Your molecule in one of BOSS’s organic solvents, ready to run in BOSS, GROMACS, OpenMM or LAMMPS.
Powered by BOSS — the group's Monte Carlo engine does the work behind this form.
Much of chemistry does not happen in water. A reaction in methanol, a compound in chloroform or DMSO — to simulate any of these, a program needs the molecule surrounded by the right solvent, in a box relaxed to the liquid’s real density.
Organic Solvents does it in one step. Give it a molecule — as a SMILES string, a drawing, a name or a structure file — and choose a solvent. The solvents are the ones stored in BOSS, the group’s simulation engine: the published united-atom OPLS models, used exactly as BOSS uses them. Each comes as a box of 512 solvent molecules, made the way BOSS 5.1 makes them, from its stored box of 512 argon atoms. BOSS places your molecule in the box, removes the solvent molecules in its way and relaxes everything by Monte Carlo at 1 atm.
You get the box for BOSS, GROMACS, OpenMM and LAMMPS, and its density, compared with experiment.
| Solvent | Formula | Density, g/cm³ (25 °C) BOSS · experiment | Often used for |
|---|---|---|---|
| Methanol | CH3OH | 0.761 · 0.787 | Polar, protic solvent; reactions, crystallization |
| Acetonitrile | CH3CN | 0.758 · 0.777 | Polar, aprotic; chromatography, electrochemistry |
| Chloroform | CHCl3 | 1.474 · 1.479 | Extraction, NMR, natural products |
| Dichloromethane | CH2Cl2 | 1.310 · 1.317 | Organic synthesis, extraction |
| Carbon tetrachloride | CCl4 | 1.570 · 1.584 | A non-polar reference solvent |
| DMSO | (CH3)2SO | 1.109 · 1.095 | Compound libraries, assays, polar aprotic reactions |
| THF | C4H8O | 0.883 · 0.883 | Organic synthesis, organometallics |
BOSS’s stored solvents are united-atom models (CH3, CH2 and CH groups are one site each) with the parameters in BOSS’s oplsaa.par, and the molecules are rigid. BOSS densities: the pure 512-molecule box at 25 °C and 1 atm. Experimental densities from the CRC Handbook of Chemistry and Physics.
| BOSS Quick Start | TIP3P, TIP4P & TIP5P | Organic Solvents this page | LigParGen | |
|---|---|---|---|---|
| It answers | What shape does my molecule take, and how does it behave in water? | How do I get my molecule into a box of water, ready to simulate? | How do I get my molecule into an organic solvent? | What numbers does my MD program need for this molecule? |
| You get | The most stable shape, hydration free energy, dipole, surface area | Your molecule in thousands of water molecules, with ions, relaxed by BOSS | Your molecule in 512 solvent molecules, relaxed by BOSS | Force-field parameters |
| Files for | Docking, quantum chemistry, viewing | GROMACS, OpenMM, LAMMPS, AMBER, BOSS — ready to run | BOSS, GROMACS, OpenMM, LAMMPS — ready to run | GROMACS, OpenMM, CHARMM and 7 more |
| Solvent | Continuum water (GB/SA) | Real water molecules | Seven organic solvents | None |
| Time | Seconds to a few minutes | A few minutes | A few minutes | A few seconds |
Find your molecule’s best shape with BOSS Quick Start → put it in water on TIP3P, TIP4P & TIP5P, or in another solvent here — or take only its force field from LigParGen.
Final Monte Carlo configuration — your molecule in color, the solvent as thin lines. Drag to rotate, scroll to zoom.
calculations run since launch
Calculations that finished on this page since it went live, counted by country. Each run is recorded only with its date, country and whether it worked.
The solvent: the model’s own paper, which the files name — for example chloroform: Jorgensen, W. L.; Briggs, J. M.; Contreras, M. L. J. Phys. Chem. 1990, 94, 1683–1686.
BOSS: Jorgensen, W. L.; Tirado-Rives, J. J. Comput. Chem. 2005, 26, 1689–1700. doi:10.1002/jcc.20297
OPLS-AA: Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225–11236. doi:10.1021/ja9621760
1.14*CM1A-LBCC charges: Dodda, L. S.; Vilseck, J. Z.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2017, 121, 3864–3870. doi:10.1021/acs.jpcb.7b00272