption spectra cover $\sim 20$ cm$^{-1}$ which are indicative of a pronounced effect of the surrounding protein matrix on the vibrational spectroscopy of the ligand. Electronic structure calculations show that H$_2$ forms a stable complex with the heme-iron (stabilized by $\sim -12$ kcal/mol) but splitting of H$_2$ is unlikely due to a high activation energy ($\sim 50$ kcal/mol). |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2409_08737 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Diffusion and Spectroscopy of H$_2$ in Myoglobin Käser, Jiri Töpfer, Kai Meuwly, Markus Chemical Physics Biomolecules The diffusional dynamics and vibrational spectroscopy of molecular hydrogen (H$_2$) in myoglobin (Mb) is characterized. Hydrogen has been implicated in a number of physiologically relevant processes, including cellular aging or inflammation. Here, the internal diffusion through the protein matrix was characterized and the vibrational spectroscopy was investigated using conventional empirical energy functions and improved models able to describe higher-order electrostatic moments of the ligand. H$_2$ can occupy the same internal defects as already found for Xe or CO (Xe1 to Xe4 and B-state). Furthermore, 4 additional sites were found, some of which had been discovered in earlier simulation studies. The vibrational spectra using the most refined energy function indicate that depending on the docking site the spectroscopy of H$_2$ differs. The maxima of the absorption spectra cover $\sim 20$ cm$^{-1}$ which are indicative of a pronounced effect of the surrounding protein matrix on the vibrational spectroscopy of the ligand. Electronic structure calculations show that H$_2$ forms a stable complex with the heme-iron (stabilized by $\sim -12$ kcal/mol) but splitting of H$_2$ is unlikely due to a high activation energy ($\sim 50$ kcal/mol). |
| title | Diffusion and Spectroscopy of H$_2$ in Myoglobin |
| topic | Chemical Physics Biomolecules |
| url | https://arxiv.org/abs/2409.08737 |