Structural Insight into Locked Nucleic Acid based Novel Antisense Modifications: A DFT calculations at monomer and MD simulations at oligomer level

Author(s):  
Mallikarjunachari V.N. Uppuladinne ◽  
Dikshita Dowerah ◽  
Uddhavesh B. Sonavane ◽  
Suvendra Kumar Ray ◽  
Ramesh C. Deka ◽  
...  
2019 ◽  
Vol 55 (84) ◽  
pp. 12635-12638 ◽  
Author(s):  
Carlos Bornes ◽  
Mariana Sardo ◽  
Zhi Lin ◽  
Jeffrey Amelse ◽  
Auguste Fernandes ◽  
...  

2D 1H–31P NMR and DFT calculations extend the understanding of TMPO:Brønsted complexes formed at HZSM-5 zeolite surfaces, providing structural insight into the proton-transfer mechanism.


2011 ◽  
Vol 1313 ◽  
Author(s):  
Ken Tasaki ◽  
Alexander Goldberg ◽  
Jian-Jie Liang ◽  
Martin Winter

ABSTRACTDensity functional theory (DFT) calculations and classical molecular dynamics (MD) simulations have been performed to gain insight into the difference in cycling behaviors between the ethylene carbonate (EC)-based and the propylene carbonate (PC)-based electrolytes in lithium-ion battery cells. DFT calculations for the ternary graphite intercalation compounds (Li+(S)iCn: S=EC or PC), in which the solvated lithium ion Li+(S)i (i=1~3) was inserted into a graphite cell, suggested that Li+(EC)iCn was more stable than Li+(PC)iCn in general. Furthermore, Li+(PC)3Cn was found to be energetically unfavorable, while Li+(PC)2Cn was stable, relative to their corresponding Li+(PC)i in the bulk electrolyte. The calculations also revealed severe structural distortions of the PC molecule in Li+(PC)3Cn, suggesting a rapid kinetic effect on PC decomposition reactions, as compared to decompositions of EC. In addition, MD simulations were carried out to examine the solvation structures at a high salt concentration: 2.45 mo kg-1. The results showed that the solvation structure was significantly interrupted by the counter anions, having a smaller solvation number than that at a lower salt concentration (0.83 mol kg-1). We propose that at high salt concentrations, the lithium desolvation may be facilitated due to the increased contact ion pairs, so that a stable ternary GIC with less solvent molecules can be formed without the destruction of graphite particles, followed by solid-electrolyte-interface film formation reactions. The results from both DFT calculations and MD simulations are consistent with the recent experimental observations.


2017 ◽  
Vol 19 (11) ◽  
pp. 7476-7480 ◽  
Author(s):  
Tian Sheng ◽  
Jin-Yu Ye ◽  
Wen-Feng Lin ◽  
Shi-Gang Sun

In this work, we have studied methanol oxidation mechanisms on RuO2(100) by using density functional theory (DFT) calculations and ab initio molecular dynamics (MD) simulations with some explicit interfacial water molecules.


2020 ◽  
Vol 21 (7) ◽  
pp. 2601 ◽  
Author(s):  
Shuang Zhao ◽  
Yan-Yan Zhu ◽  
Xiao-Yu Wang ◽  
Yong-Sheng Liu ◽  
Yun-Xiang Sun ◽  
...  

Sirtuin 6 (SIRT6) is an NAD+-dependent deacetylase with a significant role in 20% of all cancers, such as colon cancers and rectal adenocarcinoma. However, there is currently no effective drug for cancers related to SIRT6. To explore potential inhibitors of SIRT6, it is essential to reveal details of the interaction mechanisms between inhibitors and SIRT6 at the atomic level. The nature of small molecules from herbs have many advantages as inhibitors. Based on the conformational characteristics of the inhibitor Compound 9 (Asinex ID: BAS13555470), we explored the natural molecule Scutellarin, one compound of Huang Qin, which is an effective herb for curing cancer that has been described in the Traditional Chinese Medicine (TCMS) library. We investigated the interactions between SIRT6 and the inhibitors using molecular dynamics (MD) simulations. We illustrated that the structurally similar inhibitors have a similar binding mode to SIRT6 with residues—Leu9, Phe64, Val115, His133 and Trp188. Hydrophobic and π-stacking interactions play important roles in the interactions between SIRT6 and inhibitors. In summary, our results reveal the interactive mechanism of SIRT6 and the inhibitors and we also provide Scutellarin as a new potential inhibitor of SIRT6. Our study provides a new potential way to explore potential inhibitors from TCMS.


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>


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