The options for idealizing hydrogen atom positions depend on the connectivity table which is set up using CONN, BIND, FREE and PART; with experience, this can also be used to generate hydrogen atoms attached to disordered groups and to atoms on special positions. d determines the bond lengths in the idealized groups, and sof and U OVERRIDE the values in the atom list for all atoms until the next AFIX instruction. U is not applied if the atom is already anisotropic, but is used if an isotropic atom is to be made anisotropic using ANIS. Any legal U value may be used, e.g. 31 (a free variable reference) or -1.2 (1.2 times Ueq of the preceding normal atom). Each AFIX instruction must be followed by the required number of hydrogen or other atoms. The individual AFIX options are as follows; the default X-H distances depend on both the chemical environment and the temperature (to allow for librational effects) which is specified by means of the TEMP instruction.
m = 0 No action.
m = 1 Idealized tertiary C-H with all X-C-H angles equal. There must
be three and only three other bonds in the connectivity table to
the immediately preceding atom, which is assumed to be carbon.
m = 1 is often combined with a riding model refinement (n = 3).
m = 2 Idealized secondary CH2 with all X-C-H and Y-C-H angles equal,
and H-C-H determined by X-C-Y (i.e. approximately tetrahedral,
but widened if X-C-Y is much less than tetrahedral). This option
is also suitable for riding refinement (n = 3).
m = 3 Idealized CH3 group with tetrahedral angles. The group is
staggered with respect to the shortest other bond to the atom to
which the -CH3 is attached. If there is no such bond (e.g. an
acetonitrile solvent molecule) this method cannot be used (but
m = 13 is still viable).
m = 4 Aromatic C-H or amide N-H with the hydrogen atom on the external
bisector of the X-C-Y or X-N-Y angle. m = 4 is suitable for a
riding model refinement, i.e. AFIX 43 before the H atom.
m = 5 Next five non-hydrogen atoms are fitted to a regular pentagon,
default d = 1.42 A.
m = 6 Next six non-hydrogen atoms are fitted to a regular hexagon,
default d = 1.39 A.
m = 7 Identical to m = 6 (included for upwards compatibility from
SHELX-76). In SHELX-76 only the first, third and fifth atoms of
the six-membered ring were used as target atoms; in SHELXL-93
this will still be the case if the other three are given zero
coordinates, but the procedure is more general because any one,
two or three atoms may be left out by giving them zero
coordinates.
m = 8 Idealized OH group, with X-O-H angle tetrahedral. If the oxygen
is attached to a saturated carbon, all three staggered positions
are considered for the hydrogen. If it is attached to an
aromatic ring, both positions in the plane are considered. The
final choice is based on forming the 'best' hydrogen bond to a
nitrogen, oxygen, chlorine or fluorine atom. The algorithm
involves generating a potential position for such an atom by
extrapolating the O-H vector, then finding the nearest N, O, F
or Cl atom to this position, taking symmetry equivalents into
account. If another atom which, (according to the connectivity
table) is bonded to the N, O, F or Cl atom, is nearer to the
ideal position, the N, O, F or Cl atom is not considered. Note
that m = 8 had a different effect in SHELX-76 (but was rarely
employed).
m = 9 Idealized terminal X=CH2 or X=NH2+ with the hydrogen atoms in
the plane of the nearest substituent on the atom X. Suitable
for riding model refinement (AFIX 93 before the two H atoms).
m = 10 Idealized pentamethylcyclopentadienyl (Cp*). This AFIX must be
followed by the 5 ring carbons and then the 5 methyl carbons in
cyclic order, so that the first methyl group (atom 6) is attached
to the first carbon (atom 1). The default d is 1.42 A, with the
C-CH3 distance set to 1.063d. A variable-metric rigid group
refinement (AFIX 109) would be appropriate, and would allow for
librational shortening of the bonds. Hydrogen atoms (e.g. with
AFIX 37 or 127) may be included after the corresponding carbon
atoms, in which case AFIX 0 or 5 (in the case of a rigid group
refinement) must be inserted before the next carbon atom.
m = 11 Idealized naphthalene group with equal bonds (default d = 1.39 A)
The atoms should be numbered as a symmetrical figure of eight,
starting with the alpha C and followed by the beta, so that the
first six atoms (and also the last six) describe a hexagon in
cyclic order. m = 11 is also appropriate for rigid group
refinement (AFIX 116).
m = 12 Idealized disordered methyl group; as m = 3 but with two
positions rotated from each other by 60 degrees. The corres-
ponding occupation factors should normally be set to add up to
one, e.g. by giving them as 21 (i.e. 1*fv(2) ) and -21 ( 1*(1-
fv(2)) ). If HFIX is used to generate an AFIX instruction with
m=12, the occupation factors are fixed at 0.5. AFIX 12n is
suitable for a para methyl on a phenyl group with no meta
substituents, and should be followed by 6 half hydrogen atoms
(first the three belonging to one -CH3 component, then the three
belonging to the other, so that hydrogens n and n+3 are opposite
one another). Disordered -CF3 groups may also be generated in
this way (with d=1.32).
m = 13 Idealized CH3 group with tetrahedral angles. If the coordinates
of the first hydrogen atom are non-zero, they define the torsion
angle of the methyl group. Otherwise (or if the AFIX instruction
is being generated via HFIX) a structure-factor calculation is
performed (of course only once, even if many hydrogens are
involved) and the torsion angle is set which maximizes the sum of
the electron density at the three calculated hydrogen positions.
Since even this is not an infallible method of getting the
correct torsion angle, it should normally be combined with a
rigid or rotating group refinement for the methyl group (e.g. mn
= 137 before the first H). In subsequent least-squares cycles
the group is re-idealized retaining the current torsion angle.
-CF3 groups may be generated in the same way (with d = 1.32).
m = 14 Idealized OH group, with X-O-H angle tetrahedral. If the coor-
dinates of the hydrogen atom are non-zero, they are used to
define the torsion angle. Otherwise (or if HFIX was used to set
up the AFIX instruction) the torsion angle is chosen which
maximizes the electron density (see m = 13). Since this torsion
angle is unlikely to be very accurate, the use of a rotating
group refinement is recommended (i.e. mn = 147 before the H atom)
m = 15 BH group in which the boron atom is bonded to either four or five
other atoms as part of an polyhedral fragment. The hydrogen atom
is placed on the vector which represents the negative sum of the
unit vectors along the four or five other bonds to the boron atom
m = 16 Acetylenic C-H, with X-C-H linear. Usually refined with the
riding model, i.e. AFIX 163.
m > 16 A group defined in a FRAG...FEND section with code = m is
fitted, usually as a preliminary to rigid group refinement.
The FRAG...FEND section MUST precede the corresponding AFIX
instruction in the '.ins' file, but there may be any number of
AFIX instructions with the same m corresponding to a single
FRAG...FEND section.
When a group is fitted (m = 5, 6, 10 or 11, or m > 16), atoms with non-zero
coordinates are used as target atoms with equal weight. Atoms with all three
coordinates zero are ignored. Any three or more non-colinear atoms may be
used as target atoms. 'Riding' (n = 3, 4) and 'rotating' (n = 7, 8) hydrogen atoms, but not other idealized groups, are re-idealized (if m is 1, 2, 3, 4, 8, 9, 12, 13, 14, 15 or 16) before each refinement cycle (after the first cycle, the coordinates of the first hydrogen of a group are always non-zero, so the torsion angle is retained on reidealizing). For n = 4 and 8, the angles are reidealized but the (refined) X-H bond length is retained, unless the hydrogen coordinates are all zero, in which case d (on the AFIX instruction) or (if d is not given) a standard value which depends on the chemical environment and temperature (TEMP) is used instead.
n = 0 No action.
n = 1 The coordinates, s.o.f. and U or Uij are fixed.
n = 2 The s.o.f. and U (or Uij) are fixed, but the coordinates are
free to refine.
n = 3 The coordinates, but not the s.o.f. or U (or Uij) 'ride' on
the coordinates of the previous atom with n not equal to 3.
The same shifts are applied to the coordinates of both atoms,
and both contribute to the derivative calculation. The atom on
which riding is performed may not itself be a riding atom, but
it may be in a rigid group (m = 5, 6 or 9).
n = 4 This constraint is the same as n = 3 except that the X-H distance
is free to refine. The X-H vector direction does not change.
This constraint requires better quality reflection data than
n = 3, but allows for variations in apparent X-H distances caused
by libration and bonding effects. If there is more than one
equivalent hydrogen, the same shift is applied to each equivalent
X-H distance (e.g. to all three C-H bonds in a methyl group).
n = 4 may be combined with DFIX or SADI restraints (to restrain
chemically equivalent X-H distances to be equal) or embedded
inside a rigid (n = 6) group, in which case the next atom (if
any) in the same rigid group must follow an explicit AFIX
instruction with n = 5. Note that n = 4 had a different effect
in SHELX-76.
n = 5 The next atom(s) are 'dependent' atoms in a rigid group. Note
that this is automatically generated for the atoms following an
n = 6 or n = 9 atom, so does not need to be included specifically
unless m has to be changed (e.g. AFIX 35 before the first
hydrogen of a rigid methyl group with AFIX 6 or 9 before the
preceding carbon).
n = 6 The next atom is the 'pivot atom' of a NEW rigid group, i.e. the
other atoms in the rigid group rotate about this atom, and the
same translational shifts are applied to all atoms in the rigid
group.
n = 7 The following (usually hydrogen) atoms (until the next AFIX with
n not equal to 7) are allowed to ride on the immediately prece-
ding atom X and rotate about the Y-X bond; X must be bonded to
one and only one atom Y in the connectivity list, ignoring the
n = 7 atoms (which, if they are F rather than H, may be present
in the connectivity list). The motion of the atoms of this
'rotating group' is a combination of riding motion (c.f. n = 3)
on the atom X plus a tangential component perpendicular to the
Y-X and X-H bonds, so that the X-H distances, Y-X-H and H-X-H
angles remain unchanged. This constraint is intended for -OH,
-CH3 and possibly -CF3 groups. X may be part of a rigid group,
which may be resumed with an AFIX n = 5 following the n = 7
atoms.
n = 8 This constraint is similar to n = 7 except that the X-H distances
may also vary, the same shifts being applied along all the X-H
bonds. Thus only the Y-X-H and H-X-H angles are held constant;
the relationship of n = 8 to n = 7 corresponds to that of n = 4
to n = 3. DFIX and SADI restraints may be useful for the X-H
distances. This constraint is useful for -CF3 groups or for
-CH3 groups with good data.
n = 9 The first (pivot) atom of a new 'variable metric' rigid group.
Such a group retains its 'shape' but may shrink or expand
uniformly. It is useful for C5H5 and BF4 groups, which may show
appreciable librational shortening of the bond lengths. Subse-
quent atoms of this type of rigid group should have n = 5, which
is generated automatically by the program if no other AFIX
instruction is inserted between the atoms. Riding atoms are not
permitted inside this type of rigid group. Only the pivot atom
coordinates may be fixed (by adding 10) or tied to free variables
and only the pivot atom may lie on a special position (for the
automatic generation of special position constraints).
Although there are many possible combinations of m and n, in practice only a
small number is used extensively, as discussed in the section on hydrogen
atoms. Rigid group fitting and refinement (e.g. AFIX 66 followed by six
atoms of a phenyl ring or AFIX 109 in front of a Cp* group) is particularly
useful in the initial stages of refinement; atoms not found in the structure
solution may be given zero coordinates, in which cases they will be generated
from the rigid group fit.
A rigid group or set of dependent hydrogens must