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External atoms (microiterations)

External atoms (microiterations)

An input file for Si6(CH3)6 is:

# MIN/ONIOM(B3LYP/6-31G*:PM6)
 
0 1
Si         1.072140325305          0.674813020194          1.465051372146   H
Si         1.188721352253          1.229683160626         -0.824059022819   H
Si         1.509587113137         -1.078536796924         -0.229815920089   H
Si        -1.174684242151          0.850690516075         -1.073040898584   H
Si        -1.288038513039          0.174481898509          1.180210342195   H
Si        -0.818653679090         -1.559721151184         -0.409581739300   H
C          1.700304057386          0.106828207386          3.121071775695   L   H   1
C          2.425703517393          2.327128197190         -1.675580903631   L   H   2
C          2.729898977208         -2.289656339913         -0.939483735774   L   H   3
C         -2.759542422584          1.682302545898         -1.579248345281   L   H   4
C         -2.985434963817          0.584018968807          1.821088393244   L   H   5
C         -1.969202613400         -2.922018480012         -0.938716069552   L   H   6
External Atoms
H          2.588688501005         -0.491627141158          2.983143258707   L
H          1.936356529930          0.966483422949          3.730720970057   L
H          0.940610691963         -0.484199970248          3.610920408216   L
H          3.079066772767          1.724661829911         -2.289218200209   L
H          1.905728363057          3.041343609312         -2.296807257699   L
H          3.010542511047          2.852606585939         -0.935151422937   L
H          2.831448837713         -2.118222994635         -2.000944160633   L
H          3.688618120746         -2.157468019888         -0.460125985877   L
H          2.378191382490         -3.296531319323         -0.769470370638   L
H         -3.314406359626          1.029646307452         -2.236945727189   L
H         -3.350690803140          1.895542964114         -0.700913491119   L
H         -2.533778074969          2.604596207294         -2.093840282295   L
H         -3.705404475582         -0.099386423372          1.395646302768   L
H         -2.995464441613          0.493557287521          2.897246417748   L
H         -3.241021010195          1.595681760676          1.542495198587   L
H         -1.658756712062         -3.851812748123         -0.485388418720   L
H         -2.975066592717         -2.686272822946         -0.623975476951   L
H         -1.941853132974         -3.018957127817         -2.014009008016   L
Options
MicroIt = (MMOnly)
 

Atoms shown below the External Atoms keyword are optimized before every geometrical displacement of the other atoms (microiteration). In other words, optimization is made in a geometrical subspace in which δV/δQn = 0 for coordinates of external atoms Qn. This keyword is available not only with ONIOM but also with any single-layer calculations. In double-ended (2PSHS, SCW, and DS-AFIR) calculations, the External Atoms keyword is not required in the reactant (second) structure input.

When a molecular mechanics (MM) method (UFF, AMBER, or DREIDING) is used as one layer, the atom type and the MM charge should be given for all atoms; each coordinate line should be given as follows:

[atom]-[atom type]-[MM charge] [xyz] [ONIOM-layer] [link-atom]

In double-ended (2PSHS, SCW, and DS-AFIR) calculations, designations of the atom type, the MM charge, the ONIOM layer, and the link-atom are not required in the reactant (second) structure input.

Availability
Available external software
  • Gaussian 03/09/16
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Updated At:Feb. 13, 2018, 6:19 p.m.

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