Example: FDE NMR shielding: Acetonitrile in water

Download FDE_NMR_relax.run

This examples demonstrates both the calculation of NMR shieldings using FDE, and how the approximate environment density can be improved by partial relaxation of individual solvent molecules. The test system is a cluster of acetonitrile and 12 solvent water molecules, of which for two the densities are relaxed, while for the remaining 10 the frozen density of the isolated water is used. For details, see Refs. C. R. Jacob, J. Neugebauer, and L. Visscher, A flexible implementation of frozendensity embedding for use in multilevel simulation, submitted, 2007. R. E. Bulo, Ch. R. Jacob, and L. Visscher, NMR Solvent Shifts of Acetonitrile from Frozen-Density Embedding Calculation, to be submitted, 2007

First, the isolated solvent water molecule is prepared. Again, because this will be rotated and translated afterwards, the option NOSYMFIT has to be included.

$ADFBIN/adf << eor

UNITS
  Length Angstrom
  Angle Degree
END

ATOMS
     O       -1.46800        2.60500        1.37700
     H       -0.95200        3.29800        0.96500
     H       -1.16100        1.79900        0.96100
END

FRAGMENTS
  H        t21.H.DZP
  O        t21.O.DZP
END

XC
  LDA
END

NUMERICALQUALITY GOOD

end input
eor

mv TAPE21 t21.h2o

Afterwards, the FDE calculation is performed. In addition to the nonfrozen acetonitrile molecule, three different fragments are used for the solvent water molecules. The first two fragments frag1 and frag2 are relaxed (in up to two freeze-and-thaw cycles), while the third fragment is used for the remaining 10 solvent molecules. Since a calculation of the shielding is performed afterwards, the option has to be included.

...
$ADFBIN/adf << eor
Title Input generated by PyADF

UNITS
  Length Angstrom
  Angle Degree
END

ATOMS
     C        0.83000        0.66100       -0.44400
     N        0.00000        0.00000        0.00000
     C        1.87800        1.55900       -0.81900
     H        1.78500        2.40300       -0.13500
     H        1.76200        1.94900       -1.83000
     H        2.82900        1.12200       -0.51300
     O       -1.46800        2.60500        1.37700    f=frag1/1
     H       -0.95200        3.29800        0.96500    f=frag1/1
     H       -1.16100        1.79900        0.96100    f=frag1/1
     O        2.40400       -2.51000       -0.36200    f=frag2/1
     H        2.70000       -3.41900       -0.40900    f=frag2/1
     H        1.77500       -2.50000        0.35900    f=frag2/1
     O       -3.44400        2.36700        3.13700    f=frag3/10
     H       -2.70200        2.29200        2.53700    f=frag3/10
     H       -3.47300        3.29500        3.36800    f=frag3/10
END

FRAGMENTS
  H        t21.H.DZP
  C        t21.C.DZP
  N        t21.N.DZP
  frag1  t21.h2o   type=FDE &
    fdeoptions RELAX
    RELAXCYCLES 2
  SubEnd
  frag2  t21.h2o   type=FDE &
    fdeoptions RELAX
    RELAXCYCLES 2
  SubEnd
  frag3  t21.h2o   type=FDE &
    FDEDENSTYPE SCFexact
  SubEnd
END

XC
  GGA BP86
END

NUMERICALQUALITY GOOD

SAVE TAPE10

FDE
  PW91k
END

End Input
eor

Finally, the calculation of the NMR shielding of the nitrogen atom is performed using the NMR program.

$ADFBIN/adf << eor
NMR
 out tens iso
 nuc 3
END
eor