Copper complex parametrization

Empirical Force Fields for Biologically Active Divalent Metal Cations in Water
C. Satheesan Babu, and Carmay Lim
J. Phys. Chem. A 2006, 110, 691-699

Informações:
Raio de van der Waals para o Cu2+
Este método não descreve a distorção Jahn Teller,  o efeito do elétron desemparelhado do cobre alargando as distâncias axiais ou equatoriais.

vdW parameters for Cu2+

             e        Rmin/2      deldelG         CN     Cu-O
         (kcal/mol)  (angstron)  (kcal/mol)       #   (angstron)
Model A 0.0734   0.8685   -13.3 (-0.1)  6    1.90
Model B 0.1305   1.0763   -13.5 (-0.3)  6    2.03
Model C 0.0427   1.0330   -59.9 (+1.0)  6    1.94

Qual usar? Seria melhor utilizar o modelo que descreve melhor os parâmetros estruturais:
A escolha foi a do modelo C.

Preciso fazer a conversão para o vdW do Cu2+?? Já que este é para o sistema Cu-H2O?????

Observe que no arquivo parmtop uso o Rmin/2 como está listado na tabela acima


Discussion about CuH2O structural geometry
from J. Phys. Chem. A, Vol. 114, No. 35, 2010
Development and Validation of a ReaxFF Reactive Force Field for Cu Cation/Water

Interactions and Copper Metal/Metal Oxide/Metal Hydroxide Condensed Phases

For a long time, it was generally accepted that the copper(II) ion is 6-fold coordinated in aqueous solution with a tetragonally distorted octahedral structure, as would be predicted from the Jahn-Teller effect for a d9 electronic configuration. 

This was challenged in 2001 by Pasquarello et al. who proposed a 5-fold coordination based on first-principles MD and neutron diffraction.[10] Their simulation indicated frequent exchanges of square pyramidal and trigonal bipyramidal clusters with five equal Cu-O distances. One year later Persson et al. performed extensive EXAFS and large angle X-ray
scattering (LAXS) experiments and again suggested that the ion was 6-fold coordinated.[14] They modeled the copper-water cluster using several different geometrical configurations and showed that a tetragonally distorted octahedron gave the best fit to the experimental data. In 2003, a quantum-mechanical/molecularmechanical (QM/MM) study by Schwenk et al. also indicated a 6-fold coordination with Jahn-Teller distortion.[12,13] However, another Car-Parrinello molecular dynamics (CPMD) simulation performed by Amira et al.[4] and analysis of the XANES portion of the XAS spectra by Benfatto et al.[15] and Frank et al.[16] suggested that the hydrated copper(II) ion can be better represented as a five-coordinate square pyramidal structure with one elongated axial water molecule.

More recently, Chaboy et al. performed XANES and EXAFS spectroscopy of copper ion hydration [17,18] and argued that “neither the classical Jahn-Teller geometry nor other six- or fivefold coordinated geometries may be proposed unambiguously as the single preferred structure in solution”.[18] According to them, a dynamic view of different geometries exchanging with each other is the right description of copper ion hydration. A review of the structural parameters of Cu2+ aqueous complexes is referenced.[19]

 MASS 
> CU 63.55 
> 
> BOND 
> nb-CU 75.582 2.027 
> o-CU 84.879 1.907 
> 
> ANGLE 
> ha-ca-nb 52.970 116.000 same as ha-ca-n2 
> ca-nb-CU 50.523 114.913 from g09 calculations 
> 
> DIHE 
> ca-nb-cp-ca 1 4.800 180.000 2.000 
> ca-nb-cp-cp 1 4.800 180.000 2.000 
> nb-CU-nb-cp 1 14.800 180.000 2.000 
> 
> IMPROPER 
> o- o-CU-nb 1.1 180.0 2.0 
> 
> NONBON 
> CU 1.0330 0.0427 LJ parms from 
> http://dx.doi.org/10.1021/jp054177x