scholarly journals Probing calcium solvation by XAS, MD and DFT calculations

RSC Advances ◽  
2020 ◽  
Vol 10 (46) ◽  
pp. 27315-27321 ◽  
Author(s):  
Feipeng Yang ◽  
Yi-Sheng Liu ◽  
Xuefei Feng ◽  
Kun Qian ◽  
Li Cheng Kao ◽  
...  

The solvation shell structures of Ca2+ in solutions are probed by calcium L-edge soft X-ray XAS and DFT/MD simulations.

2012 ◽  
Vol 85 (1) ◽  
pp. 53-60 ◽  
Author(s):  
Thomas J. Penfold ◽  
Christopher J. Milne ◽  
Ivano Tavernelli ◽  
Majed Chergui

Static and time-resolved X-ray absorption spectroscopy (XAS) is used to probe the solvent shell structure around iodide and iodine. In particular, we characterize the changes observed upon electron abstraction of aqueous iodide, which reflects the transition from hydrophilic to hydrophobic solvation after impulsive electron abstraction from iodide. The static spectrum of aqueous iodide, which is analyzed using quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, indicates that the hydrogens of the closest water molecules point toward the iodide, as expected for hydrophilic solvation. In addition, these simulations demonstrate a small anisotropy in the solvent shell. Following electron abstraction, most of the water molecules move away from iodine, while one comes closer to form a complex with it that survives for 3–4 ps. This lifetime is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform a hydrogen bond network in the hydrophobic solvation shell.


2020 ◽  
Author(s):  
Rishikesh Kulkarni ◽  
Anneliese Gest ◽  
Chun Kei Lam ◽  
Benjamin Raliski ◽  
Feroz James ◽  
...  

<p>High signal-to-noise optical voltage indicators will enable simultaneous interrogation of membrane potential in large ensembles of neurons. However, design principles for voltage sensors with high sensitivity and brightness remain elusive, limiting the applicability of voltage imaging. In this paper, we use molecular dynamics (MD) simulations and density functional theory (DFT) calculations to guide the design of a bright and sensitive green-fluorescent voltage-sensitive fluorophore, or VoltageFluor (VF dye), that uses photoinduced electron transfer (PeT) as a voltage-sensing mechanism. MD simulations predict an 11% increase in sensitivity due to membrane orientation, while DFT calculations predict an increase in fluorescence quantum yield, but a decrease in sensitivity due to a decrease in rate of PeT. We confirm these predictions by synthesizing a new VF dye and demonstrating that it displays the expected improvements by doubling the brightness and retaining similar sensitivity to prior VF dyes. Combining theoretical predictions and experimental validation has resulted in the synthesis of the highest signal-to-noise green VF dye to date. We use this new voltage indicator to monitor the electrophysiological maturation of human embryonic stem cell-derived medium spiny neurons. </p>


2008 ◽  
Vol 73 (6-7) ◽  
pp. 786-794 ◽  
Author(s):  
B. Andes Hess ◽  
Lidia Smentek

A conformational analysis of squalene encapsulated in squalene-hopene cyclase has been performed based on Schulz's X-ray structure and our DFT calculations. Based on this analysis it is concluded that the formation of rings A-D in the cyclization of squalene are likely to be a concerted but highly asynchronous reaction.


2021 ◽  
Author(s):  
Anna Agnieszka Hoser ◽  
Marcin Sztylko ◽  
Damian Trzybiński ◽  
Anders Østergaard Madsen

A framework for estimation of thermodynamic properties for molecular crystals via refinement of frequencies from DFT calculations against X-ray diffraction data is presented. The framework provides an efficient approach to...


2019 ◽  
Vol 23 (11n12) ◽  
pp. 1346-1354 ◽  
Author(s):  
Danielle Laurencin ◽  
Pascal G. Yot ◽  
Christel Gervais ◽  
Yannick Guari ◽  
Sébastien Clément ◽  
...  

Porphyrin nanorods were prepared by ion-association between free-base meso 5,10,15,20-tetrakis-(4-[Formula: see text]-methylpyridinium)porphyrin cations and tetraphenylborate anions. The nanorods have variable lengths (up to a few micrometers long) and diameters ([Formula: see text]50–500 nm). Their structure at the molecular level was elucidated by combining multinuclear solid state NMR spectroscopy, synchrotron X-ray powder diffraction and DFT calculations.


2000 ◽  
Vol 19 (26) ◽  
pp. 5589-5596 ◽  
Author(s):  
Michael Bühl ◽  
Mikael Håkansson ◽  
Amir H. Mahmoudkhani ◽  
Lars Öhrström
Keyword(s):  

2010 ◽  
Vol 21 (4) ◽  
pp. 761-769 ◽  
Author(s):  
B. Machura ◽  
M. Wolff ◽  
A. Świtlicka ◽  
R. Kruszynski ◽  
J. Mroziński

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