  Modeling molecular absorption by Earth's atmosphere is important for a wide
range of astronomical observations, including broadband NIR photometry and
high-resolution NIR spectroscopy. Using a line-by-line radiative transfer
approach, we calculate theoretical transmission spectra in the deep red optical
(700 to 1050 nm) for Apache Point Observatory. In this region the spectrum is
dominated by H2O, which is known to be highly variable in concentration on
short timescales. We fit our telluric models to high-resolution observations of
A stars and estimate the relative optical depth of H2O absorption under a wide
range of observing conditions. We compare these optical depth estimates to
simultaneous measurements of Precipitable Water Vapor (PWV) based on data from
a Global Positioning System (GPS) receiver located at Apache Point. We find
that measured PWV correlates strongly with the scaling of H2O absorption lines
in our spectra, indicating that GPS-based PWV measurements combined with
atmospheric models may be a powerful tool for the real-time estimation of total
molecular absorption in broad NIR bands. Using photometric measurements from
the Sloan Digital Sky Survey (SDSS) DR8 database we demonstrate that PWV biases
the calibrated r-z colors and z-band fluxes of mid-M stars but not mid-G stars.
While this effect is small compared to other sources of noise in the SDSS
z-band observations, future surveys like the Large Synoptic Survey Telescope
aim for higher precision and will need to take time-variable molecular
transmission into account for the global calibration of NIR measurements of
objects having strong spectral features at these wavelengths. Empirical
calibrations based on PWV may be immediately applicable to ongoing efforts to
make mmag differential measurements of M stars to detect transiting exoplanets.
