Coarctate cyclization reactions: a primer

The cleavage of five-membered heterocycles possessing an exocyclic carbene or nitrene to form conjugated ene–ene–yne systems has been documented for over 40 years; however, the reverse reaction, using a conjugated “ene–ene–yne” precursor to form a heterocycle is a relatively new approach. Over the past decade, the Haley and Herges groups have studied computationally and experimentally the cyclization of the “hetero-ene–ene–yne” motif via an unusual class of concerted reactions known as coarctate reactions. This feature article details our synthetic and mechanistic work involving triazene–arene–alkynes and structurally-related systems to generate heterocycles using coarctate chemistry

GIWAXS Characterization of Metal–Organic Framework Thin Films and Heterostructures: Quantifying Structure and Orientation

For optoelectronic applications of metal–organic framework (MOF) thin films, it is important to be able to fabricate films and heterostructures that are highly oriented relative to the substrate\u27s surface normal. However, process optimization to achieve this is difficult without sufficiently detailed structural characterization of the deposited films. It is demonstrated that 2D grazing-incidence wide-angle X-ray scattering (GIWAXS) data from a laboratory system go a long way to providing such characterization and can 1) better test structural models than 1D scans, 2) provide a quantitative estimate—useful for process optimization—of the fraction of the deposited film that has the desired surface-oriented texture (2D powder), and 3) deliver such information as a function of depth into the film—useful for heterostructure characterization. Herein, GIWAXS data collection and analysis are introduced in the context of understanding MOF thin films, then it is shown how the desired oriented fraction (2D powder fraction) of UiO-66 fabricated by vapor-assisted conversion can be increased from 4% to over 95% by minimizing nucleation in solution. Finally, it is demonstrated that heterostructures of UiO-66 and UiO-67 can be grown wherein both layers are highly ordered (UiO-66 83%, UiO-67 >94%) once synthetic protocols are optimized

Photoswitching in nanoporous, crystalline solids: an experimental and theoretical study for azobenzene linkers incorporated in MOFs

In this article, we use the popular photoswitchable molecule, azobenzene, to demonstrate that the embedding in a nanoporous, crystalline solid enables a precise understanding of light-induced, reversible molecular motion. We investigate two similar azobenzene-containing, pillared-layer metal–organic frameworks (MOFs): Cu2(AzoBPDC)2(BiPy) and Cu2(NDC)2(AzoBiPy). Experimental results from UV-vis spectroscopy and molecular uptake experiments as well as theoretical results based on density-functional theory (DFT) show that in the Cu2(AzoBPDC)2(BiPy) MOF structure, the azobenzene side groups undergo photoisomerization when irradiated with UV or visible light. In a very similar MOF structure, Cu2(NDC)2(AzoBiPy), the experimental studies show an unexpected absence of photoisomerization. The DFT calculations reveal that in both MOFs the initial and final states of the photoswitching process (the trans and the cis conformation) have similar energies, which strongly suggests that the reason for the effective blocking of photoswitching in the AzoBiPy-based MOFs must be related to the switching process itself. More detailed calculations show that in Cu2(NDC)2(AzoBiPy) a naphthalene linker from the molecular framework blocks the photoisomerization trajectory which leads from the trans to the cis conformation. For Cu2(AzoBPDC)2(BiPy), as a result of the different geometry, such a steric hindrance is absent

An effective all-atom potential for proteins

We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed alpha/beta protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49--67-residue systems with high statistical accuracy, using only modest computational resources by today's standards

Spin states of zigzag-edged Mobius graphene nanoribbons from first principles

Mobius graphene nanoribbons have only one edge topologically. How the magnetic structures, previously associated with the two edges of zigzag-edged flat nanoribbons or cyclic nanorings, would change for their Mobius counterparts is an intriguing question. Using spin-polarized density functional theory, we shed light on this question. We examine spin states of zigzag-edged Mobius graphene nanoribbons (ZMGNRs) with different widths and lengths. We find a triplet ground state for a Mobius cyclacene, while the corresponding two-edged cyclacene has an open-shell singlet ground state. For wider ZMGNRs, the total magnetization of the ground state is found to increase with the ribbon length. For example, a quintet ground state is found for a ZMGNR. Local magnetic moments on the edge carbon atoms form domains of majority and minor spins along the edge. Spins at the domain boundaries are found to be frustrated. Our findings show that the Mobius topology (i.e., only one edge) causes ZMGNRs to favor one spin over the other, leading to a ground state with non-zero total magnetization.Comment: 17 pages, 4 figure

Photochemistry of Furyl- and Thienyldiazomethanes: Spectroscopic Characterization of Triplet 3-Thienylcarbene

Photolysis (λ \u3e 543 nm) of 3-thienyldiazomethane (1), matrix isolated in Ar or N2 at 10 K, yields triplet 3-thienylcarbene (13) and α-thial-methylenecyclopropene (9). Carbene 13 was characterized by IR, UV/vis, and EPR spectroscopy. The conformational isomers of 3-thienylcarbene (s-E and s-Z) exhibit an unusually large difference in zero-field splitting parameters in the triplet EPR spectrum (|D/hc| = 0.508 cm–1, |E/hc| = 0.0554 cm–1; |D/hc| = 0.579 cm–1, |E/hc| = 0.0315 cm–1). Natural Bond Orbital (NBO) calculations reveal substantially differing spin densities in the 3-thienyl ring at the positions adjacent to the carbene center, which is one factor contributing to the large difference in D values. NBO calculations also reveal a stabilizing interaction between the sp orbital of the carbene carbon in the s-Z rotamer of 13 and the antibonding σ orbital between sulfur and the neighboring carbon—an interaction that is not observed in the s-E rotamer of 13. In contrast to the EPR spectra, the electronic absorption spectra of the rotamers of triplet 3-thienylcarbene (13) are indistinguishable under our experimental conditions. The carbene exhibits a weak electronic absorption in the visible spectrum (λmax = 467 nm) that is characteristic of triplet arylcarbenes. Although studies of 2-thienyldiazomethane (2), 3-furyldiazomethane (3), or 2-furyldiazomethane (4) provided further insight into the photochemical interconversions among C5H4S or C5H4O isomers, these studies did not lead to the spectroscopic detection of the corresponding triplet carbenes (2-thienylcarbene (11), 3-furylcarbene (23), or 2-furylcarbene (22), respectively)

Optimized Folding Simulations of Protein A

We describe optimized parallel tempering simulations of the 46-residue B-fragment of protein A. Native-like configurations with a root-mean-square deviation of approximately 3A to the experimentally determined structure (Protein Data Bank identifier 1BDD) are found. However, at biologically relevant temperatures such conformations appear with only about 10% frequency in our simulations. Possible short comings in our energy function are discussed.Comment: 6 pages, 8 figure

Photoswitching in nanoporous, crystalline solids: An experimental and theoretical study for azobenzene linkers incorporated in MOFs

In this article, we use the popular photoswitchable molecule, azobenzene, to demonstrate that the embedding in a nanoporous, crystalline solid enables a precise understanding of light-induced, reversible molecular motion. We investigate two similar azobenzene-containing, pillared-layer metal-organic frameworks (MOFs): Cu2(AzoBPDC)2(BiPy) and Cu2(NDC)2(AzoBiPy). Experimental results from UV-vis spectroscopy and molecular uptake experiments as well as theoretical results based on density-functional theory (DFT) show that in the Cu2(AzoBPDC)2(BiPy) MOF structure, the azobenzene side groups undergo photoisomerization when irradiated with UV or visible light. In a very similar MOF structure, Cu2(NDC)2(AzoBiPy), the experimental studies show an unexpected absence of photoisomerization. The DFT calculations reveal that in both MOFs the initial and final states of the photoswitching process (the trans and the cis conformation) have similar energies, which strongly suggests that the reason for the effective blocking of photoswitching in the AzoBiPy-based MOFs must be related to the switching process itself. More detailed calculations show that in Cu2(NDC)2(AzoBiPy) a naphthalene linker from the molecular framework blocks the photoisomerization trajectory which leads from the trans to the cis conformation. For Cu2(AzoBPDC)2(BiPy), as a result of the different geometry, such a steric hindrance is absent

Breaking the photoswitch speed limit

The forthcoming generation of materials, including artificial muscles, recyclable and healable systems, photochromic heterogeneous catalysts, or tailorable supercapacitors, relies on the fundamental concept of rapid switching between two or more discrete forms in the solid state. Herein, we report a breakthrough in the “speed limit” of photochromic molecules on the example of sterically-demanding spiropyran derivatives through their integration within solvent-free confined space, allowing for engineering of the photoresponsive moiety environment and tailoring their photoisomerization rates. The presented conceptual approach realized through construction of the spiropyran environment results in ~1000 times switching enhancement even in the solid state compared to its behavior in solution, setting a record in the field of photochromic compounds. Moreover, integration of two distinct photochromic moieties in the same framework provided access to a dynamic range of rates as well as complementary switching in the material’s optical profile, uncovering a previously inaccessible pathway for interstate rapid photoisomerization.</p