Coordinates in the $molecule section can be given either in Cartesian form or in Z-matrix form, as discussed below.
In either case, Q-Chem rotates the user-specified coordinates into the so-called standard nuclear orientation,
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defined as the principle axes of nuclear charge. This helps to make outputs more reproducible, because different
structure-building tools might provide coordinates in different orientations, and quadrature grids used in DFT and some other
types of calculations are not strictly rotationally invariant.
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Thus, two structures with identical internal coordinates but differing by a rigid rotation can give slightly different energies.
By rotating the user’s input into a standard orientation, identical structures prepared with different graphical user interfaces
should afford the same energy. Occassionally, however, one might want to use the absolute (laboratory-fixed) coordinate frame
that is defined by the coordinates provided in the $molecule section. This can be obtained by setting NO_REORIENT = TRUE
in the $rem section, which disables rotation into the standard orientation. The coordinate system that Q-Chem uses, whether it is
the standard one or the user’s, is printed in the Q-Chem output file immediately below where the input file is reproduced.
NO_REORIENT
NO_REORIENT
Disable rotation into the standard nuclear orientation.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
FALSE
Use the standard nuclear orientation.
TRUE
Use the coordinate system defined by the $molecule section.
RECOMMENDATION:
Use the default unless you have a reason to want a different coordinate system.
Q-Chem can accept a list of atoms and their Cartesian coordinates. The atoms can be entered either as atomic numbers or atomic symbols where each line corresponds to a single atom. The Q-Chem format for declaring a molecular geometry using Cartesian coordinates (in Ångstroms) is:
atom x-coordinate y-coordinate z-coordinate
Note: The geometry can by specified in bohr by setting the $rem variable INPUT_BOHR equal to TRUE.
Example 3.3.1 Atomic number Cartesian coordinate input for HO. The first line species the molecular charge and multiplicity, respectively.
$molecule 0 1 8 0.000000 0.000000 -0.212195 1 1.370265 0.000000 0.848778 1 -1.370265 0.000000 0.848778 $end
Example 3.3.2 Atomic symbol Cartesian coordinate input for HO.
$molecule 0 1 O 0.000000 0.000000 -0.212195 H 1.370265 0.000000 0.848778 H -1.370265 0.000000 0.848778 $end
Note: 1. Atoms can be declared by either atomic number or symbol. 2. Coordinates can be entered either as variables/parameters or real numbers. 3. Variables/parameters can be declared in any order. 4. A single blank line separates parameters from the atom declaration.
Once all the molecular Cartesian coordinates have been entered, terminate the molecular coordinate input with the $end keyword.
For small molecules, Z-matrix notation is a common input format. The Z-matrix defines the positions of atoms relative to previously defined atoms using a length, an angle and a dihedral angle. Again, note that all bond lengths and angles must be in Ångstroms and degrees, unless INPUT_BOHR is set to TRUE, in which case bond lengths are specified in bohr.
The first three atom entries of a Z-matrix are different from the subsequent entries. The first Z-matrix line declares a single atom. The second line of the Z-matrix input declares a second atom, refers to the first atom and gives the distance between them. The third line declares the third atom, refers to either the first or second atom, gives the distance between them, refers to the remaining atom and gives the angle between them. All subsequent entries begin with an atom declaration, a reference atom and a distance, a second reference atom and an angle, a third reference atom and a dihedral angle. This can be summarized as:
First atom.
Second atom, reference atom, distance.
Third atom, reference atom A, distance between A and the third atom, reference atom B, angle defined by atoms A, B and the third atom.
Fourth atom, reference atom A, distance, reference atom B, angle, reference atom C, dihedral angle (A, B, C and the fourth atom).
All subsequent atoms follow the same basic form as (4)
Example 3.3.3 Z-matrix input for hydrogen peroxide
O1 O2 O1 oo H1 O1 ho O2 hoo H2 O2 ho O1 hoo H1 hooh
Line 1 declares an oxygen atom (O1). Line 2 declares the second oxygen atom (O2), followed by a reference to the first atom (O1) and a distance between them denoted oo. Line 3 declares the first hydrogen atom (H1), indicates it is separated from the first oxygen atom (O1) by a distance HO and makes an angle with the second oxygen atom (O2) of hoo. Line 4 declares the fourth atom and the second hydrogen atom (H2), indicates it is separated from the second oxygen atom (O2) by a distance HO and makes an angle with the first oxygen atom (O1) of hoo and makes a dihedral angle with the first hydrogen atom (H1) of hooh.
Some further points to note are:
Atoms can be declared by either atomic number or symbol.
If declared by atomic number, connectivity needs to be indicated by Z-matrix line number.
If declared by atomic symbol either number similar atoms (e.g., H1, H2, O1, O2 etc.) and refer connectivity using this symbol, or indicate connectivity by the line number of the referred atom.
Bond lengths and angles can be entered either as variables/parameters or real numbers.
Variables/parameters can be declared in any order.
A single blank line separates parameters from the Z-matrix.
All the following examples are equivalent in the information forwarded to the Q-Chem program.
Example 3.3.4 Using parameters to define bond lengths and angles, and using numbered symbols to define atoms and indicate connectivity.
$molecule 0 1 O1 O2 O1 oo H1 O1 ho O2 hoo H2 O2 ho O1 hoo H1 hooh oo = 1.5 oh = 1.0 hoo = 120.0 hooh = 180.0 $end
Example 3.3.5 Not using parameters to define bond lengths and angles, and using numbered symbols to define atoms and indicate connectivity.
$molecule 0 1 O1 O2 O1 1.5 H1 O1 1.0 O2 120.0 H2 O2 1.0 O1 120.0 H1 180.0 $end
Example 3.3.6 Using parameters to define bond lengths and angles, and referring to atom connectivities by line number.
$molecule 0 1 8 8 1 oo 1 1 ho 2 hoo 1 2 ho 1 hoo 3 hooh oo = 1.5 oh = 1.0 hoo = 120.0 hooh = 180.0 $end
Example 3.3.7 Referring to atom connectivities by line number, and entering bond length and angles directly.
$molecule 0 1 8 8 1 1.5 1 1 1.0 2 120.0 1 2 1.0 1 120.0 3 180.0 $end
Obviously, a number of the formats outlined above are less appealing to the eye and more difficult for us to interpret than the others, but each communicates exactly the same Z-matrix to the Q-Chem program.
Dummy atoms are indicated by the identifier and followed, if necessary, by an integer. (e.g., , . Dummy atoms are often useful for molecules where symmetry axes and planes are not centered on a real atom, and have also been useful in the past for choosing variables for structure optimization and introducing symmetry constraints.
Note: Dummy atoms play no role in the quantum mechanical calculation, and are used merely for convenience in specifying other atomic positions or geometric variables.