An Extended Rudolph Diagram: B3H5 and B3H6+ Relate 3D-, 2D-, 1D-, and 0D-Boron Allotropes.

The structural chemistry of boron goes beyond the sp, sp2, and sp3 hybridization paradigms of carbon chemistry. We relate the apparently unconnected polyhedral boranes and 3D allotropes on the one hand and 2D clusters, borophenes, and multilayer borophenes on the other hand, through an extended Rudolph diagram. All-boron equivalents of cyclopropenium cation viz the flat B3H5 and the nonplanar B3H6+ constitute the missing links. The nonplanar B3H6+ (C3v) is the starting point for construction of polyhedral boranes; e.g., fusion of two of them leads to octahedral B6H62-. On the other hand, planar B3H6+ and B3H5 relate to borophenes with hexagonal holes. These borophene sheets can be further stacked with diverse interlayer BB bonds, ranging from bilayers to infinite layers. The tendency to achieve electron sufficiency as in the parent C3H3+ dictates the preference for hexagonal holes in the constituent layers and the interlayer bonds between them in multilayer borophenes. The design principles and theoretical validations for the formation of multilayer borophenes are also presented, indicating the variety and complexities involved.

Rearrangement of dicarboranyl methyl cation to icosahedral C3 B9 H12 + : An ab initio dynamics view.

Closo-carborane anions are prominent, whereas the cations of the same are less abundant in the literature. As these ions have similar size and are weakly coordinating, the ionic liquids of these two ions could have important applications in many areas of chemistry. In view of limited number of polyhedral carborane cations available, we revisited the rearrangement of dicarboranyl methyl cation (7-CH2 7,9-nido-C2 B9 H10 + ) using ab initio molecular dynamics calculations with metadynamics. Our simulations confirmed the concerted mechanism of the rearrangement. We believe this work will resume the interest in its synthesis and carborane cations in general.

Towards solvent regulated self-activation of N-terminal disulfide bond oxidoreductase-D.

N-terminal disulfide bond oxidoreductase-D (nDsbD), an essential redox enzyme in Gram-negative bacteria, consists of a single disulfide bond (Cys103-Cys109) in its active site. The enzymatic functions are believed to be regulated by an electron transfer mediated redox switching of the disulfide bond, which is vital in controlling bacterial virulence factors. In light of the disulfide bond's inclination towards nucleophilic cleavage, it is also plausible that an internal nucleophile could second the existing electron transfer mechanism in nDsbD. Using QM/MM MD metadynamics simulations, we explore different possibilities of generating an internal nucleophile near the nDsbD active site, which could serve as a fail-over mechanism in cleaving the disulfide bond. The simulations show the formation of the internal nucleophile Tyr42O- (F ≈ 9 kcal mol-1) and its stabilization through the solvent medium. The static gas-phase calculations show that Tyr42O- could be a potential nucleophile for cleaving the S-S bond. Most strikingly, it is also seen that Tyr42O- and Asp68OH communicate with each other through a proton-hole like water wire (F ≈ 12 kcal mol-1), thus modulating the nucleophile formation. Accordingly, we propose the role of a solvent in regulating the internal nucleophilic reactions and the subsequent self-activation of nDsbD. We believe that this could be deterministic while designing enzyme-targeted inhibitor compounds.

Thermomechanical effect in molecular crystals: the role of halogen-bonding interactions.

The design and synthesis of mechanically responsive materials is interesting because they are potential candidates to convert thermal energy into mechanical work. Reported in this paper are thermosalient effects in a series of halogen derivatives of salinazids. The chloro derivative, with higher electronegativity and a weaker inter-halogen bond strength (Cl⋯Cl) exhibits an excellent thermal response, whereas the response is weaker in the iodo derivative with stronger I⋯I halogen bonding. 3,5-Di-chloro-salinazid (Compound-A) exists in three polymorphic forms, two room-temperature polymorphs (Forms I and II) and one high-temperature modification (Form III). The transformation of Form I to Form III upon heating at 328-333 K is a reversible thermosalient transition, whereas the transformation of Form II to Form III is irreversible and non-thermosalient. 3,5-Di-bromo- (Compound-B) and 3-bromo-5-chloro- (Compound-C) salinazid are both dimorphic: the Form I to Form II transition in Compound-B is irreversible, whereas Compound-C shows a reversible thermosalient effect (362-365 K). In the case of 3,5-di-iodo-salinazid (Compound-D) and 3,5-di-fluoro-salinazid (Compound-E), no phase transitions or thermal effects were observed. The thermosalient behaviour of these halosalinazid molecular crystals is understood from the anisotropy in the cell parameters (an increase in the a axis and a decrease in the b and c axes upon heating) and the sudden release of accumulated strain during the phase transition. The di-halogen salinazid derivatives (chlorine to iodine) show a decrease in thermal effects with an increase in halogen-bond strength. Interestingly, Compound-B shows solid-state photochromism in its polymorphs along with the thermosalient effect, wherein Form I is cyan and Form II is light orange.

Solution to the π-Distortivity Problem.

Traditionally, the delocalized π system of benzene is believed to be responsible for its perfectly symmetric D6h geometry. However, it has also been suggested that the π system prefers a distorted D3h geometry. Arguments for this have been based on clever use of VB methods as well as through shifts in the frequency of the distortive b2u mode. Evidence has been provided through different ways of partitioning the total electronic energy between the σ and the π systems. These methods are plagued by the fact that there is no unique way to partition the energy, leading to questions regarding the validity of the conclusions. Here we note that even though energy cannot be partitioned exactly, force acting on a nucleus depends only on the single particle density and can hence be partitioned exactly. Using good-quality wave functions that are numerically found to obey the Hellmann-Feynman theorem to good accuracy, we calculate the σ and π components of the force and provide conclusive evidence of π-distortivity at the HF level. Our approach provides an unambiguous way to approach the problem with wave functions that account for electron correlation. Our calculations suggest that the conclusion is valid at the MP2 level, too.