Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation
Abstract
:1. Introduction
2. Results
3. Discussion
4. Materials and Methods
5. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Bond | Kr (kcal(mol∙Å2)−1 | req (Å) |
h1–ob | 546.139 | 0.970 |
ob–B | 350.221 | 1.372 |
ob–c3 | 219.866 | 1.435 |
Angle | Kθ (kcal/(mol∙radian2) | θeq (°) |
h1–ob–B | 50.184 | 110.55 |
ob–B –ob | 104.357 | 120.00 |
B –ob–c3 | 110.735 | 121.35 |
ob–c3–c3 | 114.01 | 111.44 |
ob–c3–h1 | 77.700 | 107.94 |
Dihedral | Divider | Vn (kcal/mol) | γ | n | |
---|---|---|---|---|---|
h1–ob–B –ob | 1 | 2.350 | 0.000 | −1.000 | |
h1–ob–B –ob | 1 | 1.654 | 0.000 | 2.000 | |
ob–B –ob–c3 | 1 | 1.980 | 180.000 | −1.000 | |
ob–B –ob–c3 | 1 | 1.472 | 180.000 | 2.000 | |
B –ob–c3–c3 | 2 | 5.400 | 180.000 | 2.000 | same as GAFF X –c–os–X [2] |
B –ob–c3–h1 | 1 | 5.400 | 180.000 | 2.000 | same as GAFF X –c–os–X [2] |
ob–c3–c3–h1 | 1 | 0.300 | 180.000 | 2.000 | same as GAFF X –c–c–X [2] |
Improper | Vn (kcal/mol) | γ | n |
---|---|---|---|
ob–ob–B–ob | 40.5 | 180.0 | 2.0 |
Molecule | RMSD-AD | RMSD-L | RMSD-A |
---|---|---|---|
IVEKAW02 | 0.206 | 0.0468 | 2.179 (1.442) |
TEAMBO04 | 0.212 | 0.0765 | 5.976 (3.381) |
Average | 0.209 | 0.06165 | 4.077 (2.411) |
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Kurt, B.; Temel, H. Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation. Molecules 2020, 25, 2196. https://doi.org/10.3390/molecules25092196
Kurt B, Temel H. Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation. Molecules. 2020; 25(9):2196. https://doi.org/10.3390/molecules25092196
Chicago/Turabian StyleKurt, Barış, and Hamdi Temel. 2020. "Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation" Molecules 25, no. 9: 2196. https://doi.org/10.3390/molecules25092196