A thermodynamic atlas of carbon redox chemical space.
A thermodynamic atlas of carbon redox chemical space.
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DOI：
10.1073/pnas.2005642117
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发表时间：
2020-12-29
影响因子：
11.1
通讯作者：
Aspuru-Guzik A
中科院分区：
文献类型：
--
作者：
Jinich A;Sanchez-Lengeling B;Ren H;Goldford JE;Noor E;Sanders JN;Segrè D;Aspuru-Guzik A
碳氧化还原化学在生物学中起着重要的作用。然而，涉及氧化还原生物化学的代谢物上升的热力学和物理化学原理仍然知之甚少。我们的工作介绍了理论和技术，使我们能够量化和理解碳氧化还原生物化学的全球能源格局。我们分析了具有2到5个碳原子的线性链分子的所有可能的氧化态的空间，并生成了代谢物与非生物分子相比的热力学稳定性的详细图谱。尽管生命的出现需要潜在的化学物质来引导自身脱离平衡，但对益生元分子依赖于环境的热力学景观的定量理解，对未来生命起源模型的建立将具有极大的价值。氧化还原生物化学在生命系统的化学能转导中起着关键作用。然而，在代谢氧化还原反应中观察到的化合物是化学空间的极小部分。目前尚不清楚最终被选择为代谢物的化合物是否表现出与非生物化合物不同的特定特性。在这里，我们介绍了一种系统的方法来比较线性链碳分子所有可能的氧化还原状态的化学空间与生物学中出现的相应代谢物。利用化学信息学和量子化学，我们分析了生物和非生物化合物的物理化学和热力学性质。我们发现，在所有化合物中，醛糖糖与其他分子的氧化还原连接可能最多。代谢物富含羧酸官能团，缺乏酮类和醛类，比非生物化合物具有更高的溶解度。在构建整个化学空间的能量景观作为pH值和电子供体电位的函数后，我们发现代谢物往往比非生物分子具有更低的吉布斯能。最后，我们生成了作为热力学图谱的Pourbaix相图，以指示在一组pH值和电子给体电位中哪些化合物在氧化还原化学空间中能量最小。虽然从热力学平衡向动力学驱动状态的逃逸是生命及其起源的标志，但我们设想，对假定的益生元分子的环境依赖的热力学景观的更深入的定量理解将为未来的生命起源模型提供重要参考。
Carbon redox chemistry plays a fundamental role in biology. However, the thermodynamic and physicochemical principles underlying the rise of metabolites involved in redox biochemistry remain poorly understood. Our work introduces the theory and techniques that allow us to quantify and understand the global energy landscape of carbon redox biochemistry. We analyze the space of all possible oxidation states of linear-chain molecules with two to five carbon atoms and generate a detailed atlas of the thermodynamic stability of metabolites in comparison to nonbiological molecules. Although the emergence of life required the underlying chemistry to bootstrap itself out of equilibrium, a quantitative understanding of the environment-dependent thermodynamic landscape of prebiotic molecules will be extremely valuable for future origins of life models. 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.
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影响因子：
3.7
作者：
Jakobsdottir G;Xu J;Molin G;Ahrné S;Nyman M
通讯作者：
Nyman M
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影响因子：
16
作者：
Donohoe, Dallas R.;Collins, Leonard B.;Wali, Aminah;Bigler, Rebecca;Sun, Wei;Bultman, Scott J.
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Bultman, Scott J.
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作者：
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作者：
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通讯作者：
Rabinowitz, Joshua D.
影响因子：
56.9
作者：
HOCHACHKA, PW;STOREY, KB
通讯作者：
STOREY, KB