Bader's Topological Bond Path Does Not Necessarily Indicate Stabilizing Interaction-Proof Studies Based on the Ng@[3n]cyclophane Endohedral Complexes.

According to Bader's quantum theory of atoms in molecules (QTAIM), the simultaneous presence of a bond path and the corresponding bond critical point between any two atoms is both a necessary and sufficient condition for the atoms to be bonded to one another. In principle, this means that this pair of atoms should make a stabilizing contribution to the molecular system. However, the multitude of so-called counterintuitive bond paths strongly suggests that this statement is not necessarily true. Particularly 'troublesome' are endohedral complexes, in which encapsulation-enforced proximity between the trapped guest (e.g., an atom) and the host's cage system usually 'produces' many counterintuitive bond paths. In the author's opinion, the best evidence to demonstrate the repulsive nature of the intra-cage guest⋯host interaction is the use of some trapping systems containing small escape channels and then showing that the initially trapped entity spontaneously escapes outside the host's cage during geometry optimization of the initially built guest@host endohedral complex. For this purpose, a group of 24 Ng@[3n]cyclophane (3≤n≤6) endohedral complexes is used. As a result, arguments are presented showing that Bader's topological bond path does not necessarily indicate a stabilizing interaction.

The physical nature of the ultrashort spike-ring interaction in iron maiden molecules.

The so-called 'iron maiden' molecules belong to one of the most interesting subgroups of cyclophanes due to the presence of the ultrashort interaction between the CX apical bond and the benzene ring. This article presents an in-depth theoretical study of 16 'iron maiden' molecules, in which X = H, F, Cl or Br and the side chains are of various lengths and types: CSC, CSCC, CCC, and CCCC. It is shown that the H → F → Cl → Br substitution leads to a significant expansion of the 'iron maiden' molecule. Shorter chains lead to more pronounced effects, while insertion of sulfur atoms into the side chains lowers them. Structural changes are associated with an increase in energetic destabilization of X. Moreover, unlike for H, in the case of X = halogen, the out → in isomerization is energetically disadvantageous. The 'iron maiden' molecules are characterized by the presence of only three X⋯CAr bond paths. Particularly noteworthy are unusually large (even up to 32) values of the X⋯CAr bond ellipticity, which results from flat electron density distribution. The X⋯π interaction in each of the investigated 'iron maiden' molecule turned out to be multi-center, stabilizing and almost purely covalent in nature as indicated by the definitely dominant percentage (94.8%-101.6%) of the exchange-correlation energy. The spatial hindrance within the 'iron maiden' molecules appears to be not so much due to the X⋯π repulsion, but due to unfavorable steric interactions between X and the CC side bonds. It is also confirmed that some CH⋯HC interactions in aliphatic chains can be very weakly stabilizing.

Small, Clickable, and Monovalent Magnetofluorescent Nanoparticles Enable Mechanogenetic Regulation of Receptors in a Crowded Live-Cell Microenvironment.

Multifunctional magnetic nanoparticles have shown great promise as next-generation imaging and perturbation probes for deciphering molecular and cellular processes. As a consequence of multicomponent integration into a single nanosystem, pre-existing nanoprobes are typically large and show limited access to biological targets present in a crowded microenvironment. Here, we apply organic-phase surface PEGylation, click chemistry, and charge-based valency discrimination principles to develop compact, modular, and monovalent magnetofluorescent nanoparticles (MFNs). We show that MFNs exhibit highly efficient labeling to target receptors present in cells with a dense and thick glycocalyx layer. We use these MFNs to interrogate the E-cadherin-mediated adherens junction formation and F-actin polymerization in a three-dimensional space, demonstrating the utility as modular and versatile mechanogenetic probes in the most demanding single-cell perturbation applications.

Exopolyhedral Ligand Orientation Controls Diastereoisomer in Mixed-Metal Bis(carboranes).

Heterobimetallic derivatives of a bis(carborane), [µ7,8-(1',3'-3'-Cl-3'-PPh3-closo-3',1',2'-RhC2B9H10)-2-(p-cymene)-closo-2,1,8-RuC2B9H10] (1) and [µ7,8-(1',3'-3'-Cl-3'-PPh3-closo-3',1',2'-RhC2B9H10)-2-Cp-closo-2,1,8-CoC2B9H10] (2) have been synthesised and characterised, including crystallographic studies. A minor co-product during the synthesis of compound 2 is the new species [8-{8'-2'-H-2',2'-(PPh3)2-closo-2',1',8'-RhC2B9H10}-2-Cp-closo-2,1,8-CoC2B9H10] (3), isolated as a mixture of diastereoisomers. Although, in principle, compounds 1 and 2 could also exist as two diastereoisomers, only one (the same in both cases) is formed. It is suggested that the preferred exopolyhedral ligand orientation in the rhodacarboranes in the non-observed diastereoisomers would lead to unacceptable steric crowding between the PPh3 ligand and either the p-cymene (compound 1) or Cp (compound 2) ligand of the ruthenacarborane or cobaltacarborane, respectively.

Intramolecular interactions in sterically crowded hydrocarbon molecules.

A molecular fragmentation method has been used to analyze the intramolecular interactions in the three molecules coupled diamantane, hexaphenylethane, and all-meta-tert-butyl substituted hexaphenylethane. The significance of these systems lies in the fact, that steric crowding effects enable a stabilization of the central carbon bond that possesses an extended length (1.6 to 1.7 Å) beyond conventional carbon-carbon bonds due to the steric repulsion of the attached hydrocarbon groups. The total stability of these molecules therefore depends on a delicate balance between attractive interaction forces on the one hand and on repulsive forces on the other hand. We have quantified the different interaction energy contributions using symmetry-adapted perturbation theory based on a density functional theory description of the monomers. It has been found that the attractive dispersion interactions increase more strongly with the level of crowding in the systems than the counteracting exchange interactions. This shows that steric crowding effects can have a significant impact on the structure and stability of large and branched molecules. © 2017 Wiley Periodicals, Inc.

The Trivalent Neodymium Complex [(C5 Me5 )3 Nd] Is a One-Electron Reductant!

A Se22- complex, Ph3 P, and (C5 Me5 )2 are formed in the reduction of Se=PPh3 by the NdIII complex [(C5 Me5 )3 Nd] [Eq. (a)]. The latter is thus reminiscent of [(C5 Me5 )3 Sm], which, however, appears to be a stronger reductant than [(C5 Me5 )3 Nd]. This suggests that the reductive reactivity of [(C5 Me5 )3 Ln] complexes can be tuned by varying the size of the metal atom.

Insights into the distal heme pocket of H-NOX using fluoride as a probe for H-bonding interactions.

Nitric oxide (NO) and dioxygen (O2) are gases of similar size, shape, and electrostatic potential, but different physiological function. In aerobic organisms, the cellular concentration of O2 far exceeds that of NO; instead NO relies heavily on the ability of its receptor to discriminate against O2. In mammals, soluble guanylate cyclase (sGC) serves this role, binding NO with picomolar sensitivity and excluding O2 binding. Interestingly, some bacterial homologs of sGC, including the H-NOX (heme-nitric oxide/oxygen) domain from Thermoanaerobacter tengcongensis, tightly bind O2. Three distal pocket residues (Trp9, Asn74, and Tyr140) form a hydrogen-bonding network that stabilizes O2 binding to TtH-NOX. Therefore, a current hypothesis to explain sGC ligand specificity is that sGC lacks H-bond donors that preferentially stabilize O2 binding. The wavelength maximum of the charge-transfer band (CT1) in the electronic spectrum of the fluoride complex of ferric hemoproteins is a sensitive probe of H-bonding. Here, in order to gain further understanding of the distal pocket H-bonding network in TtH-NOX, we employ fluoride as a spectroscopic probe. As expected, our results indicate that Y140 donates a strong H-bond to the heme-bound ligand. We find that an H-bond from Asn74 as well as distal pocket crowding contributes to positioning Tyr140 for a strong and directed H-bond to iron-bound ligands; indeed crowding may be the primary role for Trp9. We clarify the role of H-bonding in sGC ligand discrimination and suggest that sterics also regulate ligand binding in the H-NOX family.