![]() ![]() However, there are still no consistent one-size-fits-all standard for structural enumeration. Robust and exhaustive processes to generate chemical structures have been described previously in different contexts, ,, ,, ,. 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.Initial structures (Z-matrix or Cartesian coordinate) are important starting points for the in silico investigation of chemical species. ![]() 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. 3.5.1 Dummy Atomsĭummy atoms are indicated by the identifier and followed, if necessary, by an integer. 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. Variables/parameters can be declared in any order.Ī single blank line separates parameters from the Z-matrix.Īll the following examples are equivalent in the information forwarded to the Q-Chem program.Įxample 3.9 Using parameters to define bond lengths and angles, and using numbered symbols to define atoms and indicate connectivity.Įxample 3.10 Not using parameters to define bond lengths and angles, and using numbered symbols to define atoms and indicate connectivity.Įxample 3.11 Using parameters to define bond lengths and angles, and referring to atom connectivities by line number.Įxample 3.12 Referring to atom connectivities by line number, and entering bond length and angles directly. 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.īond lengths and angles can be entered either as variables/parameters or real numbers. If declared by atomic number, connectivity needs to be indicated by Z-matrix line number. 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.Ītoms can be declared by either atomic number or symbol. 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 2 declares the second oxygen atom (O2), followed by a reference to the first atom (O1) and a distance between them denoted oo. 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.įourth atom, reference atom A, distance, reference atom B, angle, reference atom C, dihedral angle (A, B, C and the fourth atom).Īll subsequent atoms follow the same basic form as (4)Įxample 3.8 Z-matrix for hydrogen peroxide ![]() 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. 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. The second line of the Z-matrix input declares a second atom, refers to the first atom and gives the distance between them. The first Z-matrix line declares a single atom. The first three atom entries of a Z-matrix are different from the subsequent entries. Note: As with the Cartesian coordinate input method, Q-Chem begins a calculation by taking the user-defined coordinates and translating and rotating them into a Standard Nuclear Orientation. Again, note that all bond lengths and angles must be in Angstroms and degrees. The Z-matrix defines the positions of atoms relative to previously defined atoms using a length, an angle and a dihedral angle. Z-matrix notation is one of the most common molecular coordinate input forms. ![]()
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