[2000.6]
M. Baaden, F. Berny, G. Wipff and C. Madic
J. Phys. Chem. A 2000,104,7659
A molecular dynamics
and quantum mechanics study of M3+ lanthanide cation solvation by
acetonitrile: the role of cation size, counterions and
polarization effects investigated.
[2001.2]
M. Baaden, M. Burgard, C. Boehme and G. Wipff
Phys. Chem. Chem. Phys. 2001 ,3,
1317
Lanthanide cation
binding to a phosphoryl-calix{4}arene: the importance of solvent
and counterions investigated by molecular dynamics and quantum
mechanical simulations
[2001.3]
M. Baaden, M. Burgard, and G. Wipff
J. Phys. Chem. B 2001,105, 11131
TBP at the water - oil
interface: the effect of TBP concentration and water acidity
investigated by molecular dynamics simulations
Amber parameters and input files
================================
Marc Baaden
1. Prep files
=============
1.1. Ions
---------
Filename PDBS Comment
...................... ....................... ......................
H3O.bin H3O+.pdb Hydronium (+1)
Eu3+.bin EU3+.pdb Europium (3+)
Yb3+.bin YB3+.pdb Ytterbium (3+)
La3+.bin La3+.pdb Lanthanum (3+)
NO3.bin NO3-.pdb Nitrate (-)
PCL.bin PCL-.pdb Perchlorate (-)
TFL.bin TFL-.pdb Triflate (-)
1.2. Organic Molecules
----------------------
Filename PDBS Comment
...................... ....................... ......................
ACN.bin HNO3.pdb Nitric acid
CA1.bin TETA.pdb Scaffold for
calixarenes
CON.bin DPDA.pdb,DPPM.pdb Calix-cone part
DPP.bin DPDA.pdb,DPPM.pdb diphenylphosphineoxide
arm
TBU.bin DPDA.pdb,DPPM.pdb tert-butyl-unit
AMI.bin TETA.pdb,DPDA.pdb Amide moiety for
calixarenes
PHO.bin 1tbp.pdb Neutral PO from TBP
POP.bin tbph+.pdb Protonated POH from
TBPH+ (+1)
OBU.bin 1tbp.pdb,tbph+.pdb O-butyl moiety of TBP
2. PDB files
============
2.1. Ions
---------
Filename residues reference charge description
............. ............. ............. ............. .............
H3O+.pdb H3O [2001.3] +1 Hydronium ion
EU3+.pdb M [2000.6] +3 Europium
YB3+.pdb M [2000.6] +3 Ytterbium
NO3-.pdb NO3 [2001.3] -1 Nitrate
PCL-.pdb PCL [2000.6] -1 Perchlorate
TFL-.pdb TFL [2000.6] -1 Triflate
2.2. Organic Molecules
----------------------
Filename residues reference charge description
............. ............. ............. ............. .............
HNO3.pdb ACN [2001.3] 0 Nitric acid
1tbp.pdb PHO, OBU [2001.3] 0 tri-n-butyl-phosphate
tbph+.pdb POP, OBU [2001.3] +1 tri-n-butyl-phosphate
DPPM.pdb CON, DPP, TBU [2000.4][2001.2] 0 tetraphosphineoxide
calix[4]
DPDA.pdb CON, DPP, TBU [2000.4] 0 di-phosphineoxide-diamide
calix[4]
3. Errata
=========
In [2001.3] there is an error concerning the TBP and TBPH+ charges.
The Second CT in OS-CT-CT-.. has to bear a +0.06 charge and not a
-0.06 one.
In [2000.4] there are two errors concerning the charges. One for the
amide fragment, where the alpha amide carbon is not charged -0.323 but
+0.323. One for the phosphine-oxide, where the bottom HA is indicated
as 0.0122 and should be 0.122 (these have been corrected in the
downloadable files here).