PMID- 37200472
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20230601
LR  - 20230601
IS  - 1520-5207 (Electronic)
IS  - 1520-5207 (Linking)
VI  - 127
IP  - 21
DP  - 2023 Jun 1
TI  - Automatic Multiscale Method of Building up a Cross-linked Polymer Reaction 
      System: Bridging SMILES to the Multiscale Molecular Dynamics Simulation.
PG  - 4905-4914
LID - 10.1021/acs.jpcb.3c01555 [doi]
AB  - An automatic method is introduced to generate the initial configuration and input 
      file from SMILES for multiscale molecular dynamics (MD) simulation of 
      cross-linked polymer reaction systems. Inputs are a modified version of SMILES of 
      all the components and conditions of coarse-grained (CG) and all-atom (AA) 
      simulations. The overall process comprises the following steps: (1) Modified 
      SMILES inputs of all the components are converted to 3-dimensional coordinates of 
      molecular structures. (2) Molecular structures are mapped to the coarse-grained 
      scale, followed by a CG reaction simulation. (3) CG beads are backmapped to the 
      atomic scale after the CG reaction. (4) An AA productive run is finally performed 
      to analyze volume shrinkage, glass transition, and atomic detail of network 
      structure. The method is applied to two common epoxy resin reactions, that is, 
      the cross-linking process of DGEVA (diglycidyl ether of vanillyl alcohol) and 
      DHAVA (dihydroxyaminopropane of vanillyl alcohol) and that of DGEBA (diglycidyl 
      ether of bisphenol A) and DETA (diethylenetriamine). These components form 
      network structures after the CG cross-linking reaction and are then backmapped to 
      calculate properties in the atomic scale. The result demonstrates that the method 
      can accurately predict volume shrinkage, glass transition, and all-atom structure 
      of cross-linked polymers. The method bridges from SMILES to MD simulation 
      trajectories in an automatic way, which shortens the time of building up 
      cross-linked polymer reaction model and suitable for high-throughput 
      computations.
FAU - Pei, Han-Wen
AU  - Pei HW
AUID- ORCID: 0000-0002-2743-8550
AD  - State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of 
      Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's 
      Republic of China.
AD  - School of Applied Chemistry and Engineering, University of Science and Technology 
      of China, Hefei 230026, People's Republic of China.
FAU - Zhu, You-Liang
AU  - Zhu YL
AUID- ORCID: 0000-0002-9561-0770
AD  - College of Chemistry, Jilin University, Changchun 130012, People's Republic of 
      China.
FAU - Lu, Zhong-Yuan
AU  - Lu ZY
AUID- ORCID: 0000-0001-7884-0091
AD  - College of Chemistry, Jilin University, Changchun 130012, People's Republic of 
      China.
FAU - Li, Jun-Peng
AU  - Li JP
AD  - State Key Laboratory of Advanced Technologies for Comprehensive Utilization of 
      Platinum Metals, Sino-Platinum Metals Company, Limited, Kunming 650106, People's 
      Republic of China.
FAU - Sun, Zhao-Yan
AU  - Sun ZY
AUID- ORCID: 0000-0002-6357-3039
AD  - State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of 
      Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's 
      Republic of China.
AD  - School of Applied Chemistry and Engineering, University of Science and Technology 
      of China, Hefei 230026, People's Republic of China.
LA  - eng
PT  - Journal Article
DEP - 20230518
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
SB  - IM
EDAT- 2023/05/18 19:12
MHDA- 2023/05/18 19:13
CRDT- 2023/05/18 14:23
PHST- 2023/05/18 19:13 [medline]
PHST- 2023/05/18 19:12 [pubmed]
PHST- 2023/05/18 14:23 [entrez]
AID - 10.1021/acs.jpcb.3c01555 [doi]
PST - ppublish
SO  - J Phys Chem B. 2023 Jun 1;127(21):4905-4914. doi: 10.1021/acs.jpcb.3c01555. Epub 
      2023 May 18.