Yes. Under the right circumstances there is no reason why simple molecules cannot be transformed into atoms. Atoms combine into molecules and when one figures out the energetics, it can be shown that in many cases the atom version should be more stable than the molecule. Let us look at one case which is best explained by a molecule to atom transformation.
In 1998, two scientists, Stanley Fleischmann and Marvin Pons, announced that when they had carried out an electrolysis with a Palladium electrode and "Heavy Water," there was energy produced within the Palladium electrode, to the point, in one case of melting the electrode down. They ascribed this energy production to the fusion of Deuterium atoms to Helium 4 atoms, and called the process, "Cold Fusion."
The scientific community "went ballistic" at the term, "fusion." It is an item of faith in the scientific community that "fusion" can only take place at extremely high temperatures and pressures such as are found in the center of the Sun. In the almost twenty years that have passed since then a number of other workers have shown that the phenomenon reported by Fleischmann and Pons is real and have also reported other results of similar types. However, most of the establishment considers the area as "Kook science," rather than as a frontier between molecular and nuclear science where it probably should be considered. Unfortunately, explanations given for the phenomenon range from the fanciful to the bizarre.
The problems with this whole ares stem from the separation of nuclear chemistry from molecular chemistry which started with Chadwick's discovery of the neutron in the 1930's. and the "romance" that the scientific community has had with this particle since. The neutron was enshrined as a fundamental particle of nature, an essential unit of every nucleus except of that of Hydrogen 1, This choice of the neutron as a basic building block of nature was in spite of the fact that it is energetically unstable to both the electron and proton as free entities and the Hydrogen 1 atom which can be considered as isomeric to it. The neutron was not given its proper place as an alternate state of matter which can come into existence under certain high-energy conditions. As a consequence of the neutrons "mis-placement" there began the high energy particle physics field searching for other "fundamental particles," which could be found by "atom-smashing." For some seventy years these scientists have discovered more and more "fundamental particles," which. like the neutron, should be properly classified as "alternate, high-energy states of matter.
All of this has led to such inanities as the Standard Model based upon these sets of "fundamental particles. " and the ideas of "Strong and Weak Nuclear Forces." The latter are ideas that arise directly from the ascribing to neutrons their existence as such in the nuclei of atoms. If. instead of adopting the neutron as a "fundamental particle," which had to be accounted for as such in nuclei, the neutron had been given its proper place and nuclei had been considered in the same way as molecules are, that is, as centers bonded by electrons moving in paths within and among them, perhaps we would have had a much more productive 70 years.
The point of all this is that. for the Fleischmann-Pons observations, there is a very simple probable explanation if one notes that both the Deuterium molecule, D:D, and the Helium 4 atom, He4, can be properly considered as being composed of four protons bonded by four electrons. Even the shapes are somewhat similar. The D:D unit can be visualized as a "stretched tetrahedron," and the He4 nucleus as compact, perfect tetrahedron. The latter could be an instantaneous shape of a vibrational mode of the former. If there is a "receptor" available to drain off the excess vibrational energy of the "D:D form," the more stable "atom" structure can be taken on. Palladium with its plethora of energy levels is an ideal receptor for the excess energy of vibration. What Fleischman and Pons almost surely observed was what could be called an "Iso-set
isomerization" between the molecular and atomic forms of a set of protons and electrons. There are many such possibilities, some of which have apparently been observed in other "Cold Fusion" type experiments.
Surely molecules can be transformed to atoms under the proper conditions. It's an area that should be wide open to open-minded scientists.