Formation of Carbohydrate–Metal Adducts from Solvent Mixtures during Electrospray: A Molecular Dynamics and ESI-MS Study

2021 ◽  
Author(s):  
Emvia I. Calixte ◽  
O. Tara Liyanage ◽  
Darren T. Gass ◽  
Elyssia S. Gallagher
Keyword(s):  
Molecular Dynamics ◽  
Solvent Mixtures ◽  
Esi Ms ◽  
Metal Adducts

Molecular Dynamics Study of Polysaccharides in Binary Solvent Mixtures of an Ionic Liquid and Water

2011 ◽  
Vol 115 (34) ◽  
pp. 10251-10258 ◽  
Author(s):  
Hanbin Liu ◽  
Kenneth L. Sale ◽  
Blake A. Simmons ◽  
Seema Singh
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Binary Solvent ◽  
Solvent Mixtures ◽  
Binary Solvent Mixtures

scholarly journals Fast Predictions of Liquid-Phase Acid-Catalyzed Reaction Rates Using Molecular Dynamics Simulations and Convolutional Neural Networks

2020 ◽  
Author(s):  
Alex Chew ◽  
Shengli Jiang ◽  
Weiqi Zhang ◽  
Victor Zavala ◽  
Reid Van Lehn
Keyword(s):  
Neural Networks ◽  
Molecular Dynamics ◽  
Liquid Phase ◽  
Molecular Dynamics Simulations ◽  
Convolutional Neural Networks ◽  
Reaction Rates ◽  
Solvent Mixtures ◽  
Acid Catalyzed ◽  
Solvent Systems ◽  
Dynamics Simulations

The rates of liquid-phase, acid-catalyzed reactions relevant to the upgrading of biomass into high-value chemicals are highly sensitive to solvent composition and identifying suitable solvent mixtures is theoretically and experimentally challenging. We show that the atomistic configurations of reactant-solvent environments generated by classical molecular dynamics simulations can be exploited by 3D convolutional neural networks to enable fast predictions of Brønsted acid-catalyzed reaction rates for model biomass compounds. We develop a computational implementation, which we call SolventNet, and train it using experimental reaction data for seven biomass-derived oxygenates in water-cosolvent mixtures. We show that SolventNet can predict reaction rates for additional reactants and solvent systems an order of magnitude faster than prior simulation methods. This combination of machine learning with molecular dynamics enables the rapid screening of solvent systems and identification of improved biomass conversion conditions.

Molecular dynamics of β-CD in water/co-solvent mixtures

2011 ◽  
Vol 70 (3-4) ◽  
pp. 279-290 ◽  
Author(s):  
Kanokthip Srisuk Boonyarattanakalin ◽  
Peter Wolschann ◽  
Luckhana Lawtrakul
Keyword(s):  
Molecular Dynamics ◽  
Solvent Mixtures

scholarly journals Stability and Mobility of Lid Lipmnk in Acetonitrile by Molecular Dynamics Simulations Approach

2018 ◽  
Vol 15 (2) ◽  
pp. 295-299
Author(s):  
Dian Herasari ◽  
Rukman Hertadi ◽  
Fida M. Warganegara ◽  
Akhmaloka Akhmaloka
Keyword(s):  
Molecular Dynamics ◽  
Conformational Dynamics ◽  
Solvent Polarity ◽  
Thermophilic Bacterium ◽  
Solvent Mixtures ◽  
The Stability ◽  
Dynamics Simulations ◽  
Opening And Closing ◽  
Acetonitrile Concentration ◽  
Detailed Molecular Analysis

Manuk lipase (lipMNK) from the thermophilic bacterium Geobacillus sp is a double lid lipase containing short and long lid segments. A few studies demonstrated that catalytic action of lipase involved the movement of lid segments from closed to open conformation upon the substrate binding. One factor that affects conformational dynamics of the lid segments is solvent polarity. The presence of acetonitrile in certain concentration has showed to enhance lipase activity. In this study, the effect of acetonitrile to the stability and activity of lipMNK was studied at the atomic level by molecular dynamics (MD) simulation. MD was carried out by NPT ensemble at 358 K for 100 nano seconds in various ratio of acetonitrile:water solvent mixtures. The results showed that the conformation of lipMNK was stable up to 70%. However, the effect of lid movement was significantly observed since the concentration at 20% acetonitrile. Detailed molecular analysis at this acetonitrile concentration revealed that the two lids moved in different modes upon opening and closing movement. In the opening movement, the two lids appeared to move in almost simultaneously, while during the closing movement, it was observed sequentially, started by short segment followed by long segment lid.

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