气候变化领域集成服务门户(CCPortal): A thermodynamic atlas of carbon redox chemical space

CCPortal

DOI	10.1073/PNAS.2005642117
	A thermodynamic atlas of carbon redox chemical space
	Jinich A.; Sanchez-Lengeling B.; Ren H.; Goldford J.E.; Noor E.; Sanders J.N.; Segrè D.; Aspuru-Guzik A.
发表日期	2021
ISSN	00278424
起始页码	32910
结束页码	32918
卷号	117 期号:52
英文摘要	Redox biochemistry plays a key role in the transduction of chemical energy in living systems. However, the compounds observed in metabolic redox reactions are a minuscule fraction of chemical space. It is not clear whether compounds that ended up being selected as metabolites display specific properties that distinguish them from nonbiological compounds. Here, we introduce a systematic approach for comparing the chemical space of all possible redox states of linear-chain carbon molecules to the corresponding metabolites that appear in biology. Using cheminformatics and quantum chemistry, we analyze the physicochemical and thermodynamic properties of the biological and nonbiological compounds. We find that, among all compounds, aldose sugars have the highest possible number of redox connections to other molecules. Metabolites are enriched in carboxylic acid functional groups and depleted of ketones and aldehydes and have higher solubility than nonbiological compounds. Upon constructing the energy landscape for the full chemical space as a function of pH and electron-donor potential, we find that metabolites tend to have lower Gibbs energies than nonbiological molecules. Finally, we generate Pourbaix phase diagrams that serve as a thermodynamic atlas to indicate which compounds are energy minima in redox chemical space across a set of pH values and electron-donor potentials. While escape from thermodynamic equilibrium toward kinetically driven states is a hallmark of life and its origin, we envision that a deeper quantitative understanding of the environment-dependent thermodynamic landscape of putative prebiotic molecules will provide a crucial reference for future origins-of-life models. © 2020 National Academy of Sciences. All rights reserved.
英文关键词	Origins of life; Prebiotic chemistry; Redox biochemistry; Systems chemistry; Thermodynamics
语种	英语
scopus关键词	aldehyde; carbohydrate; carboxylic acid; ketone; prebiotic agent; chemistry; conformation; molecular dynamics; oxidation reduction reaction; procedures; Aldehydes; Carbohydrate Conformation; Carboxylic Acids; Cheminformatics; Ketones; Molecular Dynamics Simulation; Oxidation-Reduction; Prebiotics; Sugars
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/179682
作者单位	Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States; Division of Infectious Diseases, Weill Department of Medicine, Weill-Cornell Medical College, New York, NY 10021, United States; Bioinformatics Program and Biological Design Center, Boston University, Boston, MA 02215, United States; Institute of Molecular Systems Biology, ETH Zürich, Zürich, 8093, Switzerland; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States; Department of Biology, Boston University, Boston, MA 02215, United States; Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States; Department of Physics, Boston University, Boston, MA 02215, United States; Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada; CIFAR AI Chair, Vector Institute, Toronto, ON M5S 1M1, Ca...
推荐引用方式 GB/T 7714	Jinich A.,Sanchez-Lengeling B.,Ren H.,et al. A thermodynamic atlas of carbon redox chemical space[J],2021,117(52).
APA	Jinich A..,Sanchez-Lengeling B..,Ren H..,Goldford J.E..,Noor E..,...&Aspuru-Guzik A..(2021).A thermodynamic atlas of carbon redox chemical space.Proceedings of the National Academy of Sciences of the United States of America,117(52).
MLA	Jinich A.,et al."A thermodynamic atlas of carbon redox chemical space".Proceedings of the National Academy of Sciences of the United States of America 117.52(2021).