PROGRAM TOPO (Current version TOPO440.

exe):

Analysis of Topotactic Relationships in Phase Transformations and Solid-State Reactions

Gougoutas’ original paper on the specification of topotactic alignments appeared in 1972, and presented

an elegant, straightforward methodology for specifying the orientation of mother and daughter phases.1 A later

detailed analysis of the topotaxy of 1-methoxy-1,2-benziodoxolin-3-one, along with a step-by-step

methodology, and an Appendix containing the mathematical relationships was published by Etter in 1976.2

These two papers are essential reading for any scientist interested in establishing, by experiment, the alignment

of a mother phase and one or more daughter phases arising from a crystal-to-crystal solid-state transformation.

Despite their importance, the papers have been cited only 15 and 11 times, respectively. As we returned to the

field of topotactic transformations in 2010, we sought to use modern diffractometry to solve the problem.

It is important here to repeat the definition of topotaxy so that an important point may be addressed. In

topotaxy, a single crystal of a starting material is converted into a pseudomorph2 containing one or more

products in a definite crystallographic orientation; the conversion takes place throughout the entire volume of

the crystal.3 Thus, topotaxy pertains to either a single crystal-to-single crystal process (a solitary daughter phase

is produced) OR a process during which the mother phase is converted into more than one daughter (twinned

phases are produced). Thus, in order to keep the discussion general, we will term the processes described in the

manuscript as “crystal-to-crystal”. In fact, in the present work, all the transformations studied involve twinned

product phases. The important point is that, for topotactic transformations, the diffraction properties of the

daughter phase allow the orientation(s) of the mother and daughter phases(s) to be established experimentally,

as described in the following discussion.

In the 1970’s the alignment of mother and daughter phases in molecular crystals was established through

examination of aligned Weissenberg or precession photographs.1,2,4-6 The analysis led to the following

interlattice relationship, which is important in interpreting the topotaxy observed in the experiment (symbols

from the 1976 article are used here):2

bi = φij aj
where φij is the topotactic transformation matrix, while bi and aj are the direct basis set vectors for the product

and reactant lattices, respectively. We refer the interested reader to Etter’s paper for other elements of the

theory, and an interesting historical account of how φij was derived from observations on X-ray photographs.3

In the present day, our approach first centered on the use of the original CAD-4 command set, as

implemented in the CAD-4PC software,7 which may still be run on a modern PC! For example, after entering

the orientation matrix (taken from a *.p4p file obtaind using our Bruker-Nonius Kappa-Apex2 instrument) for a

mother phase, we could use the HB command (hkl to ‘bisecting setting’ angles: θ, φ, χ) to get the setting angles

of, for example, 100, 010, and 001 for the mother phase. Then, after cooling our crystal, and observing

appearance of the daughter unit cell, we enter the orientation matrix of the daughter crystal into CAD4-PC, and

use the BH command (‘bisecting setting’ to hkl), along with the original 100, 010, and 001 angles settings from

the mother phase. The resultant values show the correspondence between mother and daughter vectors before

and after the transformation. While this worked beautifully, we imagined that the use of an older, though

elegant, program would discourage general adoption by the community. Further, we had not yet solved the

problem of how to obtain the topotactic transformation matrix, φij.

The orientation matrix for a crystal mounted on a diffractometer has been part of standard printed output

for many decades, and now appears in one or more files, either in one or both of *.cif or *.p4p files. Thus, we

decided to write a program that, in its initial incarnation, would read *.p4p files each of a mother and daughter

phase, automatically calculate angles between all nine combinations of 100, 010 and 001 mother vs. daughter

vectors, and further, allow (a) the calculation of the corresponding values for h, k, and l for a daughter phase

referenced to the mother phase; (b) the calculation of the corresponding values for h, k, and l for a mother phase

referenced to the daughter phase; and (c) the angle between a specific h, k, l combination in the mother phase

and any chosen h, k, l combination in the daughter phase. Finally, the program would provide the opportunity

to perform the calculations either in reciprocal space or direct space. After reading in two *.p4p files, the

program automatically calculates the diffractometer coordinates (cmx, cmy, cmz) for an axial hkl set (in reciprocal

or direct space) of the mother crystal, using Rm, the orientation matrix for the mother crystal:
  cmx   hm 
   
 cmy  = Rm  km 
 cmz  l 
  m 
After getting the coordinates, we then use the inverse of the orientation matrix for the daughter crystal, R-1d , to

obtain the correspondence between the indices of the mother crystal referenced to the daughter unit cell:

 hd   cmx 
  −1
 
 kd  = R d  cmy 
l   cmz 
d   
With the above information in hand, one can obtain direction cosines, and calculate angles between mother &

daughter vectors as well. As we wrote the program in g95 Fortran 95,8 it became obvious that calculation of the

topotactic transformation matrix was a simple affair:

φij = R-1d Rm

and this information also appears in the program output.9

As the source in our 60Co gamma-irradiation apparatus reached its eighth half-life, it became apparent that the

exciting work we’d carried out on radical reactions in the solid state10,11 could no longer be carried out at

Brandeis, and alternative sources were not available to us. We thus decided to return to studies of crystal-to-

crystal, thermally-induced reactions and/or phase transformations. At the outset, we faced a dilemma: in the

1970’s the alignment of reactant and product (‘mother’ and ‘daughter’) phases was established using X-ray

photographic techniques, viz., comparison of axial relationships of carefully-aligned samples on Weissenberg or

precession photographs, taken before and after the transformation. While a modern diffractometer produces no

shortage of images, one does not work with aligned samples, and thus the images cannot be used directly to

establish relative orientations. However, using the approach described by Gougoutas et al.1,4 and by Etter,2 it is

straightforward to carry out identical analyses to those done in the 1970’s. The technique is simple and its

application provides an opportunity to experimentally establish the orientation relationship between a mother

phase and one or more daughter phases or twin orientations. In a recent contribution we describe the

methodology, simple mathematics, and a program (available from the authors) that simplifies the calculation

steps and provides all necessary information to establish orientation relationships and provide an accurate
method to visually overlay mother and daughter packing diagrams.12 Taking a lead from Peggy Etter’s

presentation style, the paper combines the scientific results with a tutorial approach.2,12

1. Gougoutas, J. Z. Isr. J. Chem. 1972, 10, 395-407. In “conservative twinning”, the symmetry of the

daughter phase conserves the symmetry of the mother phase via twinning; the concept is fully illustrated

later in the present manuscript.

2. Etter, M. C. J. Am. Chem. Soc. 1976, 98, 5331-5339. Etter defines a pseudomorphic transformation as

“one in which the morphology of the reactant crystal does not change during reaction. In a single crystal

to single crystal pseudomorphic transformation, the diffraction pattern of the reacting crystal changes

but the dimensions and shape of the crystal itself does not (color and density changes often occur also).”

3. Dent Glasser, L. S.; Glasser, F. P.; Taylor, H. F. W. Quart. Rev. 1962, 16, 343-60.

4. (a) Gougoutas, J. Z.; Clardy, J. C. J. Solid State Chem. 1972, 4, 230-242; (b) Gougoutas, J. Z.;

Lessinger, L. J. Solid State Chem. 1973, 7, 175-185; (c) Gougoutas, J. Z.; Lessinger, L. J. Solid State

Chem. 1974, 9, 155-164; (d) Gougoutas, J. Z.; Lessinger, L. J. Solid State Chem. 1975, 12, 51-62; (e)

Gougoutas, J. Z.; Naae, D. G. J. Solid State Chem. 1976, 16, 271-281; (f) Gougoutas, J. Z., Chang, K.

H.; Etter, M. C. J. Solid State Chem. 1976, 16, 283-291; (g) Etter, M. C. J. Solid State Chem. 1976, 16,

399-411; (h) Etter, M. C. J. Am. Chem. Soc. 1976, 98, 5326-5331; (i); (j) Gougoutas, J. Z. J. Am. Chem.

Soc. 1977, 99, 127-132; (k) Gougoutas, J. Z.; Naae, D. G. J. Phys. Chem. 1978, 82, 393-401; (l)

Gougoutas, J. Z.; Johnson, J. J. Am. Chem. Soc. 1978, 100, 5816-5820; (m) Gougoutas, J. Z. J. Am.

Chem. Soc. 1979, 101, 5672-5675.

5. Cheng, K.; Foxman, B. M. J. Am. Chem. Soc. 1977, 99, 8102-8103.

6. Cheng, K.; Foxman, B. M.; Gersten, S. W. Mol. Cryst. Liq. Cryst. 1979, 52, 77-82; Foxman, B. M.;

Jaufmann, J. D. J. Polym. Sci., Polym. Symp. 1983, 70, 31-43.

7. Schagen, J. D.; Straver, L.; van Meurs, F.; Williams, G. CAD4 Version 5.0; Enraf-Nonius, Delft, The

Netherlands, 1989, Chapters II and VIII; see also:

http://www.nonius.nl/cad4/manuals/user/chapter02.html and

http://www.nonius.nl/cad4/manuals/user/chapter08.html .
8. Vaught, A. G95; Mesa, Arizona, 2006; see also http://www.g95.org/index.shtml .

9. Experience to date suggests that, from experiment to experiment, and compound to compound,

variations in the observed values of interplanar/interaxial angles may range from as little as 0.3º up to

ca. 2º. In part, this depends on (a) the mechanical stability of the mounted crystal; (b) the

quality/”singleness” of the crystal at the temperatures measured; and (c) the number of data used to

obtain the orientation matrix.

10. Hickey, M. B.; Schlam, R. F.; Guo, C.; Cho, T. H.; Snider, B. B.; Foxman, B. M. CrystEngComm 2011,

13, 3146-3155.

11. Shang, W.; Hickey, M. B.; Enkelmann, V.; Snider, B. B.; Foxman, B. M. CrystEngComm 2011, 13,

4339-4350.

12. Posner, S. R.; Lorson, L. C.; Gell, A. R.; Foxman, B. M. Cryst. Growth Des., 2015, 15, 3407–3416.
 ANNOTATED INSTRUCTIONS FOR TOPO v4.40

Below we provide annotated instructions using TOPO. These pages, as well as the details provided in

reference 12, provide a complete picture of the extensive options available in the paper, as well as guidelines on

the preparation of animations that illustrate the molecular motion which occurs between the initial and final

stages of a transformation. In the following example, the transformation between the RT phase and one of the

four twin components of the LT phase of ferrocenium hexafluorophosphate is explored. The downloadable .zip

file at http://www.xray.chem.brandeis.edu contains the TOPO executable, input files and output for checking

program use. Do note that a correct experiment involves a crystal transformation carried out in a single

diffractometer session: the crystal may not be removed between data collection of Form I and the generation of

other phases!!!

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C:\Users\foxman1\Desktop\topo12\twinlaws>topo440

TOPOTAXY CALCULATOR VERSION 4.40 23 MAY 2017

NOTE: ALL NUMERICAL INPUT MUST BE SEPARATED BY COMMAS

WILL THIS BE AN EXPERT MODE RUN?

** RECOMMENDED ONLY IF YOU ARE FAMILIAR **

** WITH DIFFRACTOMETER MATRIX OPERATIONS **

[ENTER Y OR N]: n

ENTER ORIENTATION MATRIX FILE TYPE, EITHER "P4P" OR "CIF"

[DEFAULT(CR) = P4P] :

ARE THERE TWIN ORIENTATIONS TO BE CONSIDERED FOR MOTHER OR DAUGHTER?

[ENTER Y OR N]: y (In this case we have a twin)

ENTER FILE NAME, WITH EXTENSION, FOR MOTHER CRYSTAL: mom.p4p

ENTER SEQUENCE NUMBER OF TWIN IN P4P FILE FOR MOTHER CRYSTAL

[1 = PARENT MATRIX...NO TWIN]: 1 (In this case we have a twin)

ENTER FILE NAME, WITH EXTENSION, FOR DAUGHTER CRYSTAL: twin4.p4p

ENTER SEQUENCE NUMBER OF TWIN IN P4P FILE FOR DAUGHTER CRYSTAL...

[1 = PARENT MATRIX...NO TWIN]: 2 (I’ll look at twin orientation 2 for the daughter; rerun fr 1, 3, and 4 later)
 ENTER FILE NAME FOR OUTPUT [DEFAULT=TOPO.OUT]: topo440.out

Reciprocal: Part IR -- AUTOMATIC GENERATION OF ANGLES This provides an automatic look at some of
BETWEEN PRIMARY R. L. VECTORS the main intervector angles; things can jump
M = MOTHER, D= DAUGHTER out at us here!

HM KM LM HD KD LD ANGLE

1. 0. 0. 1. 0. 0. 10.409 (hmmm…I dunno what up here….)

1. 0. 0. 0. 1. 0. 90.224

1. 0. 0. 0. 0. 1. 93.646

0. 1. 0. 1. 0. 0. 90.261

0. 1. 0. 0. 1. 0. 179.350 (clearly b*[mom] and –b*[daughter] are aligned)

0. 1. 0. 0. 0. 1. 90.789

0. 0. 1. 1. 0. 0. 97.204

0. 0. 1. 0. 1. 0. 89.405

0. 0. 1. 0. 0. 1. 179.090 (clearly c*[mom] and –c*[daughter] are aligned)

TYPE<CR> to CONTINUE:

CALCULATE M-->D, D-->M CORRESPONDING VECTORS,

INTERVECTOR ANGLES, OR GO TO DIRECT LATTICE CALC [MD,DM,IV,DIRECT]: md

Reciprocal: Part IIR(a) -- GENERATE DAUGHTER INDICES THAT CORRESPOND Let’s have a look at what the
TO INPUT MOTHER INDICES
mother 100 r.l. vector
NOTE THAT DAUGHTER INDICES MAY BE FRACTIONAL! corresponds to in the daughter

ENTER H, K, L FOR MOTHER CRYSTAL [100,0,0 TO END]: 1,0,0

MOTHER DAUGHTER
H K L H K L
_______________________________________________________________

1.000 0.000 0.000 0.982 -0.002 -0.255 (mom’s 100 is daughter ‘s 4 0 -1)

ENTER H, K, L FOR MOTHER CRYSTAL [100,0,0 TO END]: 0,1,0

MOTHER DAUGHTER
H K L H K L
_______________________________________________________________

0.000 1.000 0.000 -0.004 -0.968 -0.014 (0 -1 0 just like we thought!)

ENTER H, K, L FOR MOTHER CRYSTAL [100,0,0 TO END]: 0,0,1

 MOTHER DAUGHTER
H K L H K L
_______________________________________________________________

0.000 0.000 1.000 -0.005 0.010 -0.992 (0 0 -1 just like we thought!)

ENTER H, K, L FOR MOTHER CRYSTAL [100,0,0 TO END]: 100,0,0

CALCULATE M-->D, D-->M CORRESPONDING VECTORS,

INTERVECTOR ANGLES, OR GO TO DIRECT LATTICE CALC [MD,DM,IV,DIRECT]: iv

Reciprocal: Part IIIR -- GENERATION OF ANGLES BETWEEN

SPECIFIED R. L. VECTORS

M = MOTHER, D= DAUGHTER

ENTER H, K, L FOR MOTHER CRYSTAL: 1,0,0

ENTER H, K, L FOR DAUGHTER CRYSTAL: 4,0,-1

Here we’re just checking that the
intervector angle is less than a degree
HM KM LM HD KD LD ANGLE
or two, and thus we interpreted the
1. 0. 0. 4. 0. -1. 0.423 ‘md ‘ output correctly!

ANOTHER? [Y OR N]: n

CALCULATE M-->D, D-->M CORRESPONDING VECTORS,

INTERVECTOR ANGLES, OR GO TO DIRECT LATTICE CALC [MD,DM,IV,DIRECT]: direct

Direct: PART ID -- AUTOMATIC GENERATION OF ANGLES

BETWEEN PRIMARY DIRECT LATTICE VECTORS

M = MOTHER, D= DAUGHTER

[HM KM LM] [HD KD LD] ANGLE

1. 0. 0. 1. 0. 0. 0.517

1. 0. 0. 0. 1. 0. 90.163
Very similar to the above input
1. 0. 0. 0. 0. 1. 97.207 and output, except that all this is
now in DIRECT SPACE.
0. 1. 0. 1. 0. 0. 90.262

0. 1. 0. 0. 1. 0. 179.189

0. 1. 0. 0. 0. 1. 90.555

0. 0. 1. 1. 0. 0. 93.643

0. 0. 1. 0. 1. 0. 89.200

0. 0. 1. 0. 0. 1. 169.575

TYPE<CR> to CONTINUE:

CALCULATE M-->D, D-->M CORRESPONDING VECTORS,

INTERVECTOR ANGLES, OR GO TO OBLIQUITY CALC [MD,DM,IV,OBLI]: md

Direct: Part IID(a) -- GENERATE DAUGHTER DIRECTIONS THAT CORRESPOND

TO INPUT MOTHER DIRECTIONS
 NOTE THAT DAUGHTER DIRECTIONS MAY BE FRACTIONAL!

ENTER [H, K, L] FOR MOTHER CRYSTAL [100,0,0 TO END]: 0,0,1

MOTHER DAUGHTER
[H K L] [H K L]
_______________________________________________________________

0.000 0.000 1.000 -0.262 0.015 -1.007

ENTER [H, K, L] FOR MOTHER CRYSTAL [100,0,0 TO END]: 100,0,0

CALCULATE M-->D, D-->M CORRESPONDING VECTORS,

INTERVECTOR ANGLES, OR GO TO OBLIQUITY CALC [MD,DM,IV,OBLI]: iv

Direct: Part IIID -- GENERATION OF ANGLES BETWEEN

SPECIFIED DIRECTIONS

M = MOTHER, D= DAUGHTER

Mother [001] corresponds to

ENTER [H, K, L] FOR MOTHER CRYSTAL: 0,0,1
daughter [-1 0 -4]

ENTER [H, K, L] FOR DAUGHTER CRYSTAL: -1,0,-4

HM KM LM HD KD LD ANGLE

0. 0. 1. -1. 0. -4. 0.728 …and it checks out as well

ANOTHER? [Y OR N]: n

CALCULATE M-->D, D-->M CORRESPONDING VECTORS,

INTERVECTOR ANGLES, OR GO TO OBLIQUITY CALC [MD,DM,IV,OBLI]: obli

CALCULATE PLANE-TO-DIRECTION ANGLE IN MOTHER [OBLM],

DAUGHTER [OBLD], OR QUIT [QUIT]: obld

PART IVB- -- GENERATE DAUGHTER PLANE-TO-DIRECT AXIS ANGLES

(SPECIFIC OBLIQUITY CALCULATION)

ENTER (H, K, L) FOR DAUGHTER CRYSTAL: 0,0,1

ENTER [H, K, L] FOR DAUGHTER CRYSTAL: 1,0,4

DAUGHTER (PLANE) DAUGHTER [DIRECT AXIS] OBLIQUITY

(H K L) [H K L]
_______________________________________________________________ Now we check the obliquity for this
TLQS twin, a reasonable 3.3°.
0. 0. 1. 1. 0. 4. 3.248

CALCULATE PLANE-TO-DIRECTION ANGLE IN MOTHER [OBLM],

DAUGHTER [OBLD], OR QUIT [QUIT]: quit