scholarly journals Structural and dynamical heterogeneity of water trapped inside Na+-pumping KR2 rhodopsin in the dark state

2021 ◽  
Vol 154 (21) ◽  
pp. 215101
Author(s):  
Mantu Santra ◽  
Aniruddha Seal ◽  
Kankana Bhattacharjee ◽  
Suman Chakrabarty
Keyword(s):  
Dark State ◽  
Dynamical Heterogeneity

scholarly journals Structural and dynamical heterogeneity of water trapped inside Na+-pumping KR2 rhodopsin in the dark state

2020 ◽  
Author(s):  
Mantu Santra ◽  
Aniruddha Seal ◽  
Kankana Bhattacharjee ◽  
Suman Chakrabarty
Keyword(s):  
Md Simulations ◽  
Active Role ◽  
Water Molecules ◽  
Dark State ◽  
Dynamical Heterogeneity ◽  
Structure And Dynamics ◽  
Channel Opening ◽  
Conserved Water Molecules ◽  
Ion Proton ◽  
Ion Pumping

AbstractPhotoisomerisation in retinal leads to a channel opening in the rhodopsins that triggers translocation of an ion/proton. Crystal structures of rhodopsins contain several structurally conserved water molecules. It has been suggested that water plays an active role in facilitating the ion pumping/translocation process by acting as a lubricant in these systems. In this work, we investigate the localisation, local structure and dynamics of water molecules along the channel for the resting/dark state of KR2 rhodopsin. Employing 1.5 μs long atomistic molecular dynamics (MD) simulations of this trans-membrane protein system, we demonstrate the presence of five distinct water containing pockets/cavities separated by gateways controlled by the protein side-chains. We present evidence of significant structural and dynamical heterogeneity in the water molecules present in these cavities. The exchange time-scale of these buried water with bulk ranges from tens of nanoseconds to > 1.5 μs. The translational and rotational dynamics of buried water are found to be strongly dependent on protein cavity size and local interactions with possible functional significance.

Restriction of Access to Dark State: A New Mechanistic Model for Heteroatom-Containing AIE Systems

2019 ◽  
Author(s):  
Yujie Tu ◽  
Junkai Liu ◽  
Haoke Zhang ◽  
Qian Peng ◽  
Jacky W. Y. Lam ◽  
...  
Keyword(s):  
Excited States ◽  
Radiative Decay ◽  
Molecular Design ◽  
Mechanistic Model ◽  
Zinc Ion ◽  
Easy Access ◽  
Triplet States ◽  
Dark State ◽  
Ion Probe ◽  
Π State

Aggregation-induced emission (AIE) is an unusual photophysical phenomenon and provides an effective and advantageous strategy for the design of highly emissive materials in versatile applications such as sensing, imaging, and theragnosis. "Restriction of intramolecular motion" is the well-recognized working mechanism of AIE and have guided the molecular design of most AIE materials. However, it sometimes fails to be workable to some heteroatom-containing systems. Herein, in this work, we take more than one excited state into account and specify a mechanism –"restriction of access to dark state (RADS)" – to explain the AIE effect of heteroatom-containing molecules. An anthracene-based zinc ion probe named APA is chosen as the model compound, whose weak fluorescence in solution is ascribed to the easy access from the bright (π,π*) state to the closelying dark (n,π*) state caused by the strong vibronic coupling of the two excited states. By either metal complexation or aggregation, the dark state is less accessible due to the restriction of the molecular motion leading to the dark state and elevation of the dark state energy, thus the emission of the bright state is restored. RADS is found to be powerful in elucidating the photophysics of AIE materials with excited states which favor non-radiative decay, including overlap-forbidden states such as (n,π*) and CT states, spin-forbidden triplet states, which commonly exist in heteroatom-containing molecules.

scholarly journals Intermittent decoherence blockade in a chiral ring environment

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Salvatore Lorenzo ◽  
Stefano Longhi ◽  
Albert Cabot ◽  
Roberta Zambrini ◽  
Gian Luca Giorgi
Keyword(s):  
Intrinsic Property ◽  
Destructive Interference ◽  
Light Atom ◽  
General Belief ◽  
Dark State ◽  
The Past ◽  
Collective Interaction ◽  
Quantum Feedback ◽  
Chiral Ring ◽  
Dissipative Environment

AbstractIt has long been recognized that emission of radiation from atoms is not an intrinsic property of individual atoms themselves, but it is largely affected by the characteristics of the photonic environment and by the collective interaction among the atoms. A general belief is that preventing full decay and/or decoherence requires the existence of dark states, i.e., dressed light-atom states that do not decay despite the dissipative environment. Here, we show that, contrary to such a common wisdom, decoherence suppression can be intermittently achieved on a limited time scale, without the need for any dark state, when the atom is coupled to a chiral ring environment, leading to a highly non-exponential staircase decay. This effect, that we refer to as intermittent decoherence blockade, arises from periodic destructive interference between light emitted in the present and light emitted in the past, i.e., from delayed coherent quantum feedback.

Film compensation to improve the dark state in the oblique directions of the horizontal-switching mode

2012 ◽  
Vol 39 (6) ◽  
pp. 675-681 ◽  
Author(s):  
Young Jin Lim ◽  
Bong Choon Kim ◽  
Yu Jin Choi ◽  
Seung Hee Lee ◽  
Wan-Seok Kang ◽  
...  
Keyword(s):  
Dark State ◽  
Switching Mode

scholarly journals Ultrafast excited state dynamics and light-switching of [Ru(phen)2(dppz)]2+ in G-quadruplex DNA

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Chunfan Yang ◽  
Qian Zhou ◽  
Zeqing Jiao ◽  
Hongmei Zhao ◽  
Chun-Hua Huang ◽  
...  
Keyword(s):  
Excited State ◽  
State Formation ◽  
Rational Design ◽  
Bound Water ◽  
Binding Modes ◽  
Relaxation Dynamics ◽  
Dark State ◽  
Excited State Dynamics ◽  
G Quadruplex ◽  
Mechanistic Basis

AbstractThe triplet metal to ligand charge transfer (3MLCT) luminescence of ruthenium (II) polypyridyl complexes offers attractive imaging properties, specifically towards the development of sensitive and structure-specific DNA probes. However, rapidly-deactivating dark state formation may compete with 3MLCT luminescence depending on different DNA structures. In this work, by combining femtosecond and nanosecond pump-probe spectroscopy, the 3MLCT relaxation dynamics of [Ru(phen)2(dppz)]2+ (phen = 1,10-phenanthroline, dppz = dipyridophenazine) in two iconic G-quadruplexes has been scrutinized. The binding modes of stacking of dppz ligand on the terminal G-quartet fully and partially are clearly identified based on the biexponential decay dynamics of the 3MLCT luminescence at 620 nm. Interestingly, the inhibited dark state channel in ds-DNA is open in G-quadruplex, featuring an ultrafast picosecond depopulation process from 3MLCT to a dark state. The dark state formation rates are found to be sensitive to the content of water molecules in local G-quadruplex structures, indicating different patterns of bound water. The unique excited state dynamics of [Ru(phen)2(dppz)]2+ in G-quadruplex is deciphered, providing mechanistic basis for the rational design of photoactive ruthenium metal complexes in biological applications.

DNA-Stabilized Silver Nanoclusters with High Yield of Dark State

2013 ◽  
Vol 117 (45) ◽  
pp. 24079-24083 ◽  
Author(s):  
Ivan L. Volkov ◽  
Pavel Yu. Serdobintsev ◽  
Alexei I. Kononov
Keyword(s):  
Silver Nanoclusters ◽  
High Yield ◽  
Dark State
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