We demonstrate quantum control of $^9$Be$^+$ ions directly implemented by an optical frequency comb. Based on numerical simulations of the relevant processes in $^9$Be$^+$ for different magnetic field regimes, we demonstrate a wide applicability when controlling the combs spectral properties. We introduce a novel technique for the selective and efficient generation of a spectrally tailored narrow-bandwidth optical frequency comb near 313 nm. We experimentally demonstrate internal state control and internal-motional state coupling of $^9$Be$^+$ ions implemented by stimulated-Raman manipulation using a spectrally optimized optical frequency comb. Our pulsed laser approach is a key enabling step for the implementation of quantum logic and quantum information experiments in Penning traps.
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