Because of the absence of advanced mathematics at the premedical level, the mathematical underpinnings of the discussion of Atomic Theory later, for example, are not going to be advanced enough to fully flesh out Schroedinger wave mechanics. This is not a problem, except that many students have difficulty studying this way, because it does not reconcile with their habit of achieving a satisfying, saturated understanding of the material before considering it mastered.
In my experience this can lead to a big stumbling block to being able to feel comfortable with concepts you need, such as the description of electron orbitals or the basic consequences of molecular orbital theory.
In summary, in Atomic Theory, you will need to find the boundaries of your sense of 'not getting it', accept where it is coming from, and not be afraid to understand things in a somewhat impressionistic, intuitive way.
For example, standing waves on a stretched string are a useful analogy for understanding the electron orbitals discussed in Atomic Theory and Modern Physics. At its root, the mathematics that leads to the distribution of possible electron wave forms (orbitals), is very similar to the mathematics that leads to the series of standing waves on a stretched string. In Atomic Theory, you learn the quantum electrodynamical description of the atom, which presents electrons as possessing both particle and wave nature. Standing mechanical waves are a useful starting point for understanding the quantum description of electron waves. When you describe the series of possible waves on a stretched string, the harmonic series, you use a series of numbers to describe the possible states (n = 1,2,3, etc.). These numbers are the same kind of numbers as the quantum numbers describing the possible electron standing waves in an atom.
The quantum numbers distinguish solutions to the Schroedinger wave equation for an electron in an atom, its orbitals, just as the series of numbers in our simple standing wave functions for a stretched string correspond to possible solutions for that wave type.
This is the kind of mental work to build an intuitive, conceptual comfort level in Atomic Theory and Modern Physics. You are not pretending to have an advanced understanding. What you are aiming for is a satisfied and satisfactory understanding.
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