The Shodor Scholars Program began today with Robert R. Gotwals, Jr. (Bob2) reviewing with the students the four important types of science: computational, experimental, theoretical, and observational. He asked students to observe Jenna, an intern at Shodor. They mentioned characteristics referred to as her "structure", that she had brown hair and was wearing jeans. Then they determined some of her "properties", that she was smart. Once Jenna began to interact with another intern, Laura, students were able to observe her "activity", that Jenna was friendly and outgoing. These social science observations were then compared to Chemistry. Using the same types of characteristics they used to describe Jenna, the students began to describe the water molecule.
Observing the water molecule led to a discussion about energy. Then the questions arose: how does a water molecule vibrate and in how many ways? Then Bob2 introduced the formula, "2N + 3" which calculates the number of vibrations, with N as the number of atoms in the molecule. To look further into the vibrations of this molecule, students logged into Moodle on the Shodor site and built a water molecule using Mopac. Once models of the molecule were built, they were able to see the motion of three vibrations on the water molecule that the formula suggested.
Next, families of chemicals were discussed. Specifically, the family known as carboxylic acids. Students divided up the task of modeling different acids. They ran a molecular energy calculation and recorded the calculated pKa (a measurement of acid strength), the charge of the acidic hydrogen for each molecule, the dipole moment, and the heat formation of these molecules. The goal was to determine if the charge of the acidic hydrogen, the dipole moment, and/or the heat formation could be used to determine the acidic strength (pKa). This was investigated using excel and linear regression. The conclusion was that none were very good predictors of pKa, even together.
For the second half of the day, students investigated the chemical properties of drugs. The importance of the value for logP was emphasized. The best value for logP for a drug was explained to be 1.15. If the number is too low, the drug goes through the blood, too high, it bounces off the blood or gets stuck. With this knowledge, the students went to Moodle on Shodor again, and found the OSIRIS property explorer. Together the class studied benzene, adding atoms such as carbon, and observed the effects on the harmfulness of the drug, the logP, and other properties that were affected. Then students were given the challenge to design a drug whose logP was approximately equal to 1.15, with a tolerance of 0.02, without toxicity risks, a molecular weight of less than 500, and with at least 6 carbons. Although this design challenge was set up to be quite difficult, several students came up with structures that fit the criteria, and some even found more than one.
The next task for the students was to build a model using Vensim of the process of a drug entering the body, going into the stomach, traveling into the blood, and then being excreted. The model was introduced as related to pharmacokinetics, since the model relies on information about the drug and how fast it moves. The students set up the model towards the end of the day, and planned to complete it the next day.