An automatized workflow from molecular dynamic simulation to quantum chemical methods to identify elementary reactions and compute reaction constants

Schmitz, Gunnar; Yönder, Özlem; Schnieder, Bastian; Schmid, Rochus; Hättig, Christof

doi:10.1002/jcc.26757

Cited by 8 publications

(8 citation statements)

References 64 publications

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“…There are three variants of GFNn-xTB that are developed ( n = 0, 1, and 2), which differ in accuracy and efficiency. They have been successfully applied in the optimization of organometallic complexes, structure sampling, exploring the reaction profiles, and macromolecule structure optimization. − In addition, the electronic effects are still included at the semiempirical level of theory, which are challenging systems for the DFT method . The empirical FF parameters for the GFN2-xTB method are fitted to reproduce the results of DFT (B97-3c) .…”

Section: Experimental Sectionmentioning

confidence: 99%

N-Vinyl Caprolactam/Maleic-Based Copolymers as Kinetic Hydrate Inhibitors: The Effect of Internal Hydrogen Bonding

et al. 2022

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Kinetic hydrate inhibitors (KHIs) have been used for over 25 years to prevent gas hydrate formation in oil and gas production flow lines, but they are some of the most expensive oilfield production chemicals. The main component in KHI formulations is a water-soluble polymer with many amphiphilic groups. Usually, in commercial KHI polymers, the hydrophilic part of these groups is the amide group. In addition, KHI polymers are often incompatible with film-forming corrosion inhibitors. Therefore, we sought to find cheaper but effective KHIs that could also act as a flow line corrosion inhibitor. Continuing earlier work from our group with maleic-based polymers, we have now explored maleic acid/N-vinyl caprolactam (MAcid/VCap) copolymers to introduce VCap, a well-known KHI monomer, together with the cheaper MA monomer. KHI performance screening tests were conducted under high pressure with a structure II-forming natural gas mixture in steel rocking cells using the slow (1 °C/h) constant-cooling test method. Surprisingly, the MAcid/VCap copolymer showed very poor KHI efficacy. GFN2-xTB molecular dynamics simulations revealed that MAcid/VCap exhibits intra-hydrogen bond networks that trap the polymer morphology in the globular form. In this scenario, the caprolactam ring is encapsulated inside the polymer structure due to the intra-hydrogen bonds and the hydrophobic interactions that minimize its ability to interact with the hydrate surfaces, which significantly reduces the MAcid/VCap kinetic inhibition performance. However, the polymer in such globular forms still displays an important amount of its carboxylic groups exposed to water, which explains the water solubility. In contrast to MAcid/VCap copolymers, maleimide derivatives with dibutylamino end groups were effective KHIs and even better with dibutylamine oxide end groups. A terpolymer of MA/VCap reacted with N,N-dibutylaminopropylamine followed by subsequent oxidation of the end groups to dibutylamine oxide and gave the best performance of any maleic-based polymer reported to date. The combination of caprolactam and dibutylamine oxide groups can be thought of as synergism within the same polymer, akin to the excellent synergy of the separate molecules, tributylamine oxide and PVCap.

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Section: Experimental Sectionmentioning

confidence: 99%

N-Vinyl Caprolactam/Maleic-Based Copolymers as Kinetic Hydrate Inhibitors: The Effect of Internal Hydrogen Bonding

et al. 2022

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“…Found elementary steps are then assigned to reactions (either they define a new reaction or they are another path for a known reaction to occur). Many single-ended and multiended time-independent search algorithms as well as molecular dynamics based approaches have been described in the literature that can be used for this purpose − ,− ,− and our implementation is general enough to accommodate many of them (up to the point where they could be directly compared within one software framework).…”

Section: Algorithm Development For Finding New Reactionsmentioning

confidence: 99%

“…This lack of detail is rooted in limited experimental information available on a specific process and in limited quantum chemical data that is difficult to gather by manual exploration. To alleviate this problem, automated mechanism-exploration procedures have been developed in the past decade. − Accompanying these algorithmic developments, various types of exploration software have been described; examples are NetGen , GRMM , ZStruct , Chemoton , RMG , , AARON , KinBot , ChemTrayZer , Nanoreactor , autodE , YARP , AutoMeKin2021 , and many more. − …”

Section: Introductionmentioning

confidence: 99%

Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks

Unsleber

Grimmel

Reiher

2022

J. Chem. Theory Comput.

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Fueled by advances in hardware and algorithm design, large-scale automated explorations of chemical reaction space have become possible. Here, we present our approach to an open-source, extensible framework for explorations of chemical reaction mechanisms based on the first-principles of quantum mechanics. It is intended to facilitate reaction network explorations for diverse chemical problems with a wide range of goals such as mechanism elucidation, reaction path optimization, retrosynthetic path validation, reagent design, and microkinetic modeling. The stringent first-principles basis of all algorithms in our framework is key for the general applicability that avoids any restrictions to specific chemical systems. Such an agile framework requires multiple specialized software components of which we present three modules in this work. The key module, Chemoton, drives the exploration of reaction networks. For the exploration itself, we introduce two new algorithms for elementary-step searches that are based on Newton trajectories. The performance of these algorithms is assessed for a variety of reactions characterized by a broad chemical diversity in terms of bonding patterns and chemical elements. Chemoton successfully recovers the vast majority of these. We provide the resulting data, including large numbers of reactions that were not included in our reference set, to be used as a starting point for further explorations and for future reference.

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“…In the original implementation, the smallest allowed multiplicities were always assigned, despite being well aware that such a procedure does not always yield ground-state configurations, [30] e. g. for triplet oxygen vs. singlet oxygen. As a solution for this issue, we decided to follow the example of Schmitz et al [85] and probe multiple multiplicities for reactants, products and TSs. This is the second conceptual change compared to the original implementation of the coupling scheme.…”

Section: Conceptual Updates To the Chemtrayzer Rmd-qm Coupling Schemementioning

confidence: 99%

“…This is the second conceptual change compared to the original implementation of the coupling scheme. Similar to Schmitz et al, [85] our implementation only accepts combinations of multiplicities for reactants, TSs, and products that result in a spin-conserving reaction. However, while Schmitz et al only accept reactions that connect ground-state reactants and products, we also accept reactions connecting reactants and products with higher electronic energy states.…”

Section: Conceptual Updates To the Chemtrayzer Rmd-qm Coupling Schemementioning

confidence: 99%

A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part II: A ChemTraYzer Study of Chlorinated Dibenzofuran Formation and Decomposition Processes

et al. 2023

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In our two-paper series, we first present the development of ReaxFF CHOCl parameters using the recently published ParAMS parametrization tool. In this second part, we update the reactive Molecular Dynamics -Quantum Mechanics coupling scheme ChemTraYzer and combine it with our new ReaxFF parameters from Part I to study formation and decomposition processes of chlorinated dibenzofurans. We introduce a self-learning method for recovering failed transition-state searches that improves the overall ChemTraYzer transition-state search success rate by 10 percentage points to a total of 48 %. With ChemTraYzer, we automatically find and quantify more than 500 reactions using transition state theory and DFT. Among the discovered chlorinated dibenzofuran reactions are numerous reactions that are new to the literature. In three case studies, we discuss the set of reactions that are most relevant to the dibenzofuran literature: (i) bimolecular reactions of the chlorinated-dibenzofuran precursors phenoxy radical and 1,3,5-trichlorobenzene, (ii) dibenzofuran chlorination and pyrolysis, and (iii) oxidation of chlorinated dibenzofurans.

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An automatized workflow from molecular dynamic simulation to quantum chemical methods to identify elementary reactions and compute reaction constants

Cited by 8 publications

References 64 publications

N-Vinyl Caprolactam/Maleic-Based Copolymers as Kinetic Hydrate Inhibitors: The Effect of Internal Hydrogen Bonding

N-Vinyl Caprolactam/Maleic-Based Copolymers as Kinetic Hydrate Inhibitors: The Effect of Internal Hydrogen Bonding

Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks

A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part II: A ChemTraYzer Study of Chlorinated Dibenzofuran Formation and Decomposition Processes

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