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I think you're confusing two different (but related) terms. Nyquist says that in a channel of bandwidth $B$ you can transmit up to $2B$ orthogonal pulses per second. So, $R_p \leq 2B$, where $R_p$ is the pulse rate. To achieve $R_p = 2B$, the pulses need to be sinc-shaped. Other, more practical pulses achieve slightly less than that. For example, raised ...
I don't think I've seen capacity defined like that before. In the "go-to" information theory book by Thomas Cover, capacity is defined as $C=\frac{1}{2}log_2(1+SNR)$ bits per channel use or $C=Wlog_2(1+SNR)$ bits per second. The bandwidth is the symbol rate so you could have a symbol represent multiple bits which is what happens in all digital communication ...