scholarly journals Dynamic molecular ordering in multiphasic nanoconfined ionogels detected with time-resolved diffusion NMR

2022 ◽  
Author(s):  
Marina Karagianni ◽  
Lydia Gkoura ◽  
Nikolaos Tsolakis ◽  
Georgios Romanos ◽  
Savvas Orfanidis ◽  
...  
Keyword(s):  
Molecular Motion ◽  
Silica Matrix ◽  
Ab Initio Molecular Dynamics ◽  
Microscopic Mechanism ◽  
Time Resolved ◽  
Diffusion Nmr ◽  
Single File ◽  
Molecular Ordering ◽  
A Chain ◽  
Dynamics Simulations

Abstract Molecular motion in nanosized channels can be highly complicated. For example, water molecules in hydrophobic nanopores move rapidly and coherently in a chain, following the so-called single file motion. Surprisingly, fast molecular motion is also observed in viscous charged fluids, such as room temperature ionic liquids (RTILs) confined in a nanoporous carbon or silica matrix. The microscopic mechanism of this intriguing effect is still unclear. Here, by combining NMR diffusion experiments in different relaxation windows with ab-initio molecular dynamics simulations, we show that the imidazolium-based RTIL [BMIM]+[TCM]-, entrapped in the MCM-41 silica nanopores, exhibits a complex dynamic molecular ordering (DMO); adsorbed RTIL molecules near the pore walls orient almost vertically to the walls, while at the center of the pores anion-cation pairs diffuse collectively in a single file (SFD). Enlightening this extraordinary effect is of primary importance in designing RTIL-based composite materials with tuned electrochemical properties.

scholarly journals Hydroxide Ion Carrier for Proton Pump in Bacteriorhodopsin: Primary Proton Transfer

2019 ◽  
Author(s):  
M. Imai ◽  
J. Ono ◽  
Y. Nishimura ◽  
H. Nakai
Keyword(s):  
Proton Transfer ◽  
Energy Conversion ◽  
Quantum Mechanical ◽  
Primary Proton ◽  
Proton Pumps ◽  
Microscopic Mechanism ◽  
Hydroxide Ion ◽  
Time Resolved ◽  
Internal Water ◽  
Dynamics Simulations

ABSTRACTBacteriorhodopsin (BR) is a model protein for light-driven proton pumps, where the vectorial active proton transport results in light-energy conversion. To clarify the microscopic mechanism of primary proton transfer from retinal Schiff base (SB) to Asp85 in BR, herein we performed quantum-mechanical metadynamics simulations of the whole BR system (∼3800 atoms). The simulations showed a novel proton transfer mechanism, viz. hydroxide ion mechanism, in which the deprotonation of specific internal water (Wat452) yields the protonation of Asp85 via Thr89, after which the resulting hydroxide ion accepts the remaining proton from retinal SB. Furthermore, systematic investigations adopting four sequential snapshots obtained by the time-resolved serial femtosecond crystallography revealed that proton transfer took 2–5.25 μs on the photocycle. The presence of Wat401, which is the main difference between snapshots at 2 and 5.25 μs, is found to be essential in assisting the primary proton transfer.SIGNIFICANCEBacteriorhodopsin (BR), the benchmark of light-driven proton pumps, has attracted much attention from diverse areas in terms of energy conversion. Despite the significant experimental and theoretical efforts, the microscopic mechanism of the proton transfers in BR is not completely unveiled. In this study, quantum-mechanical molecular dynamics simulations of whole BR system were performed to elucidate the primary proton transfer in the L intermediate state with the latest snapshots obtained from X-ray free electron laser. As a result, it is found that the hydroxide ion originating from the specific internal water, which appears at the active site only in the L state, acts as a carrier for the primary proton transfer, demonstrating the importance of hydroxide ions in proton pumps.

scholarly journals Real-time observation of photoionization-induced water migration dynamics in 4-methylformanilide–water by picosecond time-resolved infrared spectroscopy and ab initio molecular dynamics simulations

2021 ◽  
Author(s):  
Mitsuhiko Miyazaki ◽  
Tairiku Kamiya ◽  
Matthias Wohlgemuth ◽  
KUNTAL CHATTERJEE ◽  
Roland Mitrić ◽  
...  
Keyword(s):  
Ab Initio Molecular Dynamics ◽  
Time Resolved ◽  
Pump Probe ◽  
Energy Domain ◽  
Migration Dynamics ◽  
Time Observation ◽  
Dynamics Simulations ◽  
Time Resolved Infrared Spectroscopy ◽  
Time And Energy ◽  
Real Time Observation

A novel time-resolved pump-probe spectroscopic approach that enables to keep high resolution in both the time and energy domain, nanosecond excitation-picosecond ionization-picosecond infrared probe (ns-ps-ps TRIR) spectroscopy, has been applied...

Time-Resolved Cryo-Electron Microscopy of Oscillating Microtubules

1990 ◽  
Vol 48 (1) ◽  
pp. 502-503
Author(s):  
Eva-Maria Mandelkow ◽  
Ron Milligan
Keyword(s):  
Electron Microscopy ◽  
Dynamic Instability ◽  
Entire Solution ◽  
Reaction Scheme ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
A Chain ◽  
Ray Scattering

Microtubules form part of the cytoskeleton of eukaryotic cells. They are hollow libers of about 25 nm diameter made up of 13 protofilaments, each of which consists of a chain of heterodimers of α-and β-tubulin. Microtubules can be assembled in vitro at 37°C in the presence of GTP which is hydrolyzed during the reaction, and they are disassembled at 4°C. In contrast to most other polymers microtubules show the behavior of “dynamic instability”, i.e. they can switch between phases of growth and phases of shrinkage, even at an overall steady state [1]. In certain conditions an entire solution can be synchronized, leading to autonomous oscillations in the degree of assembly which can be observed by X-ray scattering (Fig. 1), light scattering, or electron microscopy [2-5]. In addition such solutions are capable of generating spontaneous spatial patterns [6].In an earlier study we have analyzed the structure of microtubules and their cold-induced disassembly by cryo-EM [7]. One result was that disassembly takes place by loss of protofilament fragments (tubulin oligomers) which fray apart at the microtubule ends. We also looked at microtubule oscillations by time-resolved X-ray scattering and proposed a reaction scheme [4] which involves a cyclic interconversion of tubulin, microtubules, and oligomers (Fig. 2). The present study was undertaken to answer two questions: (a) What is the nature of the oscillations as seen by time-resolved cryo-EM? (b) Do microtubules disassemble by fraying protofilament fragments during oscillations at 37°C?

Structural dynamics of P-type ATPase ion pumps

2019 ◽  
Vol 47 (5) ◽  
pp. 1247-1257 ◽  
Author(s):  
Mateusz Dyla ◽  
Sara Basse Hansen ◽  
Poul Nissen ◽  
Magnus Kjaergaard
Keyword(s):  
Structural Dynamics ◽  
Single Molecule ◽  
New Technologies ◽  
Atp Hydrolysis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Time Resolved ◽  
Dynamics Simulations ◽  
Types Of Information ◽  
P Type

Abstract P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.

Visualization and Manipulation of Molecular Motion in Solid State through Photo-Induced Clusteroluminescence

2019 ◽  
Author(s):  
Haoke Zhang ◽  
Lili Du ◽  
Lin Wang ◽  
Junkai Liu ◽  
Qing Wan ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Excited State ◽  
Solid State ◽  
Light Source ◽  
Molecular Motion ◽  
Molecular Machine ◽  
Conjugated Molecules ◽  
Time Resolved ◽  
Packing Structure ◽  
New Strategy

<p>Building molecular machine has long been a dream of scientists as it is expected to revolutionize many aspects of technology and medicine. Implementing the solid-state molecular motion is the prerequisite for a practical molecular machine. However, few works on solid-state molecular motion have been reported and it is almost impossible to “see” the motion even if it happens. Here the light-driven molecular motion in solid state is discovered in two non-conjugated molecules <i>s</i>-DPE and <i>s</i>-DPE-TM, resulting in the formation of excited-state though-space complex (ESTSC). Meanwhile, the newly formed ESTSC generates an abnormal visible emission which is termed as clusteroluminescence. Notably, the original packing structure can recover from ESTSC when the light source is removed. These processes have been confirmed by time-resolved spectroscopy and quantum mechanics calculation. This work provides a new strategy to manipulate and “see” solid-state molecular motion and gains new insights into the mechanistic picture of clusteroluminescence.<br></p>

scholarly journals A diffusion anisotropy descriptor links morphology effects of H-ZSM-5 zeolites to their catalytic cracking performance

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xiaoliang Liu ◽  
Jing Shi ◽  
Guang Yang ◽  
Jian Zhou ◽  
Chuanming Wang ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Catalytic Cracking ◽  
Catalytic Performance ◽  
Zeolite Catalysts ◽  
Time Resolved ◽  
Cracking Performance ◽  
Morphology Effect ◽  
Ft Ir ◽  
The Difference ◽  
Dynamics Simulations

AbstractZeolite morphology is crucial in determining their catalytic activity, selectivity and stability, but quantitative descriptors of such a morphology effect are challenging to define. Here we introduce a descriptor that accounts for the morphology effect in the catalytic performances of H-ZSM-5 zeolite for C4 olefin catalytic cracking. A series of H-ZSM-5 zeolites with similar sheet-like morphology but different c-axis lengths were synthesized. We found that the catalytic activity and stability is improved in samples with longer c-axis. Combining time-resolved in-situ FT-IR spectroscopy with molecular dynamics simulations, we show that the difference in catalytic performance can be attributed to the anisotropy of the intracrystalline diffusive propensity of the olefins in different channels. Our descriptor offers mechanistic insight for the design of highly effective zeolite catalysts for olefin cracking.

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