Since 1972 a course of organic chemistry has been taught to a class made up exclusively of Yale freshmen who have a strong background in chemistry and physics. At first the course enrolled fewer than 30 students, and its content was the same as that of a traditional elementary organic course, except that a little more time was spent reviewing concepts from general chemistry during the first semester.

Over time the enrollment in Chemistry 125 has more than doubled, and its emphasis, especially in the first semester, has shifted in an attempt to create a more effective bridge between science as it is commonly taught in many schools (and in many courses in colleges) and science in a university setting, where the focus is on creating new knowledge. Students come to the course knowing a good deal about chemistry. They should leave with a sound knowledge of organic chemistry and a better appreciation of the logic of creative science.

The time devoted to meeting this goal has forced some traditional "first semester" topics into the second semester and required the teacher to be more selective in choosing second semester topics. There is less time for biochemical topics than in a traditional organic course, but Chemistry 125 alumni are a year ahead of their classmates and typically take a subsequent course in biochemistry, in which they have excelled. The goals of Chemistry 125 are to master the core of organic chemistry and its logical basis and to spend enough time on selected topics to show how this discipline exemplifies much of what is most admirable in science.

One of the goals of the course is to encourage students to ask questions. Asking should never embarrass the student who asks, even when the question might embarrass the teacher. If you don't understand something, it is likely that others don't understand either but haven't realized it yet or are too shy to ask. The teacher may not have explained clearly, or perhaps hasn't thought about the subject carefully enough. Once after the teacher explained that Pekeris had calculated the energy of the helium atom to 9 or 10 significant figures, a freshman asked how this was possible when the mass of the particles was known to only 7 significant figures. Good question.

The prime question, and the theme of the course, is "How do you know?"

Too much science teaching consists of drill on facts, or supposed facts, and on half-thought-through theories that generations of students have swallowed in the struggle to get on to more advanced topics. Preparing to make new contributions to science requires developing the habit of thinking carefully. The only authority should be experimental observation and logical argument - never simple assertions of the teacher or the textbook.

Three-fourths of the first semester in Chem 125 is taken up with questions of structure (what atoms and molecules look like and what bonds are) and of what makes molecules reactive. Having mastered these topics a student can understand and predict much of organic chemistry, rather than just memorizing it. When students come into a traditional course of organic chemistry as sophomores they are supposed, rightly or wrongly, to know enough about these fundamental topics, so less time is spent on them. Freshmen are not supposed to know, so we spend enough time to learn about them.

We start with Lewis structures and resonance theory and see that, useful as they can be, there is not a whole lot of there there. Here we'll spend enough time to see how great scientists make mistakes on the way to finding the truth.

We then examine the most direct experimental evidence on the structure of atoms, molecules, and bonds. It is derived from "feeling" them by SPM (scanning probe microscopy) and "seeing" them by X-ray diffraction. We want to understand not only what these techniques show, but how they show it.

Next we learn enough quantum mechanics to understand what bonds are. Molecular quantum mechanics is very unfamiliar, but it is not really difficult if you can be content with understanding why the differential equations work the way they do, and leave solving them to computers. The qualitative ideas of energy match and overlap, HOMOs LUMOs and SOMOs will illuminate all our subsequent discussions of reactivity.

Next we address how it is possible that chemists were not surprised when the methods of experimental and theoretical physics finally could show what molecules look like. Chemists weren't surprised because they already knew! The development of the organic structural model since the early 19th Century is at the same time a great romance, a great puzzle, a great way of learning structural organic chemistry and its nomenclature, and a great example of how good science works.

After a brief interlude on how enthalpy and entropy control equilibrium and dynamics, we are ready to address organic reactions on the basis of a solid understanding of what molecules are and what makes them reactive.

Most of the material above is covered in more detail than is available in textbooks. The Chemistry 125 web page plays a key role in this part of the course.

The remaining quarter of the first semester introduces simple organic transformations and how we study them. The second semester presents additional simple transformations, spectroscopic methods, and the properties of more complex molecules (including biologically important ones like proteins and nucleic acids).

Most courses of organic chemistry spend more time on these last "text-book" topics, but the Chemistry 125 approach is certainly no less rigorous, and it has seemed to work for well-prepared Yale freshmen.