To study the Circular Dichroism of some substances with chiral chromophores

The experiment is composed of a number of steps. One may follow the steps given below to successfully run the experiment.

  1. In the "Understanding Structure of Chiral Molecules" step you will be given two samples. You can click on any sample and study its structure and conformation.

  2. Once you are satisfied you can click "Next" to go to the next Step.

  3. Next Step is "Assigning R & S Configuration". Here you are given structures of four samples as individual Jmol applets. The Table "Jmol Instructions" provides guide lines to study those structures efficiently. You have to decide whether the structure is a R or a S enantiomer and select the corresponding Radio Button for each structure. Once you decide and choose your option for both the structures you should submit your answer. You will be informed whether your decission is correct or not. You can skip this step at any point of time by clicking "Skip". To decide whether the structure is R or S you may follow the following instructions

    1. First look at the atoms that are directly attached to the stereocenter of the compound. A substituent that has a higher atomic number takes precedence over a substituent that has a lower atomic number. Hydrogen is the lowest priority substituent. When you are dealing with isotopes, the atom with the higher atomic mass received higher priority. Note: The lowest priority substituents should always go away from the viewer Note: Keep in mind that priority is determined by the first point of difference along the two similar substituent chains. After you have reached the first point of difference, the rest of the chain is irrelevant.

    2. When you have two substituents that have equal rank, we proceed along the two respective substituent chains until we find a point of difference.

    3. When you are looking for the first point of difference on similar substituent chains, you may encounter branching. If there is branching, we choose the branch that is higher in priority. When the two substituents have similar branches, you rank the elements within the branches until you reach a point of difference.

    4. When you come across double and triple bonds, treat them as if they were the same number of single bonds connected to that atom instead. Think of the atoms as duplicated or triplicated:

    5. After all your substituents have been prioritized in the correct manner, you can name it either R or S. By putting the lowest priority substituent in the back (dashed line), the rotation of the other three substituents will help determine whether the molecule is R or S. In the order of priority (1, 2, 3), if the molecule rotates to the right, it is an R. Conversely, if it rotates to the left, it is considered a S.

  4. In next step you will be measuring the CD and ORD spectrum of different chiral samples. First click the "Switch the CD mode" button. The samples will be activated for selecting. Select any sample and "Measure ORD". The ORD spectrum will be shown on screen. You can "Measure Again" or skip the step.

  5. Next Step is the "Analysis" step. At the left side of your screen you are given a picture of two ORD spectrum. And there is one CD spectrum example on the screen. Now you have to decide among the ftwo given ORD spectra, with which the given CD spectra corresponds with. Once you select one graph you should submit your result and you will informed whether you are right or wrong. If you do correctly you can load the next sample. You can skip this step also at any point of time by clicking "Skip". Otherwise you will be asked to perform the analysis for both the samples.