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How do you know that the CH2s in the boat configuration are closer together than those in the chair configuration? Then, due to fewer electron-electron repulsions, the chair configuration would have a lower potential energy and thus a higher stability right?
Think of the molecule in 3D space. In the chair conformation, one CH2 is pointed down while the one opposite of it is pointed up. There is no angle, torsional, or steric strain because of the positions of the atoms and the minimizing of electron repulsion. In a chair conformation, however, there is steric strain because the CH2s that are on opposite sides are both pointed up (or down depending on how you look at the molecule). This causes steric strain between two axial hydrogens. There is also torsional strain because only 4 pairs have eclipsed hydrogens, as opposed to the H being staggered on adjacent C in the chair conformation.
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