For all their periodic tables, styrofoam ball-and-pencil models, and mouth-garbling vocabulary, chemists really don't know jack about molecules.

Part of the problem is they can't really control what molecules do. Molecules spin, vibrate, and trade electrons, all of which affect the way they react with other molecules. Of course, scientists know enough about those scaled-up reactions to do things like make concrete, refine gasoline, and brew beer. But if you're trying to use individual molecules as tools, or manipulate them so precisely that you can snap them together like Lego pieces, you need better control. Scientists aren't all the way there yet, but recently scientists at the National Institute of Standards and Technology solved an early challenge: controlling a single molecule's behavior.

At the very basic level, controlling a molecule would let scientists learn more about it. "This is a long-standing problem," says Dietrich Leibfried, a physicist with NIST's Ion Storage Group in Boulder, Colorado. "Everything around us is made out of molecules, but it's hard to precisely find out about them." And that would have practical applications. For instance, NIST keeps tables of molecular properties that astrophysicists consult when they're reading the spectral signatures of faraway stars and exoplanets. Filling in those blanks would support predictions of whether some exoplanet can support life. With enough control, scientists won't just get a better look at molecules—they'll manipulate matter.

But for now, they are still experimenting. Scientists know how to control atoms using cold vacuum and lasers—so at NIST, scientists' limited molecular control builds on that knowledge. Their research, published yesterday in Nature, describes their experiment: They begin with a vacuum chamber, a 3-inch box containing a tiny electrode, which itself holds a single positively charged calcium atomic ion. Then come the molecules: Ionized hydrogen gas, which the scientists leak into the vacuum chamber until a single H 2 reacts with the calcium atom.

Now the ionized atom and the ionized molecule are trapped together. But they're repelled by their positive charges, and the force of the repulsion sends them vibrating—like two magnets when you bring them close. They're also spinning, like a lopsided barbell hurled into the air.

So the scientists set out to freeze the pair in place, again calling on their skills of atomic control. First they fire a low-energy laser at the calcium atom, cooling it and stopping its motion—and because it's coupled to the hydrogen molecule, the hydrogen stops vibrating as well. That's the easy part. The calcium-hydride is still rotating. "That rotation, the spinning along the horizontal or vertical plane, is the hardest thing to control," says Leibfried. Imagine trying to stick Legos together if they were spinning independently. Leibfried and his group do know how to stop, and even alter the spinning. They figured that out last year using lasers tuned to specific frequencies.

All that rigamarole is worthless if you don't know which way the molecule is pointing, though. And if you want to check in on the molecule—by firing another laser—you set it into random motion once again. So instead the NIST scientists fire a teeny tiny laser at the calcium atom, causing it to wiggle. Because it is connected to the hydrogen molecule, it picks up on the molecule's state. And Leibfried and his team can "read" that state by examining the way the laser's light scatters when it encounters the calcium atom. The whole intricate choreography between them lasts about a millisecond, and at the end they can see if the molecule behaved as it was directed.

So what's the point of all that? If you can control with certainty the orientation of a molecule, it's one step closer to sticking them together exactly how you want—no more tossing compounds in a beaker and praying for the right kind of bubbles. Or, to return to the Lego analogy, you can understand—and manipulate—how molecules stick together.

This discovery builds off work done by Leibfried's mentor, Nobel winner David Wineland, who did the foundational atomic control work behind atomic clocks based on single trapped ions. But unlike atomic clocks—which changed the scale at which scientists could measure time, and led to breakthroughs like GPS—this process isn't ready to revolutionize chemistry just yet. Scientists need to fine-tune their control, and have yet to proof the concept on molecules besides hydrogen. Having just one molecule would be like trying to build a city from Legos using only 2×4 bricks.