Constrained optimization refers to the optimization of molecular structures (transition state or minimumenergy) in which certain parameters such as bond lengths, bond angles or dihedral angles are fixed. Jon Baker’s Optimize package, implemented in QChem, makes it possible to handle constraints directly in delocalized internal coordinates using the method of Lagrange multipliers (see Appendix A). Features of constrained optimization in QChem are:
Starting geometries need not satisfy the requested constraints.
Constrained optimization is performed in delocalized internal coordinates, which is typically the most efficient coordinate system for optimization of large molecules.
QChem’s freeformat $opt section allows the user to apply constraints with ease.
Constraints are imposed via the $opt input section, whose format is shown below, and the various parts of this input section are described below.
Note: As with the rest of the QChem input file, the $opt section is caseinsensitive, but there should be no blank space at the beginning of a line.
$opt CONSTRAINT stre atom1 atom2 value ... bend atom1 atom2 atom3 value ... outp atom1 atom2 atom3 atom4 value ... tors atom1 atom2 atom3 atom4 value ... linc atom1 atom2 atom3 atom4 value ... linp atom1 atom2 atom3 atom4 value ... ENDCONSTRAINT FIXED atom coordinate_reference ... ENDFIXED DUMMY idum type list_length defining_list ... ENDDUMMY CONNECT atom list_length list ... ENDCONNECT $end
CONSTRAINT and ENDCONSTRAINT define the beginning and end, respectively, of the constraint section of $opt within which users may specify up to six different types of constraints:
interatomic distances
Values in Ångstroms; value :
stre atom1 atom2 value
angles
Values in degrees, ; atom2 is the middle atom of the bend:
bend atom1 atom2 atom3 value
outofplanebends
Values in degrees, atom2; angle between atom4 and the atom1–atom2–atom3 plane:
outp atom1 atom2 atom3 atom4 value
dihedral angles
Values in degrees, ; angle the plane atom1–atom2–atom3 makes with the plane atom2–atom3–atom4:
tors atom1 atom2 atom3 atom4 value
coplanar bends
Values in degrees, ; bending of atom1–atom2–atom3 in the plane atom2–atom3–atom4:
linc atom1 atom2 atom3 atom4 value
perpendicular bends
Values in degrees, ; bending of atom1–atom2–atom3 perpendicular to the plane atom2–atom3–atom4:
linp atom1 atom2 atom3 atom4 value
Absolute atom positions can be frozen with the FIXED section. The section starts with the FIXED keyword as the first line and ends with the ENDFIXED keyword on the last. The format to fix a coordinate or coordinates of an atom is:
atom coordinate_reference
coordinate_reference can be any combination of up to three characters , and to specify the coordinate(s) to be fixed: , , , XY, XZ, YZ, XYZ. The fixing characters must be next to each other. e.g.,
FIXED 2 XY ENDFIXED
means the coordinate and coordinate of atom 2 are fixed, whereas
FIXED 2 X Y ENDFIXED
will yield erroneous results.
Note: When the FIXED section is specified within $opt, the optimization will proceed in Cartesian coordinates.
DUMMY defines the beginning of the dummy atom section and ENDDUMMY its conclusion. Dummy atoms are used to help define constraints during constrained optimizations in Cartesian coordinates. They cannot be used with delocalized internals.
All dummy atoms are defined with reference to a list of real atoms, that is, dummy atom coordinates are generated from the coordinates of the real atoms from the dummy atoms defining list (see below). There are three types of dummy atom:
Positioned at the arithmetic mean of up to seven real atoms in the defining list.
Positioned a unit distance along the normal to a plane defined by three atoms, centered on the middle atom of the three.
Positioned a unit distance along the bisector of a given angle.
The format for declaring dummy atoms is:
DUMMY idum type list_length defining_list ENDDUMMY
idum 
Center number of defining atom (must be one greater than the total number of real atoms for the first dummy atom, two greater for second etc.). 
type 
Type of dummy atom (either 1, 2 or 3; see above). 
list_length 
Number of atoms in the defining list. 
defining_list 
List of up to seven atoms defining the position of the dummy atom. 
Once defined, dummy atoms can be used to define standard internal (distance, angle) constraints as per the constraints section, above.
Note: The use of dummy atoms of type 1 has never progressed beyond the experimental stage.
Bond and dihedral angles cannot be constrained in Cartesian optimizations to exactly or . This is because the corresponding constraint normals are zero vectors. Also, dihedral constraints near these two limiting values (within, say ) tend to oscillate and are difficult to converge.
These difficulties can be overcome by defining dummy atoms and redefining the constraints with respect to the dummy atoms. For example, a dihedral constraint of can be redefined to two constraints of with respect to a suitably positioned dummy atom. The same thing can be done with a bond angle (long a familiar use in Zmatrix construction).
Typical usage is as shown in Table 10.2. Note that the order of atoms is important to obtain the correct signature on the dihedral angles. For a dihedral constraint, atoms J and K should be switched in the definition of the second torsion constraint in Cartesian coordinates.
Internal Coordinates 
Cartesian Coordinates 
$opt 
$opt 
CONSTRAINT 
DUMMY 
tors I J K L 180.0 
M 2 I J K 
ENDCONSTRAINT 
ENDDUMMY 
$end 
CONSTRAINT 
tors I J K M 90 

tors M J K L 90 

ENDCONSTRAINT 

$end 
Note: In almost all cases the above discussion is somewhat academic, as internal coordinates are now best imposed using delocalized internal coordinates and there is no restriction on the constraint values.
Normally delocalized internal coordinates are generated automatically from the input Cartesian coordinates. This is accomplished by first determining the atomic connectivity list (i.e., which atoms are formally bonded) and then constructing a set of individual primitive internal coordinates comprising all bond stretches, all planar bends and all proper torsions that can be generated based on the atomic connectivity. The delocalized internal are in turn constructed from this set of primitives.
The atomic connectivity depends simply on distance and there are default bond lengths between all pairs of atoms in the code. In order for delocalized internals to be generated successfully, all atoms in the molecule must be formally bonded so as to form a closed system. In molecular complexes with long, weak bonds or in certain transition states where parts of the molecule are rearranging or dissociating, distances between atoms may be too great for the atoms to be regarded as formally bonded, and the standard atomic connectivity will separate the system into two or more distinct parts. In this event, the generation of delocalized internal coordinates will fail. Additional atomic connectivity can be included for the system to overcome this difficulty.
CONNECT defines the beginning of the additional connectivity section and ENDCONNECT the end. The format of the CONNECT section is:
CONNECT atom list_length list ENDCONNECT
atom 
Atom for which additional connectivity is being defined. 
list_length 
Number of atoms in the list of bonded atoms. 
list 
List of up to 8 atoms considered as being bonded to the given atom. 
Example 10.215 Methanol geometry optimization with constraints.
$comment Methanol geom opt with constraints in bond length and bond angles. $end $molecule 0 1 C 0.14192 0.33268 0.00000 O 0.14192 1.08832 0.00000 H 1.18699 0.65619 0.00000 H 0.34843 0.74268 0.88786 H 0.34843 0.74268 0.88786 H 0.77395 1.38590 0.00000 $end $rem GEOM_OPT_PRINT 6 JOBTYPE opt METHOD hf BASIS 321g $end $opt CONSTRAINT stre 1 6 1.8 bend 2 1 4 110.0 bend 2 1 5 110.0 ENDCONSTRAINT $end
In 2009, three methods for optimizing the geometry of a molecule under a constant external force were introduced, which were called ForceModified Potential Energy Surface (FMPES),[Ong et al.(2009)Ong, Leiding, Tao, Virshup, and Martnez] External Force is Explicitly Included (EFEI),[RibasArino et al.(2009)RibasArino, Shiga, and Marx] and Enforced Geometry Optimization (EGO).[Wolinski and Baker(2009)] These methods are closely related, and the interested reader is referred to Ref. Stauch:2016 for a detailed discussion of the similarities and differences between them. For simplicity, we will stick to the term EFEI in this Section. An EFEI calculation is a geometry optimization in which a constant that is equal to the external force is added to the nuclear gradient of two atoms specified by the user. The external force is applied along the vector connecting the two atoms, thus driving them apart. The geometry optimization converges when the restoring force of the molecule is equal to the external force. The EFEI method can also be used in AIMD simulations (see Section 10.7), in which case the force is added in every time step. The basic syntax for specifying EFEI calculations is as follows.
$efeiHere, atom1 and atom2 are the indices of the atoms to which a force is applied. force1 is the sum of the force values that acts on atom1 and atom2 in nanoNewtons (nN). If this value is positive, a mechanical force of magnitude force1/2 acts on each of these atoms, thus driving them apart. If it is negative, an attractive force acts between the atoms. Optionally, additional pairs of atoms that are subject to a force can be specified by adding lines in the $efei section.
$end
Example 10.216 EFEI calculation of hydrogen peroxide with a constant stretching force of 2.5 nN acting on each oxygen atom
$molecule 0 1 O 0.7059250062 0.1776745132 0.0698000882 O 0.7059250062 0.1776745132 0.0698000882 H 1.0662092915 0.5838921799 0.4181150580 H 1.0662092915 0.5838921799 0.4181150580 $end $rem JOBTYPE opt EXCHANGE b3lyp BASIS 631G* $end $efei 1 2 5 $end