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The mechanism of [2 + 2 + 1] cyclization reactions to access polycyclic sulfonyl indolines via Fe(II)-catalyzed or UV-driven has been investigated by density functional theory (DFT) methods. Mechanistic studies aided by the DFT calculations suggest that the reaction might proceed via a free radical pathway with HSO3· serving as the initiator and terminator of the free radical reaction, which has never been reported to our knowledge. The reactions involve the formation of two five-membered rings. The calculated results show that the first five-membered ring formation is the rate-determining step, with an energy barrier of 3.2 kcal/mol. And the second five-membered ring formation is an exergonic process. It is worth noting that HSO3· radicals are involved in the reaction preceding the formation of the second ring, and they facilitate formation of the second ring. Meanwhile, the most active site was predicted by the condensed Fukui function (CFF) and verified by DFT calculations. [ABSTRACT FROM AUTHOR]

The mechanism of the oxygen evolution reaction over NiFe-layered double hydroxides is investigated using first-principles DFT + U calculations. We consider three possible reaction pathways for O evolution. Our calculations show that O evolution from the OH*-OH* species has high energy barrier and from OOH* species have a little high energy barrier. Finally, we discover that O can easily release from OO* species. Graphical Abstract: The mechanism of oxygen evolution reaction (OER) over NiFe-layered double hydroxides was investigated using DFT + U method by First-principle. The present work considered two possible reaction pathways for O evolution. Our calculation suggested that O evolution from the OOH* species may be more favorable because of advantages in energy profile, oxygen adsorption, and overall energy barrier. In addition, density of states (DOS) and partial density of states (PDOSs) of NiFe-LDH and Ni(OH) showed that NiFe-LDH had a more stronger capability for electron transportation and higher activity than Ni(OH). Additionally, it was found that Bader charge of Ni had a large fluctuation in the former elementary steps, while in the later that of Fe had. The research suggested that the transitional metal Fe/Ni-based hydrotalcite was a suitable material for OER, for not only they had great activity and stability, but also they were widely used and comparatively cheap.[Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

The first-principles calculations were used to investigate the oxygen evolution reaction (OER) on the (100) surface of the spinel CoO, a high-performance oxidation catalyst. We compared the OER activities by the free-energy changes on three different covered surfaces including (i) clean, (ii) 0.5 monolayer O covered, and (iii) 0.5 monolayer OH covered surfaces, and the computed overpotential ( η) for the three surfaces followed the order: O covered ( η = 0.45 V)

The insect spruce budworm ( Choristoneura fumiferana) produces antifreeze protein (AFP) to assist in the protection of the over-wintering larval stage and contains multiple isoforms. Structures for two isoforms, known as CfAFP-501 and CfAFP-337, show that both possess similar left-handed β-helical structure, although thermal hysteresis activity of the longer isoform CfAFP-501 is three times that of CfAFP-337. The markedly enhanced activity of CfAFP-501 is not proportional to, and cannot be simply accounted for, by the increased ice-binding site resulting from the two extra coils in CfAFP-501. In order to investigate the molecular basis for the activity difference and gain better understanding of AFPs in general, we have employed several different computational methods to systematically study the structural properties and ice interactions of the AFPs and their deletion models. In the context of intact AFPs, a majority of the coils in CfAFP-501 has better ice interaction and causes stronger ice lattice disruption than CfAFP-337, strongly suggesting a cooperative or synergistic effect among β-helical coils. The synergistic effect would play a critical role and make significant contributions to the antifreeze activity β-helical antifreeze proteins. This is the first time that synergistic effect and its implication for antifreeze activity are reported for β-helical antifreeze proteins. [ABSTRACT FROM AUTHOR]

The possible interaction models for an antifreeze protein from Tenebrio molitar (TmAFP) have been systematically studied using the methods of molecular mechanics, molecular dynamics and quantum chemistry. It is hoped that these approaches would provide insights into the nature of interaction between protein monomers through sampling a number of interaction possibilities and evaluating their interaction energies between two monomers in the course of recognition. The results derived from the molecular mechanics indicate that monomerś β-sheets would be involved in interaction area and the side chains on two p-faces can match each other at the two-dimensional level. The results from molecular mechanics and ONIOM methods show that the strongest interaction energy could be gained through the formation of H-bonds when the twoβ-sheets are involved in the interaction model. Furthermore, the calculation of DFT and analysis of van der Waals bond charge density confirm further that recognition between the two TCTs mainly depends on inter-molecular hydroxyls. Therefore, our results demonstrate that during the course of interaction the most favorable association of TmAFPs is via their β-sheets. [ABSTRACT FROM AUTHOR]

Several methods including molecular mechanics, molecular dynamics, ONIOM that combines quantum chemistry with molecular mechanics and standard quantum chemistry are used to study the configuration and electron structures of an adduct of the DNA segment d(ATACATG*G*TACATA)d(TATGTACCATGTAT) with cis-[Pt(NH3)(2-Picoline)]2+. The investigation shows that the configuration optimized by ONIOM is similar to that determined by NMR. Strong chemical bonds between Pt of the complex and two N7s of neighboring guanines in the DNA duplex and hydrogen bond between the NH3of the complex and O6 of a nearby guanine have a large impact on the configuration of the adduct. Chemical bonds, the aforementioned hydrogen bond, and the interaction between a methyl of the complex and a methyl of the base in close proximity are critical for the complex to specifically recognize DNA. [ABSTRACT FROM AUTHOR]