Package name: 3-nitrooxypropyl nitrate

Package ID: 209
Force-field: OPLS-AA | Code: Gromacs
Created by Bogdan Iorga (biorga)
Created at 2016-09-03 23:03:55
Modified at 2016-09-03 23:03:55

Abstract

The topology was generated using MOL2FF, with user-defined charges. These charges were obtained using the protocol P3 from Beckstein et al. (J Comput Aided Mol Des, 2014, 28, 265-276): geometry optimization and CHelpG charges calculation using Gaussian03 (http://www.gaussian.com) at the HF/6-31G* level, then a two-stage RESP fitting using AmberTools (http://ambermd.org).

Chemical structure

General view

Detailed view

References

Authors: Beckstein O, Fourrier A, Iorga BI
Title: Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field.
Journal: J Comput Aided Mol Des
Year: 2014 Mar
Volume: 28
Pages: 265-76
DOI: 10.1007/s10822-014-9727-1
Pubmed ID:   24557853
Comments:

Reference validation values

These are experimental values or high-level quantum mechanics values, which will be used for comparison with computed values (found in individual versions).

Files and history

All deposited versions are available and can be downloaded individually. Higher version numbers are more recent. Files that changed between versions can be identified by differing SHA1 hash checksums.

Version 1 created at 2016-09-03

Score 1/5 "These parameters are not validated yet"

Computed validation values

grompp
preprocessor output "grompp-compatible"
Created at 2016-09-03 23:03:55 | Modified at 2016-09-03 23:03:55 | [download zip]
Type Description Hash (SHA1)
Topology SAMPL4_027_3.itp bf4ee3af109777bf777c5efbbc68359f6305f79f
Structure SAMPL4_027_3.pdb bd9bc32dda6e8ab93826230e28de7e9853ba009f

Compound details

Ligand code UNL
Molecule identifier E9D7926D319A526B
Displayed name 3-nitrooxypropyl nitrate
Canonical IUPAC name 3-nitrooxypropyl nitrate
Formula C3H6N2O6
Molecular weight 166.09
Charge 0
Number of atoms 17
SMILES C(O[N](=O)=O)CCO[N](=O)=O
PubChem CID 96257
CAS RN
Other names 3-nitrooxypropyl nitrate • nitric acid 3-nitrooxypropyl ester • 3457-90-7 • 1,3-Propanediol dinitrate • 1,3-Propanediol, dinitrate • 1,3-Propylene glycol dinitrate • NSC62613 • Trimethylene dinitrate • Trimethylene nitrate • 1,3-Propanediol, dinitrate (8CI)(9CI) • NSC 62613

License

Type CC BY-SA – Creative Commons Attribution-Share Alike License
Name Bogdan I. Iorga
Email (hidden)
Source MOL2FF (http://mol2ff.icsn.cnrs-gif.fr)