Cost-effective density functional theory (DFT) calculations of equilibrium isotopic fractionation in large organic molecules

Iron, Mark A.; Gropp, Jonathan

doi:10.1039/c9cp02975c

Cited by 20 publications

(23 citation statements)

References 150 publications

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“…However, there are more modern and cost-effective methods, such as M06-L (Zhao et al, 2006) or HCTH/407 (Boese & Handy, 2001), and until recently the accuracy of these and other functionals in predicting EFFs of large organic molecules has not been systematically compared. We recently conducted a thorough examination of various DFT functionals and basis sets to determine the uncertainty associated with the prediction of EFFs of H, C, N and O stable isotopes among large soluble organic molecules (Iron & Gropp, 2019). The mean unsigned error (MUE) of these calculations in predicting the hydrogen fractionation in the C α position of linear and cyclic ketones is 20.8‰, comparable to the results of Wang et al (2009a;.…”

Section: Calculating Equilibrium Fractionation Factorsmentioning

confidence: 86%

“…These theoretical predictions are invaluable in exploring isotope fractionation systematics where experimental data are lacking or hard to obtain (e.g., Rustad et al, 2008;Eldridge et al, 2016), such as for the intracellular components of biological production and oxidation of methane (methanogenesis and methanotrophy, respectively). Theoretical approaches, in particular density functional theory (DFT), have been widely applied to small molecules (Li & Liu, 2011;Fujii et al, 2014), and recently also to large organic molecules (Black et al, 2007;Rustad, 2009;Wang et al, 2009aWang et al, ,b, 2013Moynier & Fujii, 2017;Iron & Gropp, 2019) in the gas, aqueous and solid phases. The application of DFT is of special interest in methanogenesis and methanotrophy since these processes involve large organic molecules, which have received less attention than small molecules due to issues of calculation cost and accuracy (Iron & Gropp, 2019).…”

Section: Generalmentioning

confidence: 99%

“…Theoretical approaches, in particular density functional theory (DFT), have been widely applied to small molecules (Li & Liu, 2011;Fujii et al, 2014), and recently also to large organic molecules (Black et al, 2007;Rustad, 2009;Wang et al, 2009aWang et al, ,b, 2013Moynier & Fujii, 2017;Iron & Gropp, 2019) in the gas, aqueous and solid phases. The application of DFT is of special interest in methanogenesis and methanotrophy since these processes involve large organic molecules, which have received less attention than small molecules due to issues of calculation cost and accuracy (Iron & Gropp, 2019). Consequently, studies to date of the isotopic compositions in methanogenesis and methanotrophy have focused on the extracellular substrates and products, mainly H 2 , CO 2 , CH 4 and H 2 O, but have neglected the intracellular components of these processes.…”

Section: Generalmentioning

confidence: 99%

“…Based on its performance in predicting EFFs in large organic molecules (Iron & Gropp, 2019), we chose the M06-L DFT exchange-correlation functional and def2-TZVP basis set (Andrae et al, 1990;Kaupp et al, 1991;Leininger et al, 1996;Metz et al, 2000;Weigend & Ahlrichs, 2005).…”

Section: Ganic Moleculesmentioning

confidence: 99%

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Theoretical estimates of equilibrium carbon and hydrogen isotope effects in microbial methane production and anaerobic oxidation of methane

Gropp

Iron

Halevy

2021

Geochimica et Cosmochimica Acta

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Microbial production and consumption of methane are widespread in natural and artificial environments, with important economic and climatic implications. Attempts to use the isotopic composition of methane to constrain its sources are complicated by incomplete understanding of the mechanisms of variation in methane's isotopic composition. Knowledge of the equilibrium isotope fractionations among the large organic intracellular intermediates in the microbial pathways of methane production and consumption must form the basis of any exploration of the mechanisms of isotopic variation, but estimates of these equilibrium isotope fractionations are currently unavailable. To address this gap, we calculated the equilibrium isotopic fractionation of carbon (13 C/ 12 C) and hydrogen (D/H) isotopes among compounds in anaerobic methane metabolisms, as well as the abundance of multiple isotope substitutions ("clumping," e.g., 13 C-D) in these compounds. The Density Functional Theory calculations employed the M06-L/def2-TZVP level of theory and the SMD implicit solvation model, which we have recently optimized for large organic molecules and tested against measured equilibrium isotope fractionations. The computed 13 β and 2 β values decrease with decreasing average oxidation state of the carbon atom in the molecules, resulting in a preference for enrichment of the molecules with more oxidized carbon in 13 C and D. Using the computed β values, we calculated the equilibrium isotope fractionation factors in the prominent methanogenesis pathways (hydrogenotrophic, methylotrophic and acetoclastic) and in the pathway for anaerobic oxidation of methane (AOM) over a temperature range of 0-700 • C. Our calculated equilibrium fractionation factors compare favorably with experimental constrains, where available, and we used them to investigate the relation between the apparent isotope fractionation during

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Section: Calculating Equilibrium Fractionation Factorsmentioning

confidence: 86%

Section: Generalmentioning

confidence: 99%

Section: Generalmentioning

confidence: 99%

Section: Ganic Moleculesmentioning

confidence: 99%

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Theoretical estimates of equilibrium carbon and hydrogen isotope effects in microbial methane production and anaerobic oxidation of methane

Gropp

Iron

Halevy

2021

Geochimica et Cosmochimica Acta

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“…Second, a recent study evaluated the range in predictions of the bulk carbon isotope fractionation between CO2 and methane found that the models fell within 2‰ of the measurements from 300-1200°C (8). Finally, a recent study (9), has evaluated the factors that affect accuracy of calculated equilibrium isotope fractionations for carbon and hydrogen isotopes among a diverse range of organic compounds. The authors found that the deviation of the calculated isotopic value from the measured equilibrium value for B3LYP DFTs (which is also the DFT that we use in our study) averaged 4‰ for carbon isotopes and 30‰ for hydrogen isotopes at 25°C.…”

mentioning

confidence: 98%

Isotopic evidence for quasi-equilibrium chemistry in thermally mature natural gases

Thiagarajan

Xie

Ponton

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Natural gas is a key energy resource, and understanding how it forms is important for predicting where it forms in economically important volumes. However, the origin of dry thermogenic natural gas is one of the most controversial topics in petroleum geochemistry, with several differing hypotheses proposed, including kinetic processes (such as thermal cleavage, phase partitioning during migration, and demethylation of aromatic rings) and equilibrium processes (such as transition metal catalysis). The dominant paradigm is that it is a product of kinetically controlled cracking of long-chain hydrocarbons. Here we show that C2+n-alkane gases (ethane, propane, butane, and pentane) are initially produced by irreversible cracking chemistry, but, as thermal maturity increases, the isotopic distribution of these species approaches thermodynamic equilibrium, either at the conditions of gas formation or during reservoir storage, becoming indistinguishable from equilibrium in the most thermally mature gases. We also find that the pair of CO2 and C1 (methane) exhibit a separate pattern of mutual isotopic equilibrium (generally at reservoir conditions), suggesting that they form a second, quasi-equilibrated population, separate from the C2 to C5 compounds. This conclusion implies that new approaches should be taken to predicting the compositions of natural gases as functions of time, temperature, and source substrate. Additionally, an isotopically equilibrated state can serve as a reference frame for recognizing many secondary processes that may modify natural gases after their formation, such as biodegradation.

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Experimental and theoretical exploration on single crystal, structural, and quantum chemical parameters of (E)‐7‐(arylidene)‐1,2,6,7‐tetrahydro‐8H‐indeno[5,4‐b]furan‐8‐one derivatives: A comparative study

Adole¹,

Jagdale²,

Pawar³

et al. 2020

J Chinese Chemical Soc

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In the present research work, biologically important halogen-substituted (E)-7-(arylidene)-1,2,6,7-tetrahydro-8H-indeno[5,4-b]furan-8-one derivatives are studied from a structural investigation point of view. For a detailed molecular structure description, some quantum-chemical calculations were performed by using the density functional theory method with a basis set 6-311++G(d,p). The optimized molecular geometry, bond length, atomic charges, bond angle, and harmonic vibrational frequencies have been investigated. The quantum and structural entities such as total energy, electron density distribution in highest occupied molecular orbital and lowest unoccupied molecular orbital, charge distribution, electronegativity, absolute hardness (η), softness, electrophilicity, chemical potential, and charge transfer in molecules (ΔN max) have been computed using 6-311++G(d,p) basis set. Importantly, single-crystal analysis study for (E)-7-(2-chlorobenzylidene)-1,2,6,7-tetrahydro-8H-indeno[5,4-b] furan-8-one (CBIF) has been presented. The single-crystal examination reveals CBIF has triclinic crystal lattice with nonclassical intermolecular short contact interactions. The vibrational wavenumbers are calculated and the scaled values are compared with the experimental FT-IR spectrum. Furthermore, the molecular electrostatic potential (MEP) and some thermodynamic functions were also explored using computational work. The theoretical geometrical parameters have been compared with the experimental results obtained from the single-crystal examination.

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Cost-effective density functional theory (DFT) calculations of equilibrium isotopic fractionation in large organic molecules

Abstract: The application of stable isotopes to large molecules is hindered by experimental and computational costs. Here, we describe a cost-effective computational framework for predicting equilibrium isotope effects and the associated uncertainties.

Cited by 20 publications

References 150 publications

Theoretical estimates of equilibrium carbon and hydrogen isotope effects in microbial methane production and anaerobic oxidation of methane

Theoretical estimates of equilibrium carbon and hydrogen isotope effects in microbial methane production and anaerobic oxidation of methane

Isotopic evidence for quasi-equilibrium chemistry in thermally mature natural gases

Experimental and theoretical exploration on single crystal, structural, and quantum chemical parameters of (E)‐7‐(arylidene)‐1,2,6,7‐tetrahydro‐8H‐indeno[5,4‐b]furan‐8‐one derivatives: A comparative study

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