Trapped atomic ion systems are currently the most advanced platform for quantum information processing. Their long coherence times, pristine state initialization and detection, and precisely controllable and versatile interactions make them excellent quantum systems for experiments in quantum computation and quantum simulation. One of the more promising schemes for quantum computing consists of performing single and multi-qubit quantum gates on qubits in a linear ion crystal. Some of the key challenges of scaling such a system are the individual addressing of arbitrary subsets of ions and controlling the growing complexity of motional mode interactions as the number of qubits increases or when the gates are performed faster. Traditional entangling quantum gates between ion qubits use laser pulses to couple the qubit states to the collective motion of the crystal, thereby generating a spin-spin interaction that can produce entanglement between selected qubits. The intrinsic limitations on the performance of gates using this method can be alleviated by applying optimally shaped pulses instead of pulses with constant amplitude. This thesis explains the theory behind this pulse shaping scheme and how it is implemented on a chain of Yb ions held in a linear radiofrequency `Paul' trap. Several experiments demonstrate the technique in chains of two, three, and five ions using various types of pulse shapes. A tightly focused individual addressing beam allows us to apply the entangling gates to a target pair of ions, and technical issues related to such tight focusing are discussed. Other advantages to the pulse shaping scheme include a robustness against detuning errors and the possibility of suppressing undesirable coupling due to optical spillover on neighboring ions. Combined with ion shuttling, we harness these features to perform sequential gates to different qubit pairs in order to create genuine tripartite entangled states and demonstrate the programmable quantum information processing capability of our system.