Okay, let's tackle at least one problem here. Consider the rotation of 1,2-dichloroethane (BP86/cc-pVDZ):
![rotation of dichloroethane][1]
These conformational changes can be further rationalised:
- **C** and **C'** are the same conformation, since these are mirror images.
- The same applies to **B** and **B'**.
- **A** and **C** are local minima and can be referred to as *conformes* in the above given way
- **B** and **D** are transition states - they are not stable.
If you consider the rotation **A** to **C** as a reaction, this state would mark the maximum energy needed for the conversion. I believe with *reactions* it is meant, that an accurate description of the transition state by InChI is not possible.
----------
For the term non-local chirality I suggest you look at [BINAP][2] or [BINOL][3].
![structure of BINAP][4]
In this case I have used a slightly abridged version of BINAP for educational purposes, where $\ce{Ph -> Me}$.
![R-BINAP][5]
(This is a display of R-BINAP - unfortunately imgur does not want to eat the S-BINAP file at the moment. I might have to come back to that.)
----------
[Markush Structures][6] are a kind of summary structure for certain compound classes. A very simple example would be a monosubstituted biphenyl system, where the upper structure is a representation of all three below. However, it is noteworthy, that each instance of a Markush structure can be well explained by InChI.
![biphenyl markush structure][7]
More complicated structures are often used in patents and in other scientific publications, usually specifically referring to a very general procedure or mechanism. I found one on wikipedia commons, that could well represent a million molecules:
![markush structure][8]
----------
#Appendix
The following section contains the nuclear coordinates in `*.xyz`(XMol) file format and angstroms as unit.
**A**
C 0.000000000 0.000000000 0.000000000
C 0.000000000 0.000000000 1.521307000
Cl 1.723641000 0.000000000 -0.593797000
H -0.486731000 -0.904743000 -0.410753000
H -0.486731000 0.904743000 -0.410753000
Cl -1.723641000 0.000000000 2.115104000
H 0.486731000 -0.904743000 1.932060000
H 0.486731000 0.904743000 1.932060000
**B**
C 0.030242000 0.085780000 -0.007620000
C -0.030242000 0.085780000 1.528927000
Cl 1.518312000 -0.758527000 -0.631286000
H -0.837191000 -0.442465000 -0.444148000
H 0.070555000 1.115212000 -0.412109000
Cl -1.518312000 -0.758527000 2.152593000
H 0.837191000 -0.442465000 1.965455000
H -0.070555000 1.115212000 1.933416000
**C**
C 0.066377000 0.127741000 0.004558000
C -0.066377000 0.127741000 1.516749000
Cl 1.083384000 -1.241726000 -0.615213000
H -0.919786000 0.050600000 -0.492443000
H 0.568277000 1.063384000 -0.317636000
Cl -1.083384000 -1.241726000 2.136520000
H 0.919786000 0.050600000 2.013750000
H -0.568277000 1.063384000 1.838943000
**D**
C 0.164887000 0.141535000 -0.000240000
C -0.164887000 0.141535000 1.521547000
Cl 0.337146000 -1.473219000 -0.795160000
H -0.633932000 0.666019000 -0.558099000
H 1.123149000 0.665665000 -0.177529000
Cl -0.337146000 -1.473219000 2.316468000
H 0.633932000 0.666019000 2.079406000
H -1.123149000 0.665665000 1.698836000
***R*-BINAP**
C -0.086423000 -0.055821000 -0.031546000
C -0.090885000 -0.047699000 1.480085000
C 1.148913000 -0.158515000 2.237313000
C 1.064686000 -0.139089000 3.676951000
C -0.131097000 -0.014450000 4.357670000
C -1.357362000 0.116010000 3.652970000
C -1.345263000 0.107319000 2.211098000
P 2.768926000 -0.321256000 1.451350000
H 1.988600000 -0.233144000 4.265654000
H -0.135982000 -0.008251000 5.459401000
C -2.590782000 0.269421000 4.370415000
C -2.623021000 0.305506000 1.559779000
C 0.437392000 1.073619000 -0.788457000
C 0.410661000 0.991852000 -2.228054000
C -0.079670000 -0.105834000 -2.908992000
C -0.579162000 -1.233570000 -2.204534000
C -0.579999000 -1.219208000 -0.762676000
P 1.107602000 2.557133000 -0.001640000
H 0.790955000 1.839345000 -2.816335000
H -0.077540000 -0.112552000 -4.010726000
C -1.063317000 -2.378355000 -2.921905000
C -1.047368000 -2.424579000 -0.111239000
C -3.792005000 0.431032000 3.705083000
H -2.558632000 0.263827000 5.471798000
H -4.735477000 0.552772000 4.258523000
C -3.797353000 0.457087000 2.279022000
H -2.662047000 0.340912000 0.466043000
H -4.750761000 0.602046000 1.748556000
C -1.503463000 -3.517255000 -0.830391000
H -1.036094000 -2.475958000 0.982488000
H -1.854657000 -4.415344000 -0.299810000
C -1.523650000 -3.499569000 -2.256520000
H -1.052652000 -2.347534000 -4.023279000
H -1.890198000 -4.377463000 -2.809877000
C 4.061075000 -0.509159000 2.730645000
C 2.844045000 -1.846744000 0.446017000
C 1.585856000 3.772639000 -1.280334000
C -0.173490000 3.383258000 1.008127000
H 0.254332000 4.289560000 1.485098000
H -1.067700000 3.703930000 0.418133000
H -0.532498000 2.717241000 1.815764000
H 1.997887000 4.670081000 -0.777298000
H 2.377005000 3.362349000 -1.938832000
H 0.749130000 4.118465000 -1.941170000
H 5.044249000 -0.601334000 2.227532000
H 4.100503000 0.383637000 3.385840000
H 3.944572000 -1.404262000 3.395364000
H 3.842692000 -1.931312000 -0.030903000
H 2.674387000 -2.779210000 1.039384000
H 2.087489000 -1.826871000 -0.361580000
***S*-BINAP**
C -1.383946000 -3.448543000 -2.256996000
C -1.065989000 -2.266144000 -2.910129000
C -0.652376000 -1.110469000 -2.179491000
C -0.563545000 -1.177237000 -0.738280000
C -0.899026000 -2.413534000 -0.098700000
C -1.299620000 -3.519323000 -0.838209000
C -0.154302000 -0.008671000 0.004167000
C 0.166467000 1.182512000 -0.673969000
C 0.072046000 1.221328000 -2.098779000
C -0.323252000 0.113168000 -2.831301000
C -0.061735000 -0.093981000 1.507135000
C -1.110430000 0.372113000 2.322674000
C -0.989013000 0.267385000 3.742090000
C 0.132224000 -0.289631000 4.336601000
C 1.210137000 -0.777916000 3.542877000
C 1.113248000 -0.682564000 2.103804000
C 2.206553000 -1.174312000 1.320794000
C 3.329975000 -1.726929000 1.922868000
C 3.419059000 -1.820539000 3.340084000
C 2.377998000 -1.353835000 4.130094000
P -2.590653000 1.186493000 1.502738000
C -3.750658000 -0.293139000 1.402088000
P 0.636241000 2.692004000 0.339668000
C 2.511918000 2.555623000 0.253510000
C -3.385046000 2.079953000 2.947654000
C 0.388676000 4.078351000 -0.898992000
H -1.802841000 0.635802000 4.383638000
H 0.202504000 -0.360978000 5.434128000
H 0.319305000 2.150696000 -2.632672000
H -0.386992000 0.166196000 -3.930250000
H 2.436377000 -1.419019000 5.228476000
H 4.313241000 -2.262708000 3.805535000
H 2.146133000 -1.110484000 0.224695000
H 4.157224000 -2.097887000 1.298347000
H -0.834575000 -2.478936000 0.997042000
H -1.552289000 -4.458551000 -0.322477000
H -1.128190000 -2.199481000 -4.008215000
H -1.700498000 -4.331984000 -2.832408000
H 2.950535000 3.473538000 0.698290000
H 2.842563000 1.687658000 0.858736000
H 2.884117000 2.439555000 -0.786611000
H 0.678948000 5.023670000 -0.395042000
H 0.990357000 3.982867000 -1.828352000
H -0.686746000 4.150262000 -1.160750000
H -4.302108000 2.573768000 2.564446000
H -3.673500000 1.421270000 3.794842000
H -2.700063000 2.872570000 3.312044000
H -4.742112000 0.063129000 1.051704000
H -3.359638000 -1.014277000 0.656570000
H -3.871382000 -0.807607000 2.379049000
[1]: https://i.sstatic.net/TCW7d.png
[2]: http://de.wikipedia.org/wiki/BINAP
[3]: http://de.wikipedia.org/wiki/BINOL
[4]: http://upload.wikimedia.org/wikipedia/commons/thumb/d/d6/BINAP_Enantiomers_Structural_Formulae_V.1.svg/350px-BINAP_Enantiomers_Structural_Formulae_V.1.svg.png
[5]: https://i.sstatic.net/UyAMJ.jpg
[6]: http://en.wikipedia.org/wiki/Markush_structure
[7]: https://i.sstatic.net/YE0gp.png
[8]: http://upload.wikimedia.org/wikipedia/commons/9/9e/Markush_structure.png