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
APA StyleKurt, B., & Temel, H. (2020). Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation. Molecules, 25(9), 2196. https://doi.org/10.3390/molecules25092196