Yes, there have been numerous experiments and observations that have directly studied the structure of an atom. One of the most famous experiments is the gold foil experiment conducted by Ernest Rutherford in 1911, also known as the Rutherford scattering experiment. In this experiment, Rutherford bombarded a thin sheet of gold foil with alpha particles (positively charged particles) and observed their scattering patterns.
The unexpected results of this experiment led to the discovery of the atomic nucleus and the development of the nuclear model of the atom. Rutherford found that most of the alpha particles passed through the gold foil with little deflection, indicating that atoms are mostly empty space. However, a small fraction of the alpha particles were deflected at large angles, and a very few even bounced straight back. This result suggested that the positive charge of the atom and most of its mass are concentrated in a tiny, dense region called the nucleus.
Since then, many other experiments have been conducted to study the structure of atoms. For example, the development of spectroscopy has allowed scientists to analyze the light emitted or absorbed by atoms, which provides valuable information about their energy levels and electron configurations. Techniques such as X-ray crystallography have been used to determine the arrangement of atoms within molecules and crystals.
More recently, advanced imaging techniques, such as scanning tunneling microscopy (STM) and atomic force microscopy (AFM), have made it possible to directly visualize individual atoms and manipulate them. These techniques have allowed scientists to study the surface structure of materials at the atomic scale and investigate various properties and behaviors of atoms.
Overall, through a combination of theoretical models, experimental observations, and technological advancements, scientists have made significant progress in understanding the structure of atoms and their constituent particles.