Formation of benzene in the interstellar medium Jones, Brant M.; Zhang, Fangtong; Kaiser, Ralf I. ...
Proceedings of the National Academy of Sciences - PNAS,
01/2011, Letnik:
108, Številka:
2
Journal Article
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Polycyclic aromatic hydrocarbons and related species have been suggested to play a key role in the astrochemical evolution of the interstellar medium, but the formation mechanism of even their ...simplest building block—the aromatic benzene molecule—has remained elusive for decades. Here we demonstrate in crossed molecular beam experiments combined with electronic structure and statistical calculations that benzene (C₆H₆) can be synthesized via the barrierless, exoergic reaction of the ethynyl radical and 1,3-butadiene, C₂H + H₂CCHCHCH₂ → C₆H₆ + H, under single collision conditions. This reaction portrays the simplest representative of a reaction class in which aromatic molecules with a benzene core can be formed from acyclic precursors via barrierless reactions of ethynyl radicals with substituted 1,3-butadiene molecules. Unique gas-grain astrochemical models imply that this low-temperature route controls the synthesis of the very first aromatic ring from acyclic precursors in cold molecular clouds, such as in the Taurus Molecular Cloud. Rapid, subsequent barrierless reactions of benzene with ethynyl radicals can lead to naphthalene-like structures thus effectively propagating the ethynyl-radical mediated formation of aromatic molecules in the interstellar medium.
Rhodopsins are seven α-helical membrane proteins that are of great importance in chemistry, biology, and modern biotechnology. Any in silico study on rhodopsin properties and functioning requires a ...high-quality three-dimensional structure. Due to particular difficulties with obtaining membrane protein structures from the experiment, in silico prediction of the three-dimensional rhodopsin structure based only on its primary sequence is an especially important task. For the last few years, significant progress was made in the field of protein structure prediction, especially for methods based on comparative modeling. However, the majority of this progress was made for soluble proteins and further investigations are needed to achieve similar progress for membrane proteins. In this paper, we evaluate the performance of modern protein structure prediction methodologies (implemented in the Medeller, I-TASSER, and Rosetta packages) for their ability to predict rhodopsin structures. Three widely used methodologies were considered: two general methodologies that are commonly applied to soluble proteins and a methodology that uses constraints that are specific for membrane proteins. The test pool consisted of 36 target-template pairs with different sequence similarities that was constructed on the basis of 24 experimental rhodopsin structures taken from the RCSB database. As a result, we showed that all three considered methodologies allow obtaining rhodopsin structures with the quality that is close to the crystallographic one (root mean square deviation (RMSD) of the predicted structure from the corresponding X-ray structure up to 1.5 Å) if the target-template sequence identity is higher than 40%. Moreover, all considered methodologies provided structures of average quality (RMSD < 4.0 Å) if the target-template sequence identity is higher than 20%. Such structures can be subsequently used for further investigation of molecular mechanisms of protein functioning and for the development of modern protein-based biotechnologies.
Ketohydroperoxides are important in liquid-phase autoxidation and in gas-phase partial oxidation and pre-ignition chemistry, but because of their low concentration, instability, and various ...analytical chemistry limitations, it has been challenging to experimentally determine their reactivity, and only a few pathways are known. In the present work, 75 elementary-step unimolecular reactions of the simplest γ-ketohydroperoxide, 3-hydroperoxypropanal, were discovered by a combination of density functional theory with several automated transition-state search algorithms: the Berny algorithm coupled with the freezing string method, single- and double-ended growing string methods, the heuristic KinBot algorithm, and the single-component artificial force induced reaction method (SC-AFIR). The present joint approach significantly outperforms previous manual and automated transition-state searches – 68 of the reactions of γ-ketohydroperoxide discovered here were previously unknown and completely unexpected. All of the methods found the lowest-energy transition state, which corresponds to the first step of the Korcek mechanism, but each algorithm except for SC-AFIR detected several reactions not found by any of the other methods. We show that the low-barrier chemical reactions involve promising new chemistry that may be relevant in atmospheric and combustion systems. Our study highlights the complexity of chemical space exploration and the advantage of combined application of several approaches. Overall, the present work demonstrates both the power and the weaknesses of existing fully automated approaches for reaction discovery which suggest possible directions for further method development and assessment in order to enable reliable discovery of all important reactions of any specified reactant(s).
This paper investigates the origins of common-mode voltage (CMV) noises in SiC MOSFET-based three-level T-type inverters (3LT 2 I), targeting adjustable speed drive (ASD) systems, and proposes ...methods for their mitigation. Although achieving zero common-mode voltage (ZCMV) is theoretically unattainable in a two-level voltage source inverter (2L-VSI), it can be realized in a 3LT 2 I by selecting specific switching states. However, the necessary simultaneous switching of two half-bridges in ZCMV methods generates significant CMV noises, which are due to the dead-time and differences in output voltage transition times. This work proposes a method to mitigate these CMV noises through precisely adjusting the timing of the transitions in the gate drive signals. This method can reduce electromagnetic interference (EMI) associated with CMV and minimize passive filter size. Lastly, the paper answers the critical question: Is full CMV suppression practically possible?
Detailed kinetic models (DKMs) are the most fundamental “bottom-up” approaches to computational investigation of the pyrolysis and oxidation of fuels. The weakest points of existing DKMs are ...incomplete information about the reaction types that can be involved in the potential energy surfaces (PESs) in pyrolysis and oxidation processes. Also, the computational thermodynamic parameters available in the literature vary widely with the level of theory employed. More sophisticated models require improvement both in our knowledge of the type of the reactions involved and the consistency of thermodynamic and kinetic parameters. In this paper, we aim to address these issues by developing ab initio models that can be used to describe early stages of pyrolysis of C 1 –C 3 hydrocarbons. We applied a recently developed global reaction route mapping (GRRM) strategy to systematically investigate the PES of the pyrolysis of C 1 –C 3 hydrocarbons at a consistent level of theory. The reactions are classified into 14 reaction types. The critical points on the PES for all reactions in the network are calculated at the highly accurate UCCSD(T)-F12b/cc-pVTZ//UM06-2X/cc-pVTZ level of theory. The data reported in this paper can be used for first principle calculations of kinetic constants and for a subsequent study on modeling the evolution of the species from the reaction network of the pyrolysis and oxidation of C 1 –C 3 hydrocarbons.
The OH initiated oxidation of nitric oxide (NO) is an important atmospheric reaction being, during the day time, the main channel that leads to the formation of HONO a reservoir species for both OH ...and odd nitrogen. This work reports ab initio study of the Potential Energy Surface (PES) of NO + OH using density functional theory calculations conducted at the B3LYP level of theory with a 6-311g (d,p) basis set. We confirmed experimental observations pointing out that the main channel for this reaction is the formation the HONO. From the addition of OH to NO both cis and trans isomers of HONO were found to be the formed as stable intermediate, both having a negative enthalpy of formation relative to the reactants, the cis isomer being more stable than the trans one. The ab initio calculations were extended to include the hydrogen extraction mechanism with its respective transition state to investigate the potential existence of a reaction channel leading to the formation of NO.sub.2 + H, that was found not to be of significant interest. Keywords: ab initio calculations; HONO; nitric oxide; hydroxyl radical
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► Ab initio/RRKM calculations reveal the mechanism of the C2H+1,2-butadiene reaction. ► Reaction is predicted to be barrierless and to form C6H6+H and C5H4+CH3 products. ► ...2-Ethynyl-1,3-butadiene+H are calculated as the dominant products (91–84%). ► Penta-1,4-diyne+CH3 (7–12%) and ethynylallene+CH3 (2–3%) are minor products.
Ab initio/RRKM calculations have been performed to investigate the mechanism of the C2H+1,2-butadiene reaction and to compute its product branching ratios under single-collision conditions. The reaction starts with barrierless C2H addition to various sites of H2CCCHCH3 producing different exothermic initial adducts. The chemically activated C6H7 adducts can then isomerize and decompose by splitting H or CH3. With the assumption of equal formation probabilities of all initial adducts, C6H6 (2-ethynyl-1,3-butadiene)+H are predicted as the dominant products (91–84% at collision energies of 0–7kcal/mol), whereas C5H4 (penta-1,4-diyne)+CH3 (7–12%) and ethynylallene+CH3 (2–3%) are minor products.
Crossed molecular beam experiments and electronic structure calculations on the reaction of the meta-tolyl radical with vinylacetylene were conducted to probe the formation of methyl-substituted ...naphthalene isomers. We present the compelling evidence that under single collision conditions 1- and 2-methylnaphthalene can be formed without an entrance barrier via indirect scattering dynamics through a bimolecular collision of two non-PAH reactants: the meta-tolyl radical and vinylacetylene. The electronic structure calculations, conducted at the UCCSD(T)-F12b/cc-pVDZ//UM06-2x/cc-pVTZ + ZPE(UM06-2x/cc-pVTZ) level of theory, reveal that this reaction is initiated by the barrierless addition of the meta-tolyl radical to the terminal vinyl carbon (C1) of vinylacetylene, via a van-der-Waals complex implying that this mechanism can play a key role in forming methyl-substituted PAHs in low temperature extreme environments such as the low temperature interstellar medium and hydrocarbon-rich atmospheres of planets and their moons in the outer solar system. The reaction mechanism, proposed from the C11H11 potential energy surface, involves a sequence of isomerizations involving hydrogen transfer and ring closure, followed by hydrogen dissociation, which eventually leads to 1- and 2-methylnaphthalene in an overall exoergic process.
Ketohydroperoxides are important in liquid-phase autoxidation and in gas-phase partial oxidation and pre-ignition chemistry, but because of their low concentration, instability, and various ...analytical chemistry limitations, it has been challenging to experimentally determine their reactivity, and only a few pathways are known. In the present work, 75 elementary-step unimolecular reactions of the simplest γ-ketohydroperoxide, 3-hydroperoxypropanal, were discovered by a combination of density functional theory with several automated transition-state search algorithms: the Berny algorithm coupled with the freezing string method, single- and double-ended growing string methods, the heuristic KinBot algorithm, and the single-component artificial force induced reaction method (SC-AFIR). The present joint approach significantly outperforms previous manual and automated transition-state searches – 68 of the reactions of γ-ketohydroperoxide discovered here were previously unknown and completely unexpected. All of the methods found the lowest-energy transition state, which corresponds to the first step of the Korcek mechanism, but each algorithm except for SC-AFIR detected several reactions not found by any of the other methods. We show that the low-barrier chemical reactions involve promising new chemistry that may be relevant in atmospheric and combustion systems. Our study highlights the complexity of chemical space exploration and the advantage of combined application of several approaches. Altogether, the present work demonstrates both the power and the weaknesses of existing fully automated approaches for reaction discovery which suggest possible directions for further method development and assessment in order to enable reliable discovery of all important reactions of any specified reactant(s).
ABSTRACT
Automatic kinetic mechanism generation, virtual high‐throughput screening, and automatic transition state search are currently trending applications requiring exploration of a large molecule ...space. Large‐scale search requires fast and accurate estimation of molecules' properties of interest, such as thermochemistry. Existing approaches are not satisfactory for large polycyclic molecules: considering the number of molecules being screened, quantum chemistry (even cheap density functional theory methods) can be computationally expensive, and group additivity, though fast, is not sufficiently accurate. This paper provides a fast and moderately accurate alternative by proposing a polycyclic thermochemistry estimation method that extends the group additivity method with two additional algorithms: similarity match and bicyclic decomposition. It significantly reduces Hf(298 K) estimation error from over 60 kcal/mol (group additivity method) to around 5 kcal/mol, Cp(298 K) error from 9 to 1 cal/mol/K, and S(298 K) error from 70 to 7 cal/mol/K. This method also works well for heteroatomic polycyclics. A web application for estimating thermochemistry by this method is made available at http://rmg.mit.edu/molecule_search.
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