More Like this

1. DNA scaffold supports long-lived vibronic coherence in an indodicarbocyanine (Cy5) dimer

   https://doi.org/10.1039/D0SC01127D  

   Sohail, Sara H. ; Otto, John P. ; Cunningham, Paul D. ; Kim, Young C. ; Wood, Ryan E. ; Allodi, Marco A. ; Higgins, Jacob S. ; Melinger, Joseph S. ; Engel, Gregory S. ( August 2020 , Chemical Science)

   null (Ed.)

   Vibronic coupling between pigment molecules is believed to prolong coherences in photosynthetic pigment–protein complexes. Reproducing long-lived coherences using vibronically coupled chromophores in synthetic DNA constructs presents a biomimetic route to efficient artificial light harvesting. Here, we present two-dimensional (2D) electronic spectra of one monomeric Cy5 construct and two dimeric Cy5 constructs (0 bp and 1 bp between dyes) on a DNA scaffold and perform beating frequency analysis to interpret observed coherences. Power spectra of quantum beating signals of the dimers reveal high frequency oscillations that correspond to coherences between vibronic exciton states. Beating frequency maps confirm that these oscillations, 1270 cm −1 and 1545 cm −1 for the 0-bp dimer and 1100 cm −1 for the 1-bp dimer, are coherences between vibronic exciton states and that these coherences persist for ∼300 fs. Our observations are well described by a vibronic exciton model, which predicts the excitonic coupling strength in the dimers and the resulting molecular exciton states. The energy spacing between those states closely corresponds to the observed beat frequencies. MD simulations indicate that the dyes in our constructs lie largely internal to the DNA base stacking region, similar to the native design of biological light harvesting complexes. Observed coherences persist on the timescale of photosynthetic energy transfer yielding further parallels to observed biological coherences, establishing DNA as an attractive scaffold for synthetic light harvesting applications. 

   more » « less
2. Coexistence of stable and unstable population dynamics in a nonlinear non-Hermitian mechanical dimer

   https://doi.org/10.1103/PhysRevE.107.064211  

   Martello, Enrico ; Singhal, Yaashnaa ; Gadway, Bryce ; Ozawa, Tomoki ; Price, Hannah M. ( June 2023 , Physical Review E)

   Non-Hermitian two-site dimers serve as minimal models in which to explore the interplay of gain and loss in dynamical systems. In this paper, we experimentally and theoretically investigate the dynamics of non-Hermitian dimer models with nonreciprocal hoppings between the two sites. We investigate two types of non-Hermitian couplings; one is when asymmetric hoppings are externally introduced, and the other is when the nonreciprocal hoppings depend on the population imbalance between the two sites, thus introducing the non-Hermiticity in a dynamical manner. We engineer the models in our synthetic mechanical setup comprised of two classical harmonic oscillators coupled by measurement-based feedback. For fixed nonreciprocal hoppings, we observe that, when the strength of these hoppings is increased, there is an expected transition from a PT-symmetric regime, where oscillations in the population are stable and bounded, to a PT-broken regime, where the oscillations are unstable and the population grows/decays exponentially. However, when the non-Hermiticity is dynamically introduced, we also find a third intermediate regime in which these two behaviors coexist, meaning that we can tune from stable to unstable population dynamics by simply changing the initial phase difference between the two sites. As we explain, this behavior can be understood by theoretically exploring the emergent fixed points of a related dimer model in which the nonreciprocal hoppings depend on the normalized population imbalance. Our study opens the way for the future exploration of non-Hermitian dynamics and exotic lattice models in synthetic mechanical networks. 

   more » « less
3. Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds

   https://doi.org/10.1021/acs.jpcb.0c06480  

   Mass, Olga A. ; Wilson, Christopher K. ; Roy, Simon K. ; Barclay, Matthew S. ; Patten, Lance K. ; Terpetschnig, Ewald A. ; Lee, Jeunghoon ; Pensack, Ryan D. ; Yurke, Bernard ; Knowlton, William B. ( October 2020 , The Journal of Physical Chemistry B)

   Exciton delocalization plays a prominent role in the photophysics of molecular aggregates, ultimately governing their particular function or application. DNA is a compelling scaffold in which to template molecular aggregates and promote exciton delocalization. As individual dye molecules are the basis of exciton delocalization in molecular aggregates, their judicious selection is important. Motivated by their excellent photostability and spectral properties, here we examine the ability of squaraine dyes to undergo exciton delocalization when aggregated via a DNA Holliday junction (HJ) template. A commercially available indolenine squaraine dye was chosen for the study given its strong structural resemblance to Cy5, a commercially available cyanine dye previously shown to undergo exciton delocalization in DNA HJs. Three types of DNA-dye aggregate configurations—transverse dimer, adjacent dimer, and tetramer—were investigated. Signatures of exciton delocalization were observed in all squaraine-DNA aggregates. Specifically, strong blue shift and Davydov splitting were observed in steady-state absorption spectroscopy and exciton-induced features were evident in circular dichroism spectroscopy. Strongly suppressed fluorescence emission provided additional, indirect evidence for exciton delocalization in the DNA-templated squaraine dye aggregates. To quantitatively evaluate and directly compare the excitonic Coulombic coupling responsible for exciton delocalization, the strength of excitonic hopping interactions between the dyes were obtained by simultaneous fitting the experimental steady-state absorption and CD spectra via a Holstein-like Hamiltonian in which, following the theoretical approach of Kühn, Renger, and May, the dominant vibrational mode is explicitly considered. The excitonic hopping strength within indolenine squaraines was found to be comparable to that of the analogous Cy5 DNA-templated aggregate. The squaraine aggregates adopted primarily an H-type (dyes oriented parallel to each other) spatial arrangement. Extracted geometric details of dye mutual orientation in the aggregates enabled close comparison of aggregate configurations and the elucidation of the influence of dye angular relationship on excitonic hopping interactions in squaraine aggregates. These results encourage the application of squaraine-based aggregates in next generation systems driven by molecular excitons. 

   more » « less
4. Collision cross‐section analysis of self‐assembled metallomacrocycle isomers and isobars via ion mobility mass spectrometry

   https://doi.org/10.1002/rcm.8717  

   Endres, Kevin J. ; Barthelmes, Kevin ; Winter, Andreas ; Antolovich, Robert ; Schubert, Ulrich S. ; Wesdemiotis, Chrys ( February 2020 , Rapid Communications in Mass Spectrometry)

   Coordinatively driven self‐assembly of transition metal ions and bidentate ligands gives rise to organometallic complexes that usually contain superimposed isobars, isomers, and conformers. In this study, the double dispersion ability of ion mobility mass spectrometry (IM‐MS) was used to provide a comprehensive structural characterization of the self‐assembled supramolecular complexes by their mass and charge, revealed by the MS event, and their shape and collision cross‐section (Ω), revealed by the IM event.

   Self‐assembled complexes were synthesized by reacting a bis(terpyridine) ligand exhibiting a 60^odihedral angle between the two ligating terpyridine sites (T) with divalent Zn, Ni, Cd, or Fe. The products were isolated as (Metal²⁺[T])_n(PF₆)_2nsalts and analyzed using IM‐MS after electrospray ionization (ESI) which produced several charge states from eachn‐mer, depending on the number of PF₆ˉ anions lost upon ESI. Experimental Ω data, derived using IM‐MS, and computational Ω predictions were used to elucidate the size and architecture of the complexes.

   Only macrocyclic dimers, trimers, and tetramers were observed with Cd²⁺, whereas Zn²⁺formed the same plus hexameric complexes. These two metals led to the simplest product distributions and no linear isomers. In sharp contrast, Ni²⁺and Fe²⁺formed all possible ring sizes from dimer to hexamer as well as various linear isomers. The experimental and theoretical Ω data indicated rather planar macrocyclic geometries for the dimers and trimers, twisted 3D architectures for the larger rings, and substantially larger sizes with spiral conformation for the linear congeners. Adding PF₆ˉ to the same complex was found to mainly cause size contraction due to new stabilizing anion–cation interactions.

   Complete structural identification could be accomplished using ESI‐IM‐MS. Our results affirm that self‐assembly with Cd²⁺and Zn²⁺proceeds through reversible equilibria that generate the thermodynamically most stable structures, encompassing exclusively macrocyclic architectures that readily accommodate the 60^oligand used. In contrast, complexation with Ni²⁺and Fe²⁺, which form stronger coordinative bonds, proceeds through kinetic control, leading to more complex mixtures and kinetically trapped less stable architectures, such as macrocyclic pentamers and linear isomers.

    

   more » « less
5. In Situ Conformational Changes of the Escherichia coli Serine Chemoreceptor in Different Signaling States

   https://doi.org/10.1128/mBio.00973-19  

   Yang, Wen ; Cassidy, C. Keith ; Ames, Peter ; Diebolder, Christoph A. ; Schulten, Klaus ; Luthey-Schulten, Zaida ; Parkinson, John S. ; Briegel, Ariane ; Harwood, Caroline S. ( August 2019 , mBio)

   ABSTRACT Tsr, the serine chemoreceptor in Escherichia coli , transduces signals from a periplasmic ligand-binding site to its cytoplasmic tip, where it controls the activity of the CheA kinase. To function, Tsr forms trimers of homodimers (TODs), which associate in vivo with the CheA kinase and CheW coupling protein. Together, these proteins assemble into extended hexagonal arrays. Here, we use cryo-electron tomography and molecular dynamics simulation to study Tsr in the context of a near-native array, characterizing its signaling-related conformational changes at both the individual dimer and the trimer level. In particular, we show that individual Tsr dimers within a trimer exhibit asymmetric flexibilities that are a function of the signaling state, highlighting the effect of their different protein interactions at the receptor tips. We further reveal that the dimer compactness of the Tsr trimer changes between signaling states, transitioning at the glycine hinge from a compact conformation in the kinase-OFF state to an expanded conformation in the kinase-ON state. Hence, our results support a crucial role for the glycine hinge: to allow the receptor flexibility necessary to achieve different signaling states while also maintaining structural constraints imposed by the membrane and extended array architecture. IMPORTANCE In Escherichia coli , membrane-bound chemoreceptors, the histidine kinase CheA, and coupling protein CheW form highly ordered chemosensory arrays. In core signaling complexes, chemoreceptor trimers of dimers undergo conformational changes, induced by ligand binding and sensory adaptation, which regulate kinase activation. Here, we characterize by cryo-electron tomography the kinase-ON and kinase-OFF conformations of the E. coli serine receptor in its native array context. We found distinctive structural differences between the members of a receptor trimer, which contact different partners in the signaling unit, and structural differences between the ON and OFF signaling complexes. Our results provide new insights into the signaling mechanism of chemoreceptor arrays and suggest an important functional role for a previously postulated flexible region and glycine hinge in the receptor molecule. 

   more » « less