Extension of the composite CBS-QB3 method to singlet diradical calculations

Improved Computational Modeling of the Kinetics of the Acetylperoxy + HO2 Reaction

The acetylperoxy + HO2 reaction has multiple impacts on the troposphere, with a triplet pathway leading to peracetic acid + O2 (reaction 1a) competing with singlet pathways leading to acetic...

Theoretical study of the pyrolysis of β-1,4-xylan: a detailed investigation on unimolecular concerted reactions

A theoretical study of the thermal decomposition of β-1,4-xylan, a model polymer of hemicelluloses, is proposed for the first time. A mechanism based on unimolecular concerted reactions is elaborated in a comprehensive way. Elementary reactions, such as dehydrations, retro-aldol, retro Diels-Alder, retro-ene, glycosidic bond fissions, isomerizations, etc., are applied to β-1,4-xylan, as well as to the fragments formed. At each stage of the construction of the mechanism, the fragments previously retained are decomposed and the low energy paths are selected to define new fragments. Energy barriers are computed at the CBS-QB3 level of theory and rate coefficients of important reactions are calculated. It is shown that the main reaction pathways can be modelled by reactions involving two specific fragments, which react in closed sequences, similarly to chain-propagating reactions. The proposed reaction scheme allows to predict important species observed during the pyrolysis of xylan, such as aldehydes or CO. In addition, we show that dehydrations require high activation energy and cannot compete with the other reactions. Therefore, it seems difficult to explain, by means of unimolecular homogeneous gas phase reactions, the significant formation of specific species such as furfural as reported by several authors.

Reducing Properties of Superalkalis on Pyridinic Graphene Surfaces: a Computational Study

The hyperlithiated species Li k + 1 F k (k=1, 2, 3, and 4) have been studied by quantum mechanical (QM) methods. Different structures have been localized for each molecule by the CBS-QB3 composite method: all the isomers show superalkali properties and strong tendency to donate an electron to carbon dioxide forming stable Li k + 1 F k · · · CO 2 complexes. With the aim to find molecular systems able to stabilize superalkalis, geometries of complexes between superalkalis and pyridine and superalkalis and graphene surfaces doped with a pyridinic vacancy were calculated. The pyridinic graphene sheets were modeled with two finite molecular systems C₆₉ H₂₁ N₃ and C₁₁₇ H₂₇ N₃ . The interaction with one pyridine molecule is quite weak and the superalkali maintains its structure and electron properties. The affinity for graphene sheets is instead stronger and the superalkalis tend to deform their geometry to better interact with the graphene surface. However, the superalkalis continue to show the tendency to transfer electrons to carbon dioxide reducing CO₂ , as found in graphene absence.

Accurate Base Pair Energies of Artificially Expanded Genetic Information Systems (AEGIS): Clues for Their Mutagenic Characteristics

Recently, several artificial nucleobases, such as B, S, J, V, X, K, P, and Z, have been proposed to help in the expansion of the genetic information system and diagnosis of diseases. Among these bases, P and Z were identified to form stable DNA and to participate in the replication. However, the stabilities of P:Z and other artificial base pairs are not fully understood. The abilities of these unnatural nucleobases in mispairing with themselves and with natural bases are also not known. Here, the ωB97X-D dispersion-corrected density functional theoretical and complete basis set (CBS-QB3) methods are used to obtain accurate structural and energetic data related to base pair interactions involving these unnatural nucleobases. The roles of protonation and deprotonation of certain artificial bases in inducing mutations are also studied. It is found that each artificial purine has a complementary artificial pyrimidine, the base pair interactions between which are similar to those of the natural Watson-Crick base pairs. Hence, these base pairs will function naturally and would not impart mutagenicity. Among these base pairs, the J:V complex is found to be the most stable and promising artificial base pair. Remarkably, the noncomplementary artificial nucleobases are found to form stable mispairs, which may generate mutagenic products in DNA. Similarly, the misinsertions of natural bases opposite artificial bases are also found to be mutagenic. The mechanisms of these mutations are explained in detail. These results are in agreement with earlier biochemical studies. It is thus expected that this study would aid in the advancement of the synthetic biology to design more robust artificial nucleotides.

Reduction of carbon dioxide with a superalkali

The ability of the superalkali Li₃F₂ to reduce CO₂ and N₂ is investigated using the CBS-QB3 composite method and intriguing results are presented.

Study of tert-Amyl Methyl Ether Low Temperature Oxidation Using Synchrotron Photoionization Mass Spectrometry

This paper examines the oxidation reaction of tert-amyl methyl ether (TAME), an oxygenated fuel additive, with chlorine radical initiators in the presence of oxygen. Data are collected at 298, 550, and 700 K. Reaction intermediates and products are probed by a multiplexed chemical kinetics synchrotron photoionization mass spectrometer (SPIMS) and characterized on the basis of the mass-to-charge ratio, ionization energy, and photoionization spectra. Branching fractions of primary products are obtained at the different reaction temperatures. CBS-QB3 computations are also carried out to study the potential energy surface of the investigated reactions to validate detected primary products.

Improvement of the modeling of the low-temperature oxidation of n-butane: study of the primary reactions

This paper revisits the primary reactions involved in the oxidation of n-butane from low to intermediate temperatures (550-800 K) including the negative temperature coefficient (NTC) zone. A model that was automatically generated is used as a starting point and a large number of thermochemical and kinetic data are then re-estimated. The kinetic data of the isomerization of alkylperoxy radicals giving (•)QOOH radicals and the subsequent decomposition to give cyclic ethers has been calculated at the CBS-QB3 level of theory. The newly obtained model allows a satisfactory prediction of experimental data recently obtained in a jet-stirred reactor and in rapid compression machines. A considerable improvement of the prediction of the selectivity of cyclic ethers is especially obtained compared to previous models. Linear and global sensitivity analyses have been performed to better understand which reactions are of influence in the NTC zone.

Peculiarities of β-pinene autoxidation

The thermal oxidation of the renewable olefin β-pinene with molecular oxygen was experimentally and computationally investigated. Peroxyl radicals abstract weakly bonded allylic hydrogen atoms from the substrate, yielding allylic hydroperoxides (i.e., myrtenyl and pinocarvyl hydroperoxide). In addition, peroxyl radicals add to the C=C bond of the substrate to form an epoxide. It was found that a relatively high peroxyl radical concentration, together with the high rate of peroxyl cross-reactions, make radical-radical reactions surprisingly important for this particular substrate. Approximately 60 % of these peroxyl cross-reactions lead to termination (radical destruction), keeping a radical chain length of approximately 4 at 10 % conversion. Numerical simulation of the reaction-based on the proposed reaction mechanism and known or predicted rate constants-demonstrate the importance of peroxyl cross-reactions for the formation of alkoxyl radicals, which are the precursor of alcohol and ketone products.

Towards cleaner combustion engines through groundbreaking detailed chemical kinetic models

In the context of limiting the environmental impact of transportation, this critical review discusses new directions which are being followed in the development of more predictive and more accurate detailed chemical kinetic models for the combustion of fuels. In the first part, the performance of current models, especially in terms of the prediction of pollutant formation, is evaluated. In the next parts, recent methods and ways to improve these models are described. An emphasis is given on the development of detailed models based on elementary reactions, on the production of the related thermochemical and kinetic parameters, and on the experimental techniques available to produce the data necessary to evaluate model predictions under well defined conditions (212 references).

Comparative computational analysis of active and inactive cofactors of nitric oxide synthase

Nitric oxide synthases (NOSs) are heme proteins that catalyze the formation of nitric oxide from L-Arg in the presence of oxygen. Of the two electrons required for the first step of the reaction, the second is primarily donated by the tetrahydrobiopterin (H4B) cofactor bound adjacent to the heme, which is eventually reduced back to resting state by the ultimate electron source of the reaction, the flavins of the NOS reductase domain. Density functional theory calculations were carried out to identify those protonation states of different cofactor molecules that best support radicalization of the cofactor and the coupled increase in the electron density of the heme-bound oxygen molecule. Three cofactor molecules were studied, native H4B, an active analogue, 5-methyl-H4B, and the inactive 4-amino-H4B. Findings support the emerging model where H4B and 5-methyl-H4B are coupled proton/electron sources of NOS catalysis, while 4-amino-H4B is an inhibitor due to its inability to donate the catalytically required proton.