  Many new material systems are being explored to enable smaller, more capable
and energy efficient devices. These bottom up approaches for atomic and
molecular electronics, quantum computation, and data storage all rely on a
well-developed understanding of materials at the atomic scale. Here, we report
a versatile scanning tunneling microscope (STM) charge characterization
technique, which reduces the influence of the typically perturbative STM tip
field, to develop this understanding even further. Using this technique, we can
now observe single molecule binding events to atomically defined reactive sites
(fabricated on a hydrogen-terminated silicon surface) through electronic
detection. We then developed a new error correction tool for automated hydrogen
lithography, directing molecular hydrogen binding events using these sites to
precisely repassivate surface dangling bonds (without the use of a scanned
probe). We additionally incorporated this molecular repassivation technique as
the primary rewriting mechanism in new ultra-dense atomic data storage designs
(0.88 petabits per in$^{2}$).
