Randy W. Larsen

Zeolite-like Metal−Organic Frameworks as Platforms for Applications: On Metalloporphyrin-Based Catalysts

The extra-large cavities of zeolite-like metal-organic frameworks (ZMOFs) offer great potential for their exploration in applications pertinent to larger molecules, like porphyrins. The anionic nature of the framework allowed for facile in situ encapsulation of a cationic free-base porphyrin, and the alpha-cage of our (In-imidazoledicarboxylate)-based rho-ZMOF is ideally suited to the isolation of one porphyrin molecule per cage, which prevents the oxidative self-degradation associated with self-dimerization common in homogeneous catalysis and upon aggregation in solid supports like mesoporous silicates or polymers. The encapsulation of a free-base porphyrin [5,10,15,20-tetrakis(1-methyl-4- pyridinio)porphyrin] and the stability of the rho-ZMOF to metalation conditions, allows for the preparation of a variety of metalloporphyrins (i.e., Mn, Cu, Co, Zn ions) with the ZMOF serving as a platform. The Mn-metallated porphyrin encapsulated in rho-ZMOF shows catalytic activity toward the oxidation of cyclohexane, with turn-over numbers, to the best of our knowledge, higher than reported for similar heterogeneous systems, and our system can be recycled up to 11 cycles, which represents a longer lifetime than reported for any other system.

Myoglobin-like aerotaxis transducers in Archaea and Bacteria

Haem-containing proteins such as haemoglobin and myoglobin play an essential role in oxygen transport and storage. Comparison of the amino-acid sequences of globins from Bacteria and Eukarya suggests that they share an early common ancestor, even though the proteins perform different functions in these two kingdoms. Until now, no members of the globin family have been found in the third kingdom, Archaea. Recent studies of biological signalling in the Bacteria and Eukarya have revealed a new class of haem-containing proteins that serve as sensors. Until now, no haem-based sensor has been described in the Archaea. Here we report the first myoglobin-like, haem-containing protein in the Archaea, and the first haem-based aerotactic transducer in the Bacteria (termed HemAT-Hs for the archaeon Halobacterium salinarum, and HemAT-Bs for Bacillus subtilis). These proteins exhibit spectral properties similar to those of myoglobin and trigger aerotactic responses.

How can proteins enter the interior of a MOF? Investigation of cytochrome c translocation into a MOF consisting of mesoporous cages with microporous windows.

It has been demonstrated for the first time that the heme protein cytochrome c (Cyt c) can enter the interior of a MOF despite the larger molecular dimension of the protein relative to the access pore sizes. Mechanistic studies suggest that the Cyt c molecules must undergo a significant conformational change during translocation into the MOF interior through the relatively small nanopores.

Globin-coupled sensors: a class of heme-containing sensors in Archaea and Bacteria.

The recently discovered prokaryotic signal transducer HemAT, which has been described in both Archaea and Bacteria, mediates aerotactic responses. The N-terminal regions of HemAT from the archaeon Halobacterium salinarum (HemAT-Hs) and from the Gram-positive bacterium Bacillus subtilis (HemAT-Bs) contain a myoglobin-like motif, display characteristic heme–protein absorption spectra, and bind oxygen reversibly. Recombinant HemAT-Hs and HemAT-Bs shorter than 195 and 176 residues, respectively, do not bind heme effectively. Sequence homology comparisons and three-dimensional modeling predict that His-123 is the proximal heme-binding residue in HemAT from both species. The work described here used site-specific mutagenesis and spectroscopy to confirm this prediction, thereby providing direct evidence for a functional domain of prokaryotic signal transducers that bind heme in a globin fold. We postulate that this domain is part of a globin-coupled sensor (GCS) motif that exists as a two-domain transducer having no similarity to the PER-ARNT-SIM (PAS)-domain superfamily transducers. Using the GCS motif, we have identified several two-domain sensors in a variety of prokaryotes. We have cloned, expressed, and purified two potential globin-coupled sensors and performed spectral analysis on them. Both bind heme and show myoglobin-like spectra. This observation suggests that the general function of GCS-type transducers is to bind diatomic oxygen and perhaps other gaseous ligands, and to transmit a conformational signal through a linked signaling domain.

Molecular building blocks approach to the assembly of zeolite-like metal–organic frameworks (ZMOFs) with extra-large cavities

Two novel porous anionic zeolite-like metal-organic frameworks, rho-ZMOF and sod-ZMOF, have been synthesized by metal-ligand-directed assembly of rigid and directional tetrahedral building units, InN4 synthesized in situ, and doubly deprotonated bis(bidentate) imidazoledicarboxylic acid ligands (HImDC) in the presence of different structure directing agents (SDAs).

Spectroscopic and molecular modeling studies of caffeine complexes with DNA intercalators

Recent studies have demonstrated that caffeine can act as an antimutagen and inhibit the cytoxic and/or cytostatic effects of some DNA intercalating agents. It has been suggested that this inhibitory effect may be due to complexation of the DNA intercalator with caffeine. In this study we employ optical absorption, fluorescence, and molecular modeling techniques to probe specific interactions between caffeine and various DNA intercalators. Optical absorption and steady-state fluorescence data demonstrate complexation between caffeine and the planar DNA intercalator acridine orange. The association constant of this complex is determined to be 258.4 +/- 5.1 M-1. In contrast, solutions containing caffeine and the nonplanar DNA intercalator ethidium bromide show optical shifts and steady-state fluorescence spectra indicative of a weaker complex with an association constant of 84.5 +/- 3.5 M-1. Time-resolved fluorescence data indicate that complex formation between caffeine and acridine orange or ethidium bromide results in singlet-state lifetime increases consistent with the observed increase in the steady-state fluorescence yield. In addition, dynamic polarization data indicate that these complexes form with a 1:1 stoichiometry. Molecular modeling studies are also included to examine structural factors that may influence complexation.

Ground- and excited-state properties of Zn(II) tetrakis(4-tetramethylpyridyl) pophyrin specifically encapsulated within a Zn(II) HKUST metal-organic framework.

We have examined the photophysical properties of Zn(II) tetramethylpyridyl porphyrin (ZnT4MPyP) specifically encapsulated within the cubioctahedral cavities of a ZnHKUST metal- organic framework. The encapsulated ZnT4MPyP exhibits a Soret maxima at ∼458 nm that is bathochromically shifted relative to ZnT4PyP in ethanol solution (Soret maxima centered at 440 nm). The corresponding emission spectra of the encapsulated porphyrin exhibit resolvable bands centered at 636 and 677 nm relative to a single broad emission band of the ZnT4MPyP in ethanol solution centered at 636 nm with a shoulder situated near ∼660 nm. The fluorescence lifetime of the encapsulated porphyrin is also perturbed relative to that of the free porphyrin in solution (1.88 ns for the encapsulated porphyrin relative to 1.2 ns in solution). These results are consistent with the ZnT4MPyP being in a more constrained environment in which the peripheral pyridyl groups have restricted rotational motion. The ZnT4MPyP triplet lifetime is also affected by encapsulation, giving rise to a longer lifetime (τ ≈ 3.3 ms) relative to that for the free porphyrin in solution (τ ≈ 1 ms). The triplet-state results indicate that nonplanar vibrational modes of the porphyrin leading to intersystem crossing are retained by encapsulation of the porphyrin but that either the density of vibrational states or the specific nonplanar modes coupling the singlet and triplet states may be perturbed, resulting in the longer observed lifetime.

How Fast Do Metal Organic Polyhedra Form in Solution? Kinetics of [Cu2(5-OH-bdc)2L2]12 Formation in Methanol

The present study utilizes rapid mixing techniques together with fast optical spectroscopy to probe the assembly of [Cu2(5-OH-bdc)2L2]12 formation in methanol. The data reveal five distinct kinetic steps involved in the formation of the Cu-nanoball in methanol with lifetimes of <15 ms, 26 ms, 310 ms, 4 s, and 45 s. From these results two possible mechanistic pathways are proposed based upon fragment isomerization followed by condensation. Both mechanisms involve fast building unit assembly (<15 ms) followed by either concerted or sequential fragment isomerization (activation controlled) coupled with condensation.

Photoinduced inter-cavity electron transfer between Ru(II)tris(2,2′-bipyridne) and Co(II)tris(2,2′-bipyridine) Co-encapsulated within a Zn(II)-trimesic acid metal organic framework

Photoexcitation of a Zn(II)-trimesic acid based metal organic framework containing co-encapsulated Ru(II)tris(2,2′-bipyridine) (RuBpy) and Co(II)tris(2,2′-bipyridine) (CoBpy) results in inter-molecular electron transfer (ET) between the excited state of RuBpy (3MLCT) and the ground state CoBpy The rate of inter-cavity ET, kET, is found to be 3.7 × 106 s−1. Using the semi-classical Marcus equation and the observed rate constant, it is determined that ET occurs between RuBpy and CoBpy complexes located in adjacent cavities (∼19.6 A).

Sulfono‐γ‐AApeptides as a New Class of Nonnatural Helical Foldamer

Foldamers offer an attractive opportunity for the design of novel molecules that mimic the structures and functions of proteins and enzymes including biocatalysis and biomolecular recognition. Herein we report a new class of nonnatural helical sulfono-γ-AApeptide foldamers of varying lengths. The crystal structure of the sulfono-γ-AApeptide monomer S6 illustrates the intrinsic folding propensity of sulfono-γ-AApeptides, which likely originates from the bulkiness of tertiary sulfonamide moiety. The two-dimensional solution NMR spectroscopy data for the longest sequence S1 demonstrates a 10/16 right-handed helical structure. Optical analysis using circular dichroism further supports well- defined helical conformation of sulfono-γ-AApeptides in solution containing as few as five building blocks. Future development of sulfono-γ-AApeptides may lead to new foldamers with discrete functions, enabling expanded application in chemical biology and biomedical sciences.