Relating fischer projection with cis model

[Chem_Mod]

Question: I'm having trouble relating Fischer projections with cis and trans. For cis models, are two H's drawn on same side in Fischer projection or opposite?

[Chem_Mod]

Answer: In Fischer projections, the molecules on the vertical chain is said to be projected away from you, while the molecules that are presented horizontally on the sides are said to be projected towards you. Consider the following diagram, which shows glucose in its linear and cyclic form: http://sci9bestq3bm.wikispaces.com/file ... lucose.gif . They look different, but they are in actuality the same molecule, and it will help you visualize the cis and trans nature of the substituents on each carbon. Look at carbons labeled 2 and 3. On the Fischer projection to the left, the -OH groups are located to the right for C2, and to the left for C3. In the cyclic form, you can see that the -OH groups in C2 and C3 are trans. So in response to your question, if they are on the same side, they should be cis to one another.

However, be cautious about naming cis and trans model for linear molecules. That is because atoms bonded by a single bond have free rotation about that bond. Due to the rapid rotations of atoms about their bonds, one rarely ever names such molecules as cis or trans. That is why cis and trans notation (and other similar IUPAC notations) are only used for structures like double bonds or rings where the substituents are for certain locked in place.