Modeling the hydrogen sulfide binding to heme
Abstract
The binding of hydrogen sulfide to a model heme compound is investigated by coupled-cluster singles-doubles augmented by a perturbative triple excitations, CCSD(T), and density functional theory, DFT. The minimum energy path for the H2S addition to an isolated heme center of the heme protein is evaluated by adopting as a model the heme compound FeP(Im) (P = porphyrin; Im = imidazole). The FeP(Im)-H2S aduct is bound by 13.7 kcal/mol at the CCSD(T) level of theory. Relaxed potential energy curves for the lowest lying spin states of the H2S to FeP(Im) binding using DFT reveal that the binding process is associated with a "double spin-cross-over" reaction with the existence of long-distance van der Waals minima only 5-7 kcal/mol above the FeP(Im)-H2S ground state. The fact that the energy of the singlet ground state of FeP(Im)-H2S is so close in energy to the dissociation products FeP(Im) + H2S points towards the reversibility of the H2S adsorption/desorption process in biochemical reactio...ns.
Keywords:
Heme / Imidazole / H2S binding / Electronic states / Density functional theory / Coupled cluster theorySource:
Journal of Inorganic Biochemistry, 2018, 184, 108-114Publisher:
- Elsevier Science Inc, New York
Funding / projects:
- The study of physicochemical and biochemical processes in living environment that have impacts on pollution and the investigation of possibilities for minimizing the consequences (RS-MESTD-Basic Research (BR or ON)-172001)
- Modeling and Numerical Simulations of Complex Many-Body Systems (RS-MESTD-Basic Research (BR or ON)-171017)
Note:
- The peer-reviewed version: https://cer.ihtm.bg.ac.rs/handle/123456789/4284
DOI: 10.1016/j.jinorgbio.2018.04.012
ISSN: 0162-0134
PubMed: 29705379
WoS: 000434493300013
Scopus: 2-s2.0-85046168618
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Institution/Community
IHTMTY - JOUR AU - Ostojić, Bojana AU - Schwerdtfeger, Peter AU - Đorđević, Dragana PY - 2018 UR - https://cer.ihtm.bg.ac.rs/handle/123456789/2286 AB - The binding of hydrogen sulfide to a model heme compound is investigated by coupled-cluster singles-doubles augmented by a perturbative triple excitations, CCSD(T), and density functional theory, DFT. The minimum energy path for the H2S addition to an isolated heme center of the heme protein is evaluated by adopting as a model the heme compound FeP(Im) (P = porphyrin; Im = imidazole). The FeP(Im)-H2S aduct is bound by 13.7 kcal/mol at the CCSD(T) level of theory. Relaxed potential energy curves for the lowest lying spin states of the H2S to FeP(Im) binding using DFT reveal that the binding process is associated with a "double spin-cross-over" reaction with the existence of long-distance van der Waals minima only 5-7 kcal/mol above the FeP(Im)-H2S ground state. The fact that the energy of the singlet ground state of FeP(Im)-H2S is so close in energy to the dissociation products FeP(Im) + H2S points towards the reversibility of the H2S adsorption/desorption process in biochemical reactions. PB - Elsevier Science Inc, New York T2 - Journal of Inorganic Biochemistry T1 - Modeling the hydrogen sulfide binding to heme VL - 184 SP - 108 EP - 114 DO - 10.1016/j.jinorgbio.2018.04.012 ER -
@article{ author = "Ostojić, Bojana and Schwerdtfeger, Peter and Đorđević, Dragana", year = "2018", abstract = "The binding of hydrogen sulfide to a model heme compound is investigated by coupled-cluster singles-doubles augmented by a perturbative triple excitations, CCSD(T), and density functional theory, DFT. The minimum energy path for the H2S addition to an isolated heme center of the heme protein is evaluated by adopting as a model the heme compound FeP(Im) (P = porphyrin; Im = imidazole). The FeP(Im)-H2S aduct is bound by 13.7 kcal/mol at the CCSD(T) level of theory. Relaxed potential energy curves for the lowest lying spin states of the H2S to FeP(Im) binding using DFT reveal that the binding process is associated with a "double spin-cross-over" reaction with the existence of long-distance van der Waals minima only 5-7 kcal/mol above the FeP(Im)-H2S ground state. The fact that the energy of the singlet ground state of FeP(Im)-H2S is so close in energy to the dissociation products FeP(Im) + H2S points towards the reversibility of the H2S adsorption/desorption process in biochemical reactions.", publisher = "Elsevier Science Inc, New York", journal = "Journal of Inorganic Biochemistry", title = "Modeling the hydrogen sulfide binding to heme", volume = "184", pages = "108-114", doi = "10.1016/j.jinorgbio.2018.04.012" }
Ostojić, B., Schwerdtfeger, P.,& Đorđević, D.. (2018). Modeling the hydrogen sulfide binding to heme. in Journal of Inorganic Biochemistry Elsevier Science Inc, New York., 184, 108-114. https://doi.org/10.1016/j.jinorgbio.2018.04.012
Ostojić B, Schwerdtfeger P, Đorđević D. Modeling the hydrogen sulfide binding to heme. in Journal of Inorganic Biochemistry. 2018;184:108-114. doi:10.1016/j.jinorgbio.2018.04.012 .
Ostojić, Bojana, Schwerdtfeger, Peter, Đorđević, Dragana, "Modeling the hydrogen sulfide binding to heme" in Journal of Inorganic Biochemistry, 184 (2018):108-114, https://doi.org/10.1016/j.jinorgbio.2018.04.012 . .