Global reaction route mapping of isomerization pathways of exotic C6H molecular species

High performance global exploration of isomers and isomerization channels on quantum chemical potential energy surface of H5 C2 NO2

High performance global exploration of isomers and isomerization channels on the quantum chemical potential energy surface (PES) is performed for H₅ C₂ NO₂ by using the scaled hypersphere search-anharmonic downward distortion following (SHS-ADDF) method. A multi-node operation, NeoGRRM, has achieved high performance exploration calculations for the large system by submitting SHS-ADDF sub-jobs into many cores in parallel and unifying the results of sub-jobs into the total lists of the main-job. Global exploration of equilibrium (EQ) and transition-state structures at the level of B3LYP/6-31G(d) gave 3210 EQs and 23278 TSs. Nine compounds were found in the low energy regions of 0-100 kJ/mol; the lowest energy compound is N-methylcarbamic acid, the second is methyl carbamate, and the third is glycine (the most fundamental amino acid). Interconversion pathways between the conformers of each of the low energy compounds were surveyed. Isomerization channels around glycine were explored in detail. The lowest energy barriers around some of the EQs turned to be negative after zero-point energy corrections. This indicates that those structures cannot exist as independent structures because they spontaneously collapse into more stable structures. The global PES search showed various interesting dissociating channels which indicate synthon reaction pathways in the reverse directions.

Mono-silicon isoelectronic replacement in CAl4 : van't hoff/le bel carbon or not?

In cluster studies, the isoelectronic replacement strategy has been successfully used to introduce new elements into a known structure while maintaining the desired topology. The well-known penta-atomic 18 valence electron (ve) species C Al 4 2 - and its Al^- /Si or Al/Si⁺ isoelectronically replaced clusters CAl₃ Si^- , CAl₂ Si₂ , C AlSi 3 - , and C Si 4 2 + , all possess the same anti-van't Hoff/Le Bel skeletons, that is, nontraditional planar tetracoordinate carbon (ptC) structure. In this article, however, we found that such isoelectronic replacement between Si and Al does not work for the 16ve-CAl₄ with the traditional van't Hoff/Le Bel tetrahedral carbon (thC) and its isoelectronic derivatives CAl₃ X (X = Ga/In/Tl). At the level of CCSD(T)/def2-QZVP//B3LYP/def2-QZVP, none of the global minima of the 16ve mono-Si-containing clusters CAl₂ SiX⁺ (X = Al/Ga/In/Tl) maintains thC as the parent CAl₄ does. Instead, X = Al/Ga globally favors an unusual ptC structure that has one long C─X distance yet with significant bond index value, and X = In/Tl prefers the planar tricoordinate carbon. The frustrated formation of thC in these clusters is ascribed to the CSi bonding that prefers a planar fashion. Inclusion of chloride ion would further stabilize the ptC of CAl₂ SiAl⁺ and CAl₂ SiGa⁺ . The unexpectedly disclosed CAl₂ SiAl⁺ and CAl₂ SiGa⁺ represent the first type of 16ve-cationic ptCs with multiple bonds. © 2019 Wiley Periodicals, Inc.

Chemical pathways for poly-anionic isomerisation in the metastable anions of tetra-deprotonated naphthalene: an intra-molecular inter-ring proton-transfer

An intra-molecular proton-transfer between the two different aromatic rings of naphthalene in the metastable isomeric tetra-anionic species of naphthalene is revealed by this computational work.

Study of Potential Energy Surfaces towards Global Reaction Route Mapping

The potential energy surface (PES) is just a theoretical construct based on the Born-Oppenheimer approximation, but it underlies various phenomena, including molecular vibrations, collisional ionizations, and chemical reactions. This account describes how a new idea for global reaction route mapping (GRRM), which had seemed to be impossible for chemical systems with more than three atoms, was born and has been developed during the course of the study of the PES. GRRM has pioneered new fields of chemistry. Furthermore, techniques for GRRM are still developing, and GRRM is further extending its application to various areas of chemistry and chemical physics.

Exploring the role of a single water molecule in the tropospheric reaction of glycolaldehyde with an OH radical: a mechanistic and kinetics study

This work reveals that though a single-water molecule decelerates the atmospheric reaction between the glycolaldehyde and OH radical, however, it facilitates the cis–​trans interconversion along the hydrogen-abstraction pathways.

Exploring the mechanism of isomerisation and water-migration in the water-complexes of amino-acid l-proline: electrostatic potential and vibrational analysis

This work reveals interesting pathways for water-migration and neutral ↔ zwitterionic isomerisation in the water complexes of l-proline.

Reaction sampling and reactivity prediction using the stochastic surface walking method

The new theoretical method demonstrates the ability of automated reaction sampling and activity prediction for complex organic reactions.

Water-catalysis in the gas phase reaction of dithioformic acid with hydroxyl radical: global reaction route mapping of oxidative pathways for hydrogen abstraction

Through the advanced quantum mechanical computations, this work investigates the catalytic-role of single water-molecule during hydrogen abstraction, in dithioformic acid, by the OH radical.

The mechanism of tautomerisation and geometric isomerisation in thioformic acid and its water complexes: exploring chemical pathways for water migration

A systematic and automated search for chemical pathways of isomerisation between geometric and tautomeric forms of gas-phase thioformic acid (TFA) and its water complexes is performed using a global reaction route mapping (GRRM) method, and an uncovered pathway for cis-trans isomerisation in the thiol form of TFA has been explored through computations performed at CCSD(T)/6-311++G(2d,2p)//B3LYP/6-311++G(2d,2p) level of the coupled cluster and density functional theories. To explore the routes for water migration, a detailed analysis of complexes of TFA with a single-water molecule is presented. Notably, during the isomerisation process in TFA, a positive catalytic effect of water was observed that can arise either by the stabilization of the reactant and/or of the transition state through extensive hydrogen bonding. Interesting behavior of isomeric forms of TFA along the pathways analysed is revealed through the Gibbs free-energy change and its temperature-dependence. The cis form of TFA(thiol) in the complexes of TFA with a single-water molecule is found to be thermodynamically equally feasible as the trans form which though is known to be the most dominating among the isomeric forms of TFA. Besides these, various complexes of TFA with two-water molecules have also been explored to study the hydrogen-bonding interaction through natural bond-orbital (NBO) analysis. The complexes of TFA with two-water molecules have also been characterized using spectral features including vibrational frequency analysis, and the effect of complexation has been observed by noting frequency shift.

Exploring water catalysis in the reaction of thioformic acid with hydroxyl radical: a global reaction route mapping perspective

Hydrogen abstraction pathways, in the gas-phase reaction of tautomers of thioformic acid (TFA), TFA(thiol), and TFA(thione), with hydroxyl radical in the presence and absence of single water molecule acting as a catalyst, is investigated with high-level quantum mechanical calculations at CCSD(T)/6-311++G(2d,2p)//MP2/6-311++G(2d,2p), CCSD(T)/6-311++G(d,p)//DFT/BHandHLYP/6-311++G(d,p), and DFT/B3LYP/6-311++G(2df,2p) levels of the theory. A systematic and automated search of the potential energy surface (PES) for the reaction pathways is performed using the global reaction route mapping (GRRM) method that employs an uphill walking technique to search prereaction complexes and transition states. The computations reveal significant lowering of the PES and substantial reduction in the activation energy for the hydrogen abstraction pathway in the presence of water, thereby proving water as an efficient catalyst in the reaction of both the TFA tautomers with OH radical. The hydrogen-bonding interactions are observed to be responsible for the large catalytic effect of water. Notably, in the case of TFA(thiol), formyl hydrogen abstraction is observed to be kinetically more favorable, while acidic hydrogen abstraction is observed to be thermodynamically more feasible. Interestingly, in the case of TFA(thione), reaction pathways involving only formyl hydrogen abstraction were observed to be feasible. The water-catalyzed hydrogen abstraction reaction of TFA with hydroxyl radical, investigated in this work, can provide significant insights into the corresponding reaction in the biological systems.