Why Rubidium-87 instead of Rubidium-85 for Atomic Clocks? The traditional Rubidium isotope of choice for atomic clocks is Rubidium-87, although I have found papers describing clocks built around Rubidium-85. I cannot readily find any references for why 87 is preferred in clocks.
Rubidium-85 is the naturally more common isotope (72% vs 28% for Rubidium-87) and is radioactively stable. Meanwhile, Rubidium-87 is weakly radioactive with a half life around 50 billion years, though I imagine this fact is not of much importance.
Meanwhile, the hyperfine transition frequency used in Rubidium-87 is around 6.8 GHz while that for Rubidium-85 is around 3.0 GHz. So for a given quality factor, it would appear the clock employing the 3.0 GHz transition would have a smaller linewidth than a 6.8 GHz clock, leading to higher stability.
So I haven't found a compelling reason for why Rubidium-87 would dominate the atomic clock scene. I would appreciate an identification of what I'm missing here.
 A: For what it's worth (US patent US6320472B1):

The resonance cell, containing the ensemble of alkali atoms, is placed
inside a microwave cavity tuned to the transition between which the
population inversion has been created. The light transmitted is
detected with the help of a photodetector, as shown in FIG. 1. It is
to be noted that, upon optical pumping, the cell becomes transparent
to the incident radiation since atoms are pumped out of the absorbing
level, F=1. Microwave energy is fed to the cavity and its effect on
the atoms, when tuned to the hyperfine frequency, is to alter the
population of the two levels of the ground state and, consequently,
the optical transmission of the ensemble. The ground state hyperfine
resonance signal is thus detected on the transmitted light and is used
to lock the frequency of the microwave source used to feed the cavity.
The resulting device is a system whose frequency is locked to an
atomic resonance.


Although this approach has achieved substantial
success, it has, nonetheless, several disadvantages. In particular,
the need for a microwave cavity limits availability of reduction in
the dimensions of the device. This limitation has been a main factor
in the selection of rubidium 87 (hyperfine frequency=6.8 GHz) over
rubidium 85 (hyperfine frequency=3.0 GHz), the cavity size required
being larger for rubidium 85 than for rubidium 87.

A: People always ask me "Why rubidium?" and it was fun to finally get to look into the answer. We use ${}^{87}$Rb in my lab.
And I think it's worth first asking the question in exactly that form: why rubidium?
I think the answer is largely historical.
Rubidium actually got laser cooled a little later than some other common atoms, but then it was realized that CD drives had diodes that worked at 780 nm, the wavelength needed for laser cooling Rb. This brought laser cooling into the reach of a lot of labs that didn't necessarily have huge amounts of funding for the early laser systems.
There are a couple of other good reasons for rubidium to have been historically chosen, as well. You have to understand that the holy grail of early atomic physics was getting a BEC, a Bose-Einstein condensate. And all thoughts were geared in that direction. So when they found an atom with a positive background scattering length, whose atomic cross sections also made evaporative cooling meaningfully useful, they believed they found "God's atom" (this quote might come from Eric Cornell).
***Edited to add: "historical reasons" might not seem like the best justification (which it isn't), but remember that, even now, a good number of PIs and faculty in atomic physics were grad students, postdocs, and early-career faculty when laser cooling was still new, so these historical reasons came at a time that shaped their thinking for the rest of their careers, and therefore the design of their experiments, the ones producing papers today. My PI still talks about the old dye laser systems sometimes.
As a note, ${}^{85}$Rb actually has a negative background scattering length, which makes BECs unstable unless you use a Feshbach resonance at a fairly large magnetic field to make it positive. This puts it at a historical disadvantage.
But there's actually a better reason not to use 85 in your specific application, atomic clocks. It's simple and already stated here on the thread: its ground-state hyperfine frequency of 3-ish GHz is smaller than 87's splitting of 6.8 GHz.
This is why cesium, at over 9 GHz, is still the world's standard, and why the new strontium optical lattice clocks (which work at 429 THz) are the world-record holders.
When you think about atomic clocks, the absolute first question you have to ask is "How fast can it go?" The questions of quality and stability are engineering questions; the fundamental oscillation frequency is something you can never get around except by changing the basic setup.
You want to be reaching for stability that matches the fastest oscillation you can get, not settling for a slower clock that you can get really stable.
The related statement I should make is a different way of thinking about the quality factor. This quantity is defined as $Q=\nu_0/\Delta\nu$. That is, for a given quality factor, a higher resonance frequency requires a higher linewidth. And since $Q$ is generally in the denominator of the instability, higher $Q$, means lower instability. This means higher resonance frequency gives lower instability... if you can keep the linewidth down.
Now, two isotopes of rubidium don't differ too much in the basic atomic properties. In particular the fundamental stability limit, the linewidth of the excited state, will always vary very little between isotopes. I can't seem to find a comparison of the atomic linewidths of the transitions actually used in rubidium clocks (the two-photon transitions or the actual "clock transition"), so as an example, the 5P to 5S transition, the linewidth is 6.066 MHz in ${}^{85}$Rb and 6.059 MHz in ${}^{87}$Rb. Getting down to that fundamental limit is just engineering, and any laser and vacuum systems that will work with 85 will work with 87 since they only really vary by being isotopes. (If anything, 87 I think is easier to trap due to lower vaporizing temperature, but don't quote me on that.) So the linewidth can in fact be kept about constant between the two isotopes.
So if you're going for rubidium, you want the faster oscillator with the same linewidth: ${}^{87}$Rb is the way to go.
A: Was able to lookup these two points that may offer a plausible explanation -
From the Wikipedia entry for Rubidium -

In 1995, rubidium-87 was used to produce a Bose–Einstein condensate,
for which the discoverers, Eric Allin Cornell, Carl Edwin Wieman and
Wolfgang Ketterle, won the 2001 Nobel Prize in Physics.

And also from the Wikipedia entry on Bose–Einstein_condensate -

In condensed matter physics, a Bose–Einstein condensate (BEC) is a
state of matter that is typically formed when a gas of bosons at very
low densities is cooled to temperatures very close to absolute zero
(−273.15 °C or −459.67 °F). Under such conditions, a large fraction of
bosons occupy the lowest quantum state, at which point microscopic
quantum mechanical phenomena, particularly wavefunction interference,
become apparent macroscopically. A BEC is formed by cooling a gas
of extremely low density (about 100,000 times less dense than normal
air) to ultra-low temperatures.

Perhaps these two points above can offer the explanation you are looking for?
