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 3.5 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 Ångstroms and degrees, unless INPUT_BOHR is set to TRUE, in which case bond lengths are specified in bohr. The Z-matrix defines the positions of atoms relative to previously defined atoms using a length, an angle and a dihedral angle. 3.3.1.2 Z-matrix Coordinatesįor small molecules, Z-matrix notation is a common input format. Once all the molecular Cartesian coordinates have been entered, terminate the molecular coordinate input with the $end keyword. (4) A single blank line separates parameters from the atom declaration. (3) Variables/parameters can be declared in any order. (2) Coordinates can be entered either as variables/parameters or real numbers. Note: (1) Atoms can be declared by either atomic number or symbol. The first line species the molecular charge and multiplicity, respectively.Įxample 3.4 Atomic symbol Cartesian coordinate input for H O. Note: The geometry can by specified in bohr by setting the $rem variable INPUT_BOHR equal to TRUE.Įxample 3.3 Atomic number Cartesian coordinate input for H O. The Q-Chem format for declaring a molecular geometry using Cartesian coordinates (in Ångstroms) is:Ītom x-coordinate y-coordinate z-coordinate The atoms can be entered either as atomic numbers or atomic symbols where each line corresponds to a single atom. Q-Chem can accept a list of atoms and their Cartesian coordinates. 3.3.1 Specifying the Molecular Coordinates Manually 3.3.1.1 Cartesian Coordinates Note: Q-Chem ignores commas and equal signs, and requires all distances, positions and angles to be entered as Ångstroms and degrees unless the INPUT_BOHR $rem variable is set to TRUE, in which case all lengths are assumed to be in bohr. Note: SYM_IGNORE = TRUE will also turn off determining and using of the point group symmetry. This action can be turned off by using SYM_IGNORE TRUE. This is a standard feature of most quantum chemistry programs. ![]() Q-Chem begins all calculations by rotating and translating the user-defined molecular geometry into a Standard Nuclear Orientation whereby the center of nuclear charge is placed at the origin. See Appendix A which discusses the Optimize package in further detail. Note: The coordinate system used for declaring an initial molecular geometry by default does not affect that used in a geometry optimization procedure. Each subsequent line of the molecular coordinate input corresponds to a single atom in the molecule (or dummy atom), regardless of whether using Z-matrix internal coordinates or Cartesian coordinates. ![]() The multiplicity must be between 1 and 10, inclusive (1 for a singlet, 2 for a doublet, 3 for a triplet, etc.). The net charge must be between 50 and 50, inclusive (0 for neutral molecules, 1 for cations, 1 for anions, etc.). The molecular coordinates input begins with two integers: the net charge and the spin multiplicity of the molecule. The $molecule section communicates to the program the charge, spin multiplicity, and geometry of the molecule being considered. 3.3 Molecular Coordinate Input ( $molecule)
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