Mechanisms for the inversion of chirality: global reaction route mapping of stereochemical pathways in a probable chiral extraterrestrial molecule, 2-aminopropionitrile

Chiral Linked Systems as a Model for Understanding D-Amino Acids Influence on the Structure and Properties of Amyloid Peptides

In this review, we provide an illustration of the idea discussed in the literature of using model compounds to study the effect of substitution of L- for D-amino acid residues in amyloid peptides. The need for modeling is due to the inability to study highly disordered peptides by traditional methods (high-field NMR, X-ray). At the same time, the appearance of such peptides, where L-amino acids are partially replaced by D-analogs is one of the main causes of Alzheimer’s disease. The review presents examples of the use diastereomers with L-/D-tryptophan in model process—photoinduced electron transfer (ET) for studying differences in reactivity and structure of systems with L- and D-optical isomers. The combined application of spin effects, including those calculated using the original theory, fluorescence techniques and molecular modeling has demonstrated a real difference in the structure and efficiency of ET in diastereomers with L-/D-tryptophan residues. In addition, the review compared the factors governing chiral inversion in model metallopeptides and Aβ42 amyloid.

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.

Gas-Phase Stereoinversion in Aspartic Acid: Reaction Pathways, Computational Spectroscopic Analysis, and Its Astrophysical Relevance

Noncatalytic reaction pathways for the gas-phase stereoinversion in aspartic acid are mapped employing a global reaction route mapping strategy using quantum mechanical computations. The species including the transition states (TSs) traced along the stereoinversion pathways are characterized using rotational and vibrational computational spectroscopic analysis while accounting for the vibrational corrections to rotational constants and anharmonic effects. Notably, the TS structures traced along the stereochemical pathways resemble the achiral ammonium ylide and imine intermediates as observed in the Strecker synthesis of chiral amino acids. A few of the probable stereoinversion pathways proposed proceed through the proton or hydrogen atom transfer. The feasibility of the pathways under conditions akin to interstellar medium (ISM) is further discussed in terms of natural bond orbital analysis. The stereoinversion pathways proposed in this work may proceed via photoirradiation in the ISM, which though can be revealed by exploring the excited-state potential energy surface. In this context, the spectroscopic data generated in this work can provide valuable assistance toward the astrophysical detection of chiral molecules in outer space.

Conflict in the Mechanism and Kinetics of the Barrierless Reaction between SH and NO2 Radicals

There are some unsettled issues regarding the mechanism and kinetics of an important atmospheric reaction of NO₂ radical with the SH radical. The existing mechanism is based on the formation of HSO and NO radicals, both of which can result only along one barrierless channel. However, the detection of NO radical has never been reported though the formation of HSO radical has been followed in some studies to determine the rate constants. The latter are mainly obtained by monitoring the SH decay, but rate constants are reported to be highly conflicting among the existing studies reporting its value ranging from 10^-10 to 10^-12 cm³ molecule^-1 sec^-1. The present work attempts to resolve these issues by exploring various reaction pathways through the global reaction route mapping of the potential energy surface at the level of spin-unrestricted and spin-restricted coupled-cluster and density functional theories. The initial association of two radicals was found to proceed via two barrierless modes: (1) S-N association leading to HSNO₂ and, (2) S-O association resulting in HSONO, in particular the cis-isomer. The kinetics of the barrierless pathways was investigated through rate constants computed using canonical variational transition state theory (CVTST) along with their temperature and pressure dependence investigated using the master equation. The rate constants calculated using spin-unrestricted methods are found to be in agreement with experimentally observed range of rate constant, and the formation of cis-HSONO (via mode 2) is observed to be the main contributing channel. Contrary to the results of spin-restricted calculations, the barrierless channel (mode 1) leading to the formation of HSNO₂ is predicted to involve two bottlenecks when results using spin-unrestricted calculations were analyzed. Notably, the spin-unrestricted calculations predict a prereaction complex for the formation of S-N bond (via mode 1) which has been treated using Miller's unified transition state theory with a two transition state model. The fate of all the species involved in the reaction is critically evaluated in the present work, and the predictions made can be a subject of further experimental and theoretical studies involving radical-radical reactions.

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.

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.