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## ONIOMThis keyword requests a two- or three-layer ONIOM [153,154,155,156,157,158,159]. In this procedure, the molecular system being studied is divided into two or three layers which are treated with different model chemistries. The results are then automatically combined into the final predicted results. The layers are conventionally known as the Low, Medium and High layers. By default, atoms are placed into the High layer. (From a certain point of view, any conventional calculation can be viewed as a one-layer ONIOM.) Layer assignments are specified as part of the molecule specification (see below). For ONIOM(MO:MM) jobs, the ONIOM
optimization procedure is enhanced in ONIOM(MO:MM) calculations can take advantage of electronic embedding. Electronic embedding incorporates the partial charges of the MM region into the quantum mechanical Hamiltonian. This technique provides a better description of the electrostatic interaction between the QM and MM regions and allows the QM wavefunction to be polarized. ONIOM calculations can also use an external program for the calculations for one or more layers. See the ## REQUIRED INPUTThe two or three desired model chemistries
are specified as the options to the # ONIOM(HF/6-31G(d):AM1:UFF) Atom layer assignment is done as part of the molecule specification, via additional parameters on each line according to the following syntax:
where
The In
general, For a two-layer ONIOM, if only one parameter is specified, then both scale factors will use that value. For a three-layer ONIOM, if only one parameter is specified, then all three scale factors will use that value; if only two parameters are specified, then the third scale factor will use the second value. If a scale parameter is explicitly set to 0.0, then the program will determine the corresponding scale factor in the normal way. Thus, if you want to change only the second scale factor (model system calculated at the medium level), then you must explicitly set the first scale factor to 0.0. In this case, for a three-layer ONIOM, the third scale factor will have the same value as the second parameter unless it is explicitly assigned a non-zero value (i.e., in this second context, 0.0 has the same meaning as an omitted value). ## PER-LAYER CHARGE AND SPIN MULTIPLICITYMultiple charge and spin multiplicity pairs may also be specified for ONIOM calculations. For two-layer ONIOM jobs, the format for this input line is:
where the subscript indicates the
calculation for which the values will be used. The fourth pair applies only to
Values and defaults for three-layer ONIOM calculations follow
an analogous pattern (in the subscripts below, the first character is one of:
For 3-layer ONIOM=SValue calculations, up to three additional pairs may be specified: ... Defaults for missing charge/spin multiplicity pairs are taken from the next highest calculation level and/or system size. Thus, when only a subset of the six or nine pairs are specified, the charge and spin multiplicity items default according to the following scheme, where the number in each cell indicates which pair of values applies for that calculation in the corresponding :circumstances:
Specifies scaling
parameters for MM charges during electronic embedding in the QM calculations.
The integers are multiplied by 0.2 to obtain the actual scale factors. Atoms bonded
to the inner layers use a scale factor of 0.2
Energies,
gradients and frequencies. Note that if ONIOM can also perform
CIS and TD calculations for one or more layers. The NMR calculations may be performed with the ONIOM model.
# ONIOM(B3LYP/6-31G(d,p):AM1:UFF) Opt Test 3-layer ONIOM optimization 0 1 C O,1,B1 H,1,B2,2,A1 C,1,B3,2,A2,3,180.0,0 M H C,4,B4,1,A3,2,180.0,0 L H H,4,B5,1,A4,5,D1,0 M H,4,B5,1,A4,5,-D1,0 M H,5,B6,4,A5,1,180.0,0 L H,5,B7,4,A6,8,D2,0 L H,5,B7,4,A6,8,-D2,0 L
The High layer consists of the first three atoms
(placed there by default). The other atoms are explicitly placed into the Medium
and Low layers. Note that the Z-matrix specification Here is an input file for a two-layer ONIOM calculation using a DFT method for the high layer and Amber for the low layer. The molecule specification includes atom types (which are optional with UFF but required by Amber). Note that atom types are used for both the main atom specifications and the link atoms: # ONIOM(B3LYP/6-31G(d):Amber) Geom=Connectivity 2 layer ONIOM job 0 1 0 1 0 1 This input file was created by
# ONIOM(BLYP/6-31G(d)/Auto TD=(NStates=8):UFF) This example uses density fitting for the DFT high layer time-dependent excited states calculation.
C -1 0.0 0.0 0.0 H 0 0.0 0.0 0.9 For ONIOM jobs only, if the field is set to a negative value other than -1, it is treated as part of a rigid fragment during the optimization: all atoms with the same value (< -1) move only as a rigid block. Only MM atoms can be members of such rigid fragments.
S-Values (between gridpoints) and energies: high 4 -39.322207 7 -39.305712 9 -114.479426 -153.801632 -193.107344 med 2 -39.118688 5 -39.106289 8 -114.041481 -153.160170 -192.266459 low 1 -38.588420 3 -38.577651 6 -112.341899 -150.930320 -189.507971 model mid real The integers are the gridpoints, and under each one is the energy value. Horizontally between the grid points are the S-values. These are the S-values obtained with the absolute energies. However, be aware that when applying the S-value test, relative energies and S-values need to be used (see reference [160]). |