Mechanistic Insights into S-Depalmitolyse Activity of Cln5 Protein Linked to Neurodegeneration and Batten Disease: A QM/MM Study.

Ceroid lipofuscinosis neuronal protein 5 (Cln5) is encoded by the CLN5 gene. The genetic variants of this gene are associated with the CLN5 form of Batten disease. Recently, the first crystal structure of Cln5 was reported. Cln5 shows cysteine palmitoyl thioesterase S-depalmitoylation activity, which was explored via fluorescent emission spectroscopy utilizing the fluorescent probe DDP-5. In this work, the mechanism of the reaction between Cln5 and DDP-5 was studied computationally by applying a QM/MM methodology at the ωB97X-D/6-31G(d,p):AMBER level. The results of our study clearly demonstrate the critical role of the catalytic triad Cys280-His166-Glu183 in S-depalmitoylation activity. This is evidenced through a comparison of the pathways catalyzed by the Cys280-His166-Glu183 triad and those with only Cys280 involved. The computed reaction barriers are in agreement with the catalytic efficiency. The calculated Gibb's free-energy profile suggests that S-depalmitoylation is a rate-limiting step compared to the preceding S-palmitoylation, with barriers of 26.1 and 25.3 kcal/mol, respectively. The energetics were complemented by monitoring the fluctuations in the electron density distribution through NBO charges and bond strength alterations via local mode stretching force constants during the catalytic pathways. This comprehensive protocol led to a more holistic picture of the reaction mechanism at the atomic level. It forms the foundation for future studies on the effects of gene mutations on both the S-palmitoylation and S-depalmitoylation steps, providing valuable data for the further development of enzyme replacement therapy, which is currently the only FDA-approved therapy for childhood neurodegenerative diseases, including Batten disease.

Direct oxidation of bromo-derived Fischer-Borsche oxo-ring using molecular iodine with combined experimental and computational study.

A direct oxidation of the bromo-derived Fischer-Borsche oxo-ring leading to carbazolequinone has been developed by using molecular iodine. This unprecedented transformation has been used for the modular synthesis of the anti-cardiotonic agent murrayaquinone. Furthermore, the present method has been generalized to a broad range of functional groups, with good to excellent yield.

Unraveling the Importance of Noncovalent Interactions in Asymmetric Hydroformylation Reactions.

For catalytic asymmetric hydroformylation (AHF) of alkenes to chiral aldehydes, though a topic of high interest, the contemporary developments remain largely empirical owing to rather limited molecular insights on the origin of enantioselectivity. Given this gap, herein, we present the mechanistic details of Rh-(S,S)-YanPhos-catalyzed AHF of α-methylstyrene, as obtained through a comprehensive DFT (ω-B97XD and M06) study. The challenges with the double axially chiral YanPhos, bearing an N-benzyl BINOL-phosphoramidite and a BINAP-bis(3,5-t-Bu-aryl)phosphine, are addressed through exhaustive conformational sampling. The C-H···π, π···π, and lone pair···π noncovalent interactions (NCIs) between the N-benzyl and the rest of the chiral ligand limit the N-benzyl conformers. Similarly, the C-H···π and π···π NCIs between the chiral catalyst and α-methylstyrene render the si-face binding to the Rh-center more preferred over the re-face. The transition state (TS) for the regiocontrolling migratory insertion, triggered by the Rh-hydride addition to the alkene, to the more substituted α-carbon is 3.6 kcal/mol lower than that to the ß-carbon, thus favoring the linear chiral aldehyde over the achiral branched alternative. In the linear pathway, the TS for the hydride addition to the si-face is 1.5 kcal/mol lower than that to the re-face, with a predicted ee of 85% for the S aldehyde (expt. 87%). The energetic span analysis reveals the reductive elimination as the turnover determining step for the preferred S linear aldehyde. These molecular insights could become valuable for exploiting AHF reactions for substituted alkenes and for eventual industrial implementation.

Electronic Control on Linear versus Branched Alkylation of 2-/3-Aroylbenzofurans with Acrylates: Combined DFT and Synthetic Studies.

Investigations on the factors that govern unusual branched alkylation of 2-aroylbenzofurans with acrylates by Ru-catalyzed carbonyl-directed C-H activation has been carried out by calculating the kinetics associated with the two key steps-the coordination of the acrylate with the intermediate ruthenacycle and the subsequent migratory insertion reaction-studied with the help of DFT calculations. Eight possible orientations for each mode of alkylation have been considered for the calculations. From these calculations, it has been understood that there is a synergistic operation of the steric and electronic effects favoring the branched alkylation. Further DFT investigations on the alkylation of the isomeric 3-aroylbenzofurans indicated a preference for the linear alkylation and this has been verified experimentally. Overall, the observed/calculated complementary selectivity in the alkylation of 2-/3-aroylbenzofurans with acrylates reveals that the substrate-dependent charge distribution of the Ru-C bond in the intermediate ruthenacycle is an important determining factor and thus the current work opens up a new domain of substrate design for controlling regioselectivity.

Reductive nitrosylation of nickel(ii) complex by nitric oxide followed by nitrous oxide release.

Ni(ii) complex of ligand ( = bis(2-ethyl-4-methylimidazol-5-yl)methane) in methanol solution reacts with an equivalent amount of NO resulting in a corresponding Ni(i) complex. Adding further NO equivalent affords a Ni(i)-nitrosyl intermediate with the {NiNO}(10) configuration. This nitrosyl intermediate upon subsequent reaction with additional NO results in the release of N2O and formation of a Ni(ii)-nitrito complex. Crystallographic characterization of the nitrito complex revealed a symmetric η(2)-O,O-nitrito bonding to the metal ion. This study demonstrates the reductive nitrosylation of a Ni(ii) center followed by N2O release in the presence of excess NO.

Exploring the reducing role of boron: added insights from theory.

Carbon-carbon coupling in CO molecules is a challenging proposition, and very few main group complexes have been shown to effect this process. A recently reported triply bonded diboryne system (1) is notable for coupling four CO molecules to produce a (bis)boralactone species. The current full quantum chemical computational investigation with density functional theory (DFT) provides important insights into the nature of the CO coupling process by triply bonded diboryne systems. The complete reaction pathway leading to the formation of the (bis)boralactone has been determined. Factors that make this system so successful in coupling CO groups have been elucidated, and pertinent issues, such as why the coupling process stops after four CO additions, have been explored. Also, importantly, insights have been gained through the natural bond orbital (NBO) analysis into how the back-donation from diboryne activates CO.

Iodine-catalyzed aromatization of tetrahydrocarbazoles and its utility in the synthesis of glycozoline and murrayafoline A: a combined experimental and computational investigation.

A new protocol for the aromatization of tetrahydrocarbazoles has been achieved using a catalytic amount of iodine, giving high yields. The role of iodine in the aromatization has been explained by DFT, and its wide scope is extended to the total synthesis of glycozoline and murrayafoline A. This method has proven to be tolerant of a broad range of functional groups.

Synthesis of palmyrolide A and its cis-isomer and mechanistic insight into trans-cis isomerisation of the enamide macrocycle.

Concise and protecting-group free synthesis of ent-palmyrolide A and (-)-cis-palmyrolide A were achieved starting from commercially available (S)-citronellal. The key fragment of palmyrolide A, "(5S,7S)-7-hydroxy-5,8,8-trimethylnonanamide", which makes up the most challenging part of the target molecule, was prepared in just three steps. A plausible mechanism for the trans-cis isomerization of the double bond in the macrocycle has been investigated.