Example: FDE NMR shielding: Acetonitrile in water¶
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