scholarly journals Effects of charge states, charge sites and side chain interactions on conformational preferences of a series of model peptide ions

The Analyst ◽  
2015 ◽  
Vol 140 (20) ◽  
pp. 6933-6944 ◽  
Author(s):  
Chunying Xiao ◽  
Lisa M. Pérez ◽  
David H. Russell
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Gas Phase ◽  
Dynamics Simulation ◽  
Side Chain ◽  
Peptide Ions ◽  
Conformational Preference ◽  
Model Peptide ◽  
Factors Affecting ◽  
Conformational Preferences

The factors affecting conformational preference of gas phase peptide ions are investigated by IM-MS and molecular dynamics simulation.

Conformations of 2,4-Diphenylpentane:  A Quantum Chemistry and Gas-Phase Molecular Dynamics Simulation Study

1998 ◽  
Vol 102 (24) ◽  
pp. 4694-4702 ◽  
Author(s):  
Grant D. Smith ◽  
Chakravarthy Ayyagari ◽  
Richard L. Jaffe ◽  
Matthew Pekny ◽  
Aaron Bernarbo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Quantum Chemistry ◽  
Gas Phase ◽  
Simulation Study ◽  
Dynamics Simulation

Gas-Phase Structure of the Histone Multimers Characterized by Ion Mobility Mass Spectrometry and Molecular Dynamics Simulation

2013 ◽  
Vol 85 (8) ◽  
pp. 4165-4171 ◽  
Author(s):  
Kazumi Saikusa ◽  
Sotaro Fuchigami ◽  
Kyohei Takahashi ◽  
Yuuki Asano ◽  
Aritaka Nagadoi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Gas Phase ◽  
Ion Mobility ◽  
Phase Structure ◽  
Dynamics Simulation ◽  
Ion Mobility Mass Spectrometry ◽  
Gas Phase Structure

Molecular Dynamics Simulation Study on Diamond Tool Wear in Cutting Aluminum-Based Workpieces

2013 ◽  
Vol 579-580 ◽  
pp. 211-215
Author(s):  
Guo Jun Dong ◽  
Yuan Jing Zhang ◽  
Ming Zhou
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Tool Wear ◽  
Simulation Study ◽  
Diamond Tool ◽  
Cutting Speed ◽  
Dynamics Simulation ◽  
Cutting Depth ◽  
Factors Affecting ◽  
Definite Effect

The problem of diamond tool wear is the bottleneck for machining large metal reflector with ultraprecision cutting method. In this paper, the author performed simulation study on diamond tool wear in machining large metal reflectors, and established a molecular dynamics simulation model for dynamic simulation of tool wear; and found that in the simulation process the change in cutting speed and cutting depth had definite effect on the tool wear, and the main factors affecting the tool wear was the cutting distance.

Molecular dynamics simulation study of xyloglucan adsorption on cellulose surfaces: effects of surface hydrophobicity and side-chain variation

Cellulose ◽  
2013 ◽  
Vol 21 (2) ◽  
pp. 1025-1039 ◽  
Author(s):  
Zhen Zhao ◽  
Vincent H. Crespi ◽  
James D. Kubicki ◽  
Daniel J. Cosgrove ◽  
Linghao Zhong
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Surface Hydrophobicity ◽  
Dynamics Simulation ◽  
Side Chain

scholarly journals The study on polycarboxylate superplasticizer with polyamine side chain using molecular dynamics simulation

2021 ◽  
Vol 2133 (1) ◽  
pp. 012013
Author(s):  
Xiaochen Lin ◽  
Pohsiang Chuang ◽  
Yunhui Fang
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Linear Structure ◽  
Reducing Agent ◽  
Dynamics Simulation ◽  
Side Chain ◽  
Water Molecules ◽  
Migration Ability ◽  
New Type

Abstract A new type of water-reducing agent, which contains polyamine side chains, has been theoretically studied utilizing molecular dynamics simulation (MD) in this research. The models of three types of water reducers in an aqueous solution, including SNF, PCE, and PCA, have been constructed, simulated, and analyzed. The results indicate that compared to the linear structure of SNF, the traditional PCE water-reducing agent has a stronger interaction with water molecules, so it has a better water-reducing effect. This stronger interaction is mainly provided by the side chain of PCE. PCA further enhances the hydrophilicity of its side chain based on PCE structure, leading to a stronger interaction on water molecules than traditional PCE molecules. The migration ability of water-reducing agents and other molecules in the system has been further explored. The diffusion coefficient of three water reducer molecules decreases in the following order: PCE>SNF>PCA. This is due to the interaction between molecules, especially the incompatible strength and quantity of hydrogen bonding.

Conformational Preference of Two Toad Poison Bufadienolides, Cinobufagin and Bufotalin

1998 ◽  
Vol 63 (10) ◽  
pp. 1663-1670 ◽  
Author(s):  
Yoshiaki Kamano ◽  
Ayano Kotake ◽  
Toshihiko Nogawa ◽  
Hirohumi Hashima ◽  
Machiko Tozawa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Low Temperatures ◽  
Dynamics Simulation ◽  
Conformational Preference ◽  
Solution State ◽  
Chromatographic Methods ◽  
Toad Poison

The solution state conformations of pyran-2-one ring (E ring) of two toad poison bufadienolides, cinobufagin and bufotalin, were analyzed by using NOE experiments at low temperatures and molecular dynamics simulation study. The rotation of E ring of the two bufadienolides, was found to be affected by the 14β,15β-epoxy and 16β-acetoxy groups and to be restricted at low temperatures. In the experimental, cinobufagin and bufotalin were isolated from Ch'an Su by the new chromatographic methods using the hydrophobic gel sephadex LH-20 and HP-cellulofine as carriers.

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