Simulations of Phage T7 Capsid Expansion Reveal the Role of Molecular Sterics on Dynamics

Molecular dynamics techniques provide numerous strategies for investigating biomolecular energetics, though quantitative analysis is often only accessible for relatively small (frequently monomeric) systems. To address this limit, we use simulations in combination with a simplified energetic model to study complex rearrangements in a large assembly. We use cryo-EM reconstructions to simulate the DNA packaging-associated 3 nm expansion of the protein shell of an initially assembled phage T7 capsid (called procapsid or capsid I). This is accompanied by a disorder–order transition and expansion-associated externalization displacement of the 420 N-terminal tails of the shell proteins. For the simulations, we use an all-atom structure-based model (1.07 million atoms), which is specifically designed to probe the influence of molecular sterics on dynamics. We find that the rate at which the N-terminal tails undergo translocation depends heavily on their position within hexons and pentons. Specifically, trans-shell displacements of the hexon E subunits are the most frequent and hexon A subunits are the least frequent. The simulations also implicate numerous tail translocation intermediates during tail translocation that involve topological traps, as well as sterically induced barriers. The presented study establishes a foundation for understanding the precise relationship between molecular structure and phage maturation.

Synthesis and molecular structure of pentadienyl complexes of the rare-earth metals

In combination with small and difficult to reduce rare-earth metals pdl′ undergoes CH-bond activations instead of sterically induced reductions to form dimeric complexes with a unique bridging six-membered metallacycle as the central structural motif.

Sterically induced reductive linkage of iron polypnictides with bulky lanthanide complexes by ring-opening of THF

Two new 3d/4f polyphosphide and polyarsenide complexes in which [(DippForm)2Sm(thf)2] and [Cp*Fe(η5-E5)] (E = P, As) are linked by ring-opened thf molecule were obtained and structurally characterized.

Functional Group Interconversion

Chaozhong Li of the Shanghai Institute of Organic Chemistry reported (J. Am. Chem. Soc. 2012, 134, 10401) the silver nitrate catalyzed decarboxylative fluorination of carboxylic acids, which shows interesting chemoselectivity in substrates such as 1. A related decarboxylative chlorination was also reported by Li (J. Am. Chem. Soc. 2012, 134, 4258). Masahito Ochiai at the University of Tokushima has developed (Chem. Commun. 2012, 48, 982) an iodobenzene-catalyzed Hofmann rearrangement (e.g., 3 to 4) that proceeds via hypervalent iodine intermediates. The dehydrating agent T3P (propylphosphonic anhydride), an increasingly popular reagent for acylation chemistry, has been used (Tetrahedron Lett. 2012, 53, 1406) by Vommina Sureshbabu at Bangalore University to convert amino or peptide acids such as 5 to the corresponding thioacids with sodium sulfide. Jianqing Li and co-workers at Bristol-Myers Squibb have shown (Org. Lett. 2012, 14, 214) that trimethylaluminum, which has long been known to effect the direct amidation of esters, can also achieve the direct coupling of acids and amines, such as in the preparation of amide 8. The propensity of severely hindered 2,2,6,6-tetramethylpiperidine (TMP) amides such as 9 to undergo solvolysis at room temperature has been shown (Angew. Chem. Int. Ed. 2012, 51, 548) by Guy Lloyd-Jones and Kevin Booker-Milburn at the University of Bristol. The reaction proceeds by way of the ketene and is enabled by sterically induced destabilization of the usual conformation that allows conjugation of the nitrogen lone pair with the carbonyl. Matthias Beller at Universität Rostock has found (Angew. Chem. Int. Ed. 2012, 51, 3905) that primary amides may be transamidated via copper(II) catalysis. The conditions are mild enough that an epimerization-prone amide such as 11 undergoes no observable racemization during conversion to amide 13. A photochemical transamidation has been achieved (Chem. Sci. 2012, 3, 405) by Christian Bochet at the University of Fribourg that utilizes 385-nm light to activate a dinitroindoline amide in the presence of amines such as 15, which produces the amide 16. Notably, photochemical cleavage of the Ddz protecting group occurs at a shorter wavelength of 300 nm.