Active Site Representation in First-Principles Microkinetic Models: Data-Enhanced Computational Screening for Improved Methanation Catalysts

ACS Catalysis ◽  
2020 ◽  
Vol 10 (22) ◽  
pp. 13729-13736
Author(s):  
Martin Deimel ◽  
Karsten Reuter ◽  
Mie Andersen
Keyword(s):  
Active Site ◽  
First Principles ◽  
Computational Screening

scholarly journals Computational screening of phosphite derivatives as high-performance additives in high-voltage Li-ion batteries

RSC Advances ◽  
2017 ◽  
Vol 7 (32) ◽  
pp. 20049-20056 ◽  
Author(s):  
Young-Kyu Han ◽  
Jaeik Yoo ◽  
Taeeun Yim
Keyword(s):  
High Voltage ◽  
First Principles ◽  
High Performance ◽  
First Principles Calculations ◽  
Li Ion Batteries ◽  
Computational Screening ◽  
Screening Protocol ◽  
Li Ion ◽  
Performance Additives ◽  
Additive Materials

We presented a computational screening protocol for the efficient development of cathode-electrolyte interphase (CEI)-forming additive materialsviathe first-principles calculations.

scholarly journals Computational Screening of Natural Compounds for the Discovery of Potential Aromatase Inhibitors: A Promising Therapy for Estrogen-Dependent Breast Cancer

2021 ◽  
pp. 72-78
Author(s):  
Misbahuddin M. Rafeeq ◽  
Ziaullah M. Sain ◽  
Norah A. Alturki ◽  
Ahmad Alzamami ◽  
Saeed A. Asiri ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Aromatase Inhibitors ◽  
Active Site ◽  
Natural Compounds ◽  
Computational Screening ◽  
Zinc Database ◽  
Hands On ◽  
Estrogen Receptor Positive ◽  
Er Positive ◽  
Control Compound

Aromatase plays a significant role in the progression of estrogen receptor-positive (ER-positive) breast cancer. The adverse side effects of currently used aromatase inhibitors (AIs) necessitate the development of new AIs that are more active, selective, and less toxic. This study used a computational approach to screen 503 natural compounds ZINC database against the aromatase active site. The best scoring hits ZINC69482055, ZINC69482510, and ZINC406719 exhibited strong binding with aromatase, with binding energy values of -8.45, -10.35, and -8.75 kcal/mol, respectively, which is comparatively higher than that of the control compound Anastrozole (-6.43 kcal/mol). Docking analysis showed that the selected hits interacted with the crucial residues of the aromatase active site. This study suggested that these compounds could be used as possible AIs in the cure of breast cancer. Hands-on bench work validation is needed to optimize these compounds as AIs.

Computational screening and first-principles investigations of NASICON-type LixM2(PO4)3 as solid electrolytes for Li batteries

2018 ◽  
Vol 6 (6) ◽  
pp. 2625-2631 ◽  
Author(s):  
Xudong Zhao ◽  
Zihe Zhang ◽  
Xu Zhang ◽  
Bin Tang ◽  
Zhaojun Xie ◽  
...  
Keyword(s):  
First Principles ◽  
Solid Electrolytes ◽  
Computational Screening ◽  
Nasicon Type ◽  
Li Batteries

Li-containing NASICONs were screened from the Materials Project database and seven kinds of LixM2(PO4)3 are proposed as solid electrolytes for Li batteries.

scholarly journals Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257206
Author(s):  
R. V. Sriram Uday ◽  
Rajdip Misra ◽  
Annaram Harika ◽  
Sandip Dolui ◽  
Achintya Saha ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Active Site ◽  
Protein Conformation ◽  
Hydrophobic Interactions ◽  
Experimental Studies ◽  
Allosteric Site ◽  
Hydrogen Bond Formation ◽  
Computational Screening ◽  
Π Stacking ◽  
Ns3 Protease

Dengue virus (DENV) encodes a unique protease (NS3/NS2B) essential for its maturation and infectivity and, it has become a key target for anti-viral drug design to treat dengue and other flavivirus related infections. Present investigation established that some of the drug molecules currently used mainly in cancer treatment are susceptible to bind non-active site (allosteric site/ cavity) of the NS3 protease enzyme of dengue virus. Computational screening and molecular docking analysis found that dabrafenib, idelalisib and nintedanib can bind at the allosteric site of the enzyme. The binding of the molecules to the allosteric site found to be stabilized via pi-cation and hydrophobic interactions, hydrogen-bond formation and π-stacking interaction with the molecules. Several interacting residues of the enzyme were common in all the five serotypes. However, the interaction/stabilizing forces were not uniformly distributed; the π-stacking was dominated with DENV3 proteases, whereas, a charged/ionic interaction was the major force behind interaction with DENV2 type proteases. In the allosteric cavity of protease from DENV1, the residues Lys73, Lys74, Thr118, Glu120, Val123, Asn152 and Ala164 were involved in active interaction with the three molecules (dabrafenib, idelalisib and nintedanib). Molecular dynamics (MD) analysis further revealed that the molecules on binding to NS3 protease caused significant changes in structural fluctuation and gained enhanced stability. Most importantly, the binding of the molecules effectively perturbed the protein conformation. These changes in the protein conformation and dynamics could generate allosteric modulation and thus may attenuate/alter the NS3 protease functionality and mobility at the active site. Experimental studies may strengthen the notion whether the binding reduce/enhance the catalytic activity of the enzyme, however, it is beyond the scope of this study.

First-principles design of bifunctional oxygen reduction and evolution catalysts through bimetallic centers in metal–organic frameworks

2018 ◽  
Vol 8 (14) ◽  
pp. 3666-3674 ◽  
Author(s):  
Peng Zhang ◽  
Xuejing Yang ◽  
Wang Gao ◽  
Xiuli Hou ◽  
Jianli Mi ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Oxygen Reduction ◽  
Active Site ◽  
First Principles ◽  
Metal Organic Frameworks ◽  
Metal Organic

Bi-metallic FexCo3−x(THT)2 nanosheets exhibit bifunctional catalytic activity for both the ORR and OER. The ORR occurs on the Co atom, while the active site for the OER is the Fe atom.

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