|Video of an animated molecule: kinesin, a motor protein, carrying a load along a microtubule. |
In 2006, American planetary scientist Carolyn Porco stated, to cite an example, albeit incorrect, usage of this term, in her summary argument, that she believes humans are not alone in the universe, that: 
“Sometime in the interval of 3.8 to 3.5 billion years ago, self-replicating organisms [originated] from inanimate materials in a very narrow window of time in a complicated chain of chemical events that must have occurred to evolve animated molecular structures from inanimate atoms.”
The subject of animate verses inanimate often comes to the fore in the study of the physics and chemistry of social systems. This is exemplified in English chemical physicist Philip Ball’s 2004 article “The Physical Modelling of Human Social Systems”, wherein he asks: 
“Can there really be any similarities between, say, a collection of inanimate particles in a fluid interacting via simple, mathematically defined forces of attraction and repulsion, and communities of people each of whom is governed by an unfathomable wealth of psychological complexity?”
Here, Ball defines gas particles and fluid molecules as being inanimate, and asks whether or not the laws that govern these systems can be scaled up to humans.
An example of non-moving inanimate molecule would be a molecule affixed or bonded to a surface, and thus immobilized.
An example of a simple moving in straight trajectory inanimate molecules include: gas molecules, which are said to obey the Boltzmann chaos assumption, and travel around chaotically in straight trajectories, banging into each other, at speeds of 1,200 miles per hour, or the single water molecule, which can only move in essentially straight line trajectories, and is not able to bend its atomic geometry.
Bending animate molecules
An example of simple animate "bending" molecule include the 3-element retinal molecule, which straightens in response to a single photon.
Surface-moving animate molecules
Examples of molecules animated in the form of walking or moving on a surface include: Steve Bartel's 2005 walking molecule, i.e. DTA (9,10-dithioanthracene) and 2007 molecular carriers, i.e. nano-walkers, as well as the two-legged motile protein “kinesin” that walks along microtubules carrying loads to destinations, being powered by ATP.  Kinesin is a small 6-element molecule, with molecular formula of about C400H620N100O120P50S20, that walks, carries things, and has a metabolism, so to speak.
Folding animated molecules
An example of an intermediate in complexity animated molecule is a protein molecule, a chain of polypeptides that folds inward on itself into its native state.
Boundaried animated molecules
A specific demarcation of in classifications of animate molecules are those that have a boundary or semipermeable boundary, within which an atomic turnover rate occurs. This is a complex subject. Examples in this classification include: the 15-element bacterial molecule, a 22-element fish molecule, or the 26-element human molecule (a person). 
To note, it is difficult to, as of yet, classify large planetary-sized molecules such as the earth molecule or sun molecule, being that they move, in certain trajectories, but the term “animate” does not seem applicable, so to speak. More work needs to be done of dynamics of the universe before better classifications can be made in this area.
● Animate matter
● Animate engine
● The Animate and Inanimate
● Animate thermodynamics
● Living molecule
1. Ball, Philip. (2004). “The Physical Modeling of Human Social Systems”, A Review in ComPlexUs, 1, 190, Nov.
2. Kinesin – Wikipedia.
3. Thims, Libb. (2008). The Human Molecule (issuu) (preview) (Google Books) (docstoc). LuLu.
4. Porco, Carolyn. (2006). “I believe we are not alone [in the universe], but can’t prove it” In: What We Believe but Cannot Prove (editor: John Brockman) (pgs. 14-16). Harper Perennial.