The role of metals in amyloid aggregation—Experiments and ab initio simulations

2008 ◽  
Vol 108 (11) ◽  
pp. 1992-2015 ◽  
Author(s):  
V. Minicozzi ◽  
S. Morante ◽  
G. C. Rossi ◽  
F. Stellato ◽  
N. Christian ◽  
...  
Keyword(s):  
Ab Initio ◽  
Amyloid Aggregation ◽  
Ab Initio Simulations

The role of Zn 2+ dopants in the acid-basic catalysis on MgO(001) surface: Ab initio simulations of the dissociative chemisorption of R-O-R′ and R-S-R′ (R,R′=H, CH 3 , C 2 H 5 )

2017 ◽  
Vol 661 ◽  
pp. 60-68 ◽  
Author(s):  
Carla G. Fonseca ◽  
Sérgio R. Tavares ◽  
Carla V. Soares ◽  
Bruno G. daFonseca ◽  
Fábio J.F.S. Henrique ◽  
...  
Keyword(s):  
Ab Initio ◽  
Dissociative Chemisorption ◽  
Basic Catalysis ◽  
Ab Initio Simulations ◽  
Role Of Zn

The ro^le of Metals in Amyloid Aggregation: A Test Case for ab initio Simulations

2007 ◽  
Author(s):  
V. Minicozzi ◽  
S. Morante ◽  
G. C. Rossi ◽  
F. Stellato ◽  
Theodore E. Simos ◽  
...  
Keyword(s):  
Ab Initio ◽  
Test Case ◽  
Amyloid Aggregation ◽  
Ab Initio Simulations

scholarly journals Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations

Life ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 46
Author(s):  
Juan Francisco Carrascoza Mayén ◽  
Jakub Rydzewski ◽  
Natalia Szostak ◽  
Jacek Blazewicz ◽  
Wieslaw Nowak
Keyword(s):  
Ab Initio ◽  
Elevated Temperatures ◽  
Distribution Functions ◽  
Complex Molecules ◽  
Ab Initio Simulations ◽  
Dynamics Simulations ◽  
New Compounds ◽  
Formation Efficiency ◽  
The Impact

The catalytic effects of complex minerals or meteorites are often mentioned as important factors for the origins of life. To assess the possible role of nanoconfinement within a catalyst consisting of montmorillonite (MMT) and the impact of local electric field on the formation efficiency of the simple hypothetical precursors of nucleic acid bases or amino acids, we performed ab initio Car–Parrinello molecular dynamics simulations. We prepared four condensed-phase systems corresponding to previously suggested prototypes of a primordial soup. We monitored possible chemical reactions occurring within gas-like bulk and MMT-confined four simulation boxes on a 20-ps time scale at 1 atm and 300 K, 400 K, and 600 K. Elevated temperatures did not affect the reactivity of the elementary components of the gas-like boxes considerably; however, the presence of the MMT nanoclay substantially increased the formation probability of new molecules. Approximately 20 different new compounds were found in boxes containing carbon monoxide or formaldehyde molecules. This observation and an analysis of the atom–atom radial distribution functions indicated that the presence of Ca2+ ions at the surface of the internal MMT cavities may be an important factor in the initial steps of the formation of complex molecules at the early stages of the Earth’s history.

Role of the Structural Characteristics of Dendrimers in the Manifestation of the Antiamyloid Properties

INEOS OPEN ◽  
2020 ◽  
Vol 3 ◽  
Author(s):  
S. A. Sorokina ◽  
◽  
Yu. Yu. Stroilova ◽  
V. I. Muronets ◽  
Z. B. Shifrina ◽  
...  
Keyword(s):  
Neurodegenerative Diseases ◽  
Structural Characteristics ◽  
Short Review ◽  
External Factors ◽  
Amyloid Aggregation ◽  
Amyloid Proteins ◽  
Molecular Parameters ◽  
Amyloid Aggregates ◽  
Aggregation Processes

Among the compounds able to efficiently inhibit the amyloid aggregation of proteins and decompose the amyloid aggregates that cause neurodegenerative diseases, of particular interest are dendrimers, which represent individual macromolecules with the hypercrosslinked architectures and given molecular parameters. This short review outlines the peculiarities of the antiamyloid activity of dendrimers and discusses the effect of dendrimer structures and external factors on their antiamyloid properties. The potential of application of dendrimers in further investigations on the aggregation processes of amyloid proteins as the compounds that exhibit the remarkable antiamyloid activity is evaluated.

Quantum Mechanical Interpretation of the Ultra-Low Energy Methyl-Rotation Dynamics in Porous Metal-Organic Frameworks Probed by Low-Frequency Vibrational Spectroscopy and ab initio Simulations

2018 ◽  
Author(s):  
Qi Li ◽  
Adam J. Zaczek ◽  
Timothy M. Korter ◽  
J. Axel Zeitler ◽  
Michael T. Ruggiero
Keyword(s):  
Ab Initio ◽  
Metal Organic Frameworks ◽  
Low Frequency ◽  
Rotor Dynamics ◽  
Quantum Mechanical ◽  
Valuable Insight ◽  
Void Space ◽  
Ab Initio Simulations ◽  
Metal Organic ◽  
Insight Into

<div>Understanding the nature of the interatomic interactions present within the pores of metal-organic frameworks</div><div>is critical in order to design and utilize advanced materials</div><div>with desirable applications. In ZIF-8 and its cobalt analogue</div><div>ZIF-67, the imidazolate methyl-groups, which point directly</div><div>into the void space, have been shown to freely rotate - even</div><div>down to cryogenic temperatures. Using a combination of ex-</div><div>perimental terahertz time-domain spectroscopy, low-frequency</div><div>Raman spectroscopy, and state-of-the-art ab initio simulations,</div><div>the methyl-rotor dynamics in ZIF-8 and ZIF-67 are fully charac-</div><div>terized within the context of a quantum-mechanical hindered-</div><div>rotor model. The results lend insight into the fundamental</div><div>origins of the experimentally observed methyl-rotor dynamics,</div><div>and provide valuable insight into the nature of the weak inter-</div><div>actions present within this important class of materials.</div>

The role of density reduction in lithiated amorphous silicon: Molecular dynamics and ab-initio studies

2021 ◽  
Author(s):  
Jay Krishan Dora ◽  
Charchit Saraswat ◽  
Ashish Gour ◽  
Sudipto Ghosh ◽  
Natraj Yedla ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Amorphous Silicon ◽  
Density Reduction
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