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1. Planar B ₄₁ ⁻ and B ₄₂ ⁻ clusters with double-hexagonal vacancies

   https://doi.org/10.1039/C9NR09522E  

   Bai, Hui; Chen, Teng-Teng; Chen, Qiang; Zhao, Xiao-Yun; Zhang, Yang-Yang; Chen, Wei-Jia; Li, Wan-Lu; Cheung, Ling Fung; Bai, Bing; Cavanagh, Joseph; et al (December 2019, Nanoscale)

   Since the discovery of the B 40 borospherene, research interests have been directed to the structural evolution of even larger boron clusters. An interesting question concerns if the borospherene cages persist in larger boron clusters like the fullerenes. Here we report a photoelectron spectroscopy (PES) and computational study on the structures and bonding of B 41 − and B 42 − , the largest boron clusters characterized experimentally thus far. The PE spectra of both clusters display broad and complicated features, suggesting the existence of multiple low-lying isomers. Global minimum searches for B 41 − reveal three low-lying isomers ( I–III ), which are all related to the planar B 40 − structure. Isomer II ( C s , 1 A′) possessing a double hexagonal vacancy is found to agree well with the experiment, while isomers I ( C s , 3 A′′) and III ( C s , 1 A′) both with a single hexagonal vacancy are also present as minor isomers in the experiment. The potential landscape of B 42 − is found to be much more complicated with numerous low-lying isomers ( VII–XII ). The quasi-planar structure VIII ( C 1 , 2 A) containing a double hexagonal vacancy is found to make major contributions to the observed PE spectrum of B 42 − , while the other low-lying isomers may also be present to give rise to a complicated spectral pattern. Chemical bonding analyses show isomer II of B 41 − ( C s , 1 A′) and isomer VIII of B 42 − ( C 1 , 2 A) are π aromatic, analogous to that in the polycyclic aromatic hydrocarbon C 27 H 13 + ( C 2v , 1 A 1 ). Borospherene cage isomers are also found for both B 41 − and B 42 − in the global minimum searches, but they are much higher energy isomers. 

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2. A Rigidified Macrocyclic Grubbs Complex: A Rare Example of In - and Out -Isomers that Show a Dramatic Difference in Catalytic Reactivity

   https://doi.org/10.1021/acs.organomet.4c00331  

   Davalos-Morinigo, Anibal R; Vemulapalli, Srini; Dudding, Travis; Diver, Steven T (September 2024, Organometallics)

   Chirik, Paul (Ed.)

   The design of a rigidified macrocyclic N-heterocyclic carbene (NHC) ligand led to the formation and structural characterization of in- and out-Ru carbene complexes. In this study, introduction of a conformational lock was used to rigidify heteroaryl-aryl bonds and thereby enforce a more perpendicular dihedral angle. A forcing metalation step was needed to form the isomeric Ru carbene complexes (Grubbs complexes). The major isomer had the Ru carbene fragment located outside the macrocyclic ring whereas the minor isomer had the Ru carbene inside the macrocyclic ring. The two new Ru carbene complexes are the first examples of in- and out-isomers of a Grubbs-type complex. The solid state structures of each isomeric ruthenium carbene complex was determined by x-ray diffraction studies. The two Ru complexes showed significantly different catalytic reactivity in the ring-closing metathesis (RCM) of the benchmark substrate, diethyl diallylmalonate. We performed computational studies to determine rotational barriers; scalable energetic barriers were found in the unmetallated NHC ligand, favoring the in-isomer by 2.4 kcal/mol. These calculations, coupled with attempted interconversion of isomers, support a mechanism featuring rotational isomerization of the NHC nucleophile in a preequilibrium step before metalation. 

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3. Gallocin A, an Atypical Two-Peptide Bacteriocin with Intramolecular Disulfide Bonds Required for Activity

   https://doi.org/10.1128/spectrum.05085-22  

   Proutière, Alexis; du Merle, Laurence; Garcia-Lopez, Marta; Léger, Corentin; Voegele, Alexis; Chenal, Alexandre; Harrington, Antony; Tal-Gan, Yftah; Cokelaer, Thomas; Trieu-Cuot, Patrick; et al (April 2023, Microbiology Spectrum)

   LaRock, Christopher N. (Ed.)

   ABSTRACT Streptococcus gallolyticus subsp. gallolyticus ( SGG ) is an opportunistic gut pathogen associated with colorectal cancer. We previously showed that colonization of the murine colon by SGG in tumoral conditions was strongly enhanced by the production of gallocin A, a two-peptide bacteriocin. Here, we aimed to characterize the mechanisms of its action and resistance. Using a genetic approach, we demonstrated that gallocin A is composed of two peptides, GllA1 and GllA2, which are inactive alone and act together to kill “target” bacteria. We showed that gallocin A can kill phylogenetically close relatives of the pathogen. Importantly, we demonstrated that gallocin A peptides can insert themselves into membranes and permeabilize lipid bilayer vesicles. Next, we showed that the third gene of the gallocin A operon, gip , is necessary and sufficient to confer immunity to gallocin A. Structural modeling of GllA1 and GllA2 mature peptides suggested that both peptides form alpha-helical hairpins stabilized by intramolecular disulfide bridges. The presence of a disulfide bond in GllA1 and GllA2 was confirmed experimentally. Addition of disulfide-reducing agents abrogated gallocin A activity. Likewise, deletion of a gene encoding a surface protein with a thioredoxin-like domain impaired the ability of gallocin A to kill Enterococcus faecalis . Structural modeling of GIP revealed a hairpin-like structure strongly resembling those of the GllA1 and GllA2 mature peptides, suggesting a mechanism of immunity by competition with GllA1/2. Finally, identification of other class IIb bacteriocins exhibiting a similar alpha-helical hairpin fold stabilized with an intramolecular disulfide bridge suggests the existence of a new subclass of class IIb bacteriocins. IMPORTANCE Streptococcus gallolyticus subsp. gallolyticus ( SGG ), previously named Streptococcus bovis biotype I, is an opportunistic pathogen responsible for invasive infections (septicemia, endocarditis) in elderly people and is often associated with colon tumors. SGG is one of the first bacteria to be associated with the occurrence of colorectal cancer in humans. Previously, we showed that tumor-associated conditions in the colon provide SGG with an ideal environment to proliferate at the expense of phylogenetically and metabolically closely related commensal bacteria such as enterococci (1). SGG takes advantage of CRC-associated conditions to outcompete and substitute commensal members of the gut microbiota using a specific bacteriocin named gallocin, recently renamed gallocin A following the discovery of gallocin D in a peculiar SGG isolate. Here, we showed that gallocin A is a two-peptide bacteriocin and that both GllA1 and GllA2 peptides are required for antimicrobial activity. Gallocin A was shown to permeabilize bacterial membranes and kill phylogenetically closely related bacteria such as most streptococci, lactococci, and enterococci, probably through membrane pore formation. GllA1 and GllA2 secreted peptides are unusually long (42 and 60 amino acids long) and have very few charged amino acids compared to well-known class IIb bacteriocins. In silico modeling revealed that both GllA1 and GllA2 exhibit a similar hairpin-like conformation stabilized by an intramolecular disulfide bond. We also showed that the GIP immunity peptide forms a hairpin-like structure similar to GllA1/GllA2. Thus, we hypothesize that GIP blocks the formation of the GllA1/GllA2 complex by interacting with GllA1 or GllA2. Gallocin A may constitute the first class IIb bacteriocin which displays disulfide bridges important for its structure and activity and might be the founding member of a subtype of class IIb bacteriocins. 

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4. Experimental and computational electrochemistry of quinazolinespirohexadienone molecular switches – differential electrochromic vs photochromic behavior

   https://doi.org/10.3762/bjoc.15.240  

   Webb, Eric W; Moerdyk, Jonathan P; Sluiter, Kyndra B; Pollock, Benjamin J; Speelman, Amy L; Lynch, Eugene J; Polik, William F; Gillmore, Jason G (January 2019, Beilstein Journal of Organic Chemistry)

   null (Ed.)

   Our undergraduate research group has long focused on the preparation and investigation of electron-deficient analogs of the perimidinespirohexadienone (PSHD) family of photochromic molecular switches for potential application as "photochromic photooxidants" for gating sensitivity to photoinduced charge transfer. We previously reported the photochemistry of two closely related and more reducible quinazolinespirohexadienones (QSHDs), wherein the naphthalene of the PSHD is replaced with a quinoline. In the present work, we report our investigation of the electrochemistry of these asymmetric QSHDs. In addition to the short wavelength and photochromic long-wavelength isomers, we have found that a second, distinct long-wavelength isomer is produced electrochemically. This different long-wavelength isomer arises from a difference in the regiochemistry of spirocyclic ring-opening. The structures of both long-wavelength isomers were ascertained by cyclic voltammetry and 1 H NMR analyses, in concert with computational modeling. These results are compared to those for the symmetric parent PSHD, which due to symmetry possesses only a single possible regioisomer upon either electrochemical or photochemical ring-opening. Density functional theory calculations of bond lengths, bond orders, and molecular orbitals allow the rationalization of this differential photochromic vs electrochromic behavior of the QSHDs. 

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5. Gigantic C ₁₂₀ Fullertubes: Prediction and Experimental Evidence for Isomerically Purified Metallic [5,5] C ₁₂₀ -D _5d (1) and Nonmetallic [10,0] C ₁₂₀ -D _5h (10766)

   https://doi.org/10.1021/jacs.2c06951  

   Liu, Xiaoyang; Bourret, Emmanuel; Noble, Cora A.; Cover, Kevin; Koenig, Ryan M.; Huang, Rong; Franklin, Hannah M.; Feng, Xu; Bodnar, Robert J.; Zhang, Fan; et al (September 2022, Journal of the American Chemical Society)

   We report the first experimental characterization of isomerically pure and pristine C120 fullertubes, [5,5] C120-D5d(1) and [10,0] C120-D5h(10766). These new molecules represent the highest aspect ratio fullertubes isolated to date; for example, the prior largest empty cage fullertube was [5,5] C100-D5d(1). This increase of 20 carbon atoms represents a gigantic leap in comparison to three decades of C60–C90 fullerene research. Moreover, the [10,0] C120-D5d(10766) fullertube has an end-cap derived from C80-Ih and is a new fullertube whose C40 end-cap has not yet been isolated experimentally. Theoretical and experimental analyses of anisotropic polarizability and UV–vis assign C120 isomer I as a [5,5] C120-D5d(1) fullertube. C120 isomer II matches a [10,0] C120-D5h(10766) fullertube. These structural assignments are further supported by Raman data showing metallic character for [5,5] C120-D5d(1) and nonmetallic character for C120-D5h(10766). STM imaging reveals a tubular structure with an aspect ratio consistent with a [5,5] C120-D5d(1) fullertube. With microgram quantities not amenable to crystallography, we demonstrate that DFT anisotropic polarizability, augmented by long-accepted experimental analyses (HPLC retention time, UV–vis, Raman, and STM) can be synergistically used (with DFT) to down select, predict, and assign C120 fullertube candidate structures. From 10 774 mathematically possible IPR C120 structures, this anisotropic polarizability paradigm is quite favorable to distinguish tubular structures from carbon soot. Identification of isomers I and II was surprisingly facile, i.e., two purified isomers for two possible structures of widely distinguishing features. These metallic and nonmetallic C120 fullertube isomers open the door to both fundamental research and application development. 

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