Mapping the Kinetic and Thermodynamic Landscape of Formaldehyde Oligomerization under Neutral Conditions

Kua, Jeremy; Avila, Joseph E.; Lee, Christopher G.; Smith, William D.

doi:10.1021/jp4098292

Cited by 34 publications

(95 citation statements)

References 51 publications

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“…The reasons for this, in conjunction with using half the gas phase entropy, are discussed further in Supplementary Information. On the other hand, our protocol performs well in calculating the relative free energies of stable species, typically within 0.5 kcal/mol of experimental results, [9][10]12 or an uncertainty of within a factor of 2.3 in terms of equilibrium constant ratios. …”

Section: Methodsmentioning

confidence: 84%

“…The activation barriers compared to experiment are reasonable but the agreement is not as close, and our protocol overestimates the barrier by 2-3 kcal/mol. [9][10] The barriers are calculated in reference to the separated reactants rather than a pre-associated complex. The reasons for this, in conjunction with using half the gas phase entropy, are discussed further in Supplementary Information.…”

Section: Methodsmentioning

confidence: 99%

“…We have developed a relatively fast protocol to map the thermodynamic and kinetic energy landscape for the preliminary steps of self-oligomerization of several water-soluble aldehydes in solution, namely formaldehyde, 9 3 glycolaldehye, 10 glyoxal, 11 and methylglyoxal. 12 Our protocol was put to the test with a detailed comparison of our computational results with NMR measurements for the self-oligomerization of a 1 M solution of glycolaldehyde.…”

Section: Introductionmentioning

confidence: 99%

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Free Energy Map for the Co-Oligomerization of Formaldehyde and Ammonia

et al. 2015

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Density functional theory calculations, including Poisson-Boltzmann implicit solvent and free energy corrections, are applied to construct a free energy map of formaldehyde and ammonia co-oligomerization in aqueous solution at pH 7. The stepwise route to forming hexamethylenetetramine (HMTA), the one clearly identified major product in a complex mixture, involves a series of addition reactions of formaldehyde and ammonia coupled with dehydration and cyclization reactions at key steps in the pathway. The free energy map also allows us to propose the possible identity of some major peaks observed by mass spectroscopy in the reaction mixture being the result of stable species not along the pathway to HMTA, in particular those formed by intramolecular condensation of hydroxyl groups to form six-membered rings with ether linkages. Our study complements a baseline free energy map previously worked out for the self-oligomerization of formaldehyde in solution at pH 7 using the same computational protocol and published in this journal (J. Phys. Chem. A 2013, 117, 12658).

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Section: Methodsmentioning

confidence: 84%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Free Energy Map for the Co-Oligomerization of Formaldehyde and Ammonia

et al. 2015

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“…Finally, to assess the extensiveness of our protocol we compared our reaction network with one obtained from a manual exploration. 103 Within the bounds preset for the present exploration, each intermediate and reaction path identified in a limited manual exploration by Kua et al 103 can be found in our reaction network. Figure 6: Reaction network generated from formaldehyde, glycolaldehyde, and water (the last not shown explicitly) consisting of reactions with activation barriers below 85 kJ/mol.…”

Section: Reaction Networkmentioning

confidence: 95%

Context-Driven Exploration of Complex Chemical Reaction Networks

Hernández-Lobato

Reiher

2017

J. Chem. Theory Comput.

112

146

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The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many reactants or highly reactive species), the size of such a network may grow rapidly. Here, we present a computational protocol that constructs such reaction networks in a fully automated fashion steered in an intuitive, graph-based fashion through a single graphical user interface. Starting from a set of initial reagents new intermediates are explored through intra- and intermolecular reactions of already explored intermediates or new reactants presented to the network. This is done by assembling reactive complexes based on heuristic rules derived from conceptual electronic-structure theory and exploring the corresponding approximate reaction path. A subsequent path refinement leads to a minimum-energy path which connects the new intermediate to the existing ones to form a connected reaction network. Tree traversal algorithms are then employed to detect reaction channels and catalytic cycles. We apply our protocol to the formose reaction to study different pathways of sugar formation and to rationalize its autocatalytic nature.

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“…4. It represents a possible mechanism for the rst steps of the formose reaction as described by Kua et al 37 and comprises six chemical species and ve reaction pairs (ten elementary reactions Ri). We obtained all free energies in single-point calculations as described in the ESI.…”

Section: Kinetic Simulation Algorithmmentioning

confidence: 99%

Uncertainty quantification for quantum chemical models of complex reaction networks

et al. 2016

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For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided. On the other hand, a highly resolved time evolution may not be necessary to still determine quantitative fluxes in a reaction network if one is interested in specific time scales. In this paper, we present discrete-time kinetic simulations in discrete state space taking free energy uncertainties into account. The method builds upon thermo-chemical data obtained from electronic structure calculations in a condensed-phase model. Our kinetic approach supports the analysis of general reaction networks spanning multiple time scales, which is here demonstrated for the example of the formose reaction. An important application of our approach is the detection of regions in a reaction network which require further investigation, given the uncertainties introduced by both approximate electronic structure methods and kinetic models. Such cases can then be studied in greater detail with more sophisticated first-principles calculations and kinetic simulations.

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Mapping the Kinetic and Thermodynamic Landscape of Formaldehyde Oligomerization under Neutral Conditions

Cited by 34 publications

References 51 publications

Free Energy Map for the Co-Oligomerization of Formaldehyde and Ammonia

Free Energy Map for the Co-Oligomerization of Formaldehyde and Ammonia

Context-Driven Exploration of Complex Chemical Reaction Networks

Uncertainty quantification for quantum chemical models of complex reaction networks

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