The properties of cold ion plasmas with large numbers ͑Ͼ200͒ of laser-and sympathetically cooled species are modeled in detail using molecular dynamics simulations. We describe how to extract temperatures and ion numbers from CCD images. The identification of the ion species by excitation of their oscillation modes is discussed. The sympathetic cooling efficiency, effects of the rf micromotion and of collision heating by a neutral background gas are analyzed, in part experimentally.

Gas-phase singly protonated organic molecules of mass 410 Da (Alexa Fluor 350) have been cooled from ambient temperature to the hundred millikelvin range by Coulomb interaction with laser-cooled barium ions. The molecules were generated by an electrospray ionization source, transferred to and stored in a radio-frequency trap together with the atomic ions. Observations are well described by molecular dynamics simulations, which are used to determine the spatial distribution and thermal energy of the molecules. In one example, an ensemble of 830 laser-cooled 138Ba+ ions cooled 200 molecular ions to less than 115 mK. The demonstrated technique should allow a large variety of protonated molecules to be sympathetically cooled, including molecules of much higher mass, such as proteins.

In the Letter we reported wrong numbers for the temperature cooling and heating rates H dT=dt for Ba and AF ions derived from MD simulations. The correct numbers on page 4, 2nd paragraph, are, in order of appearance:(1) 10:4 K=s instead of 7:6 K=s; (2) 18:5 K=s instead of 4:3 K=s, 138 mK instead of 115 mK, 4:1 K=s instead of 2:5 K=s; (3) 10:6 K=s instead of 3:7 K=s, 88 mK instead of 95 mK; (4) the upper limit for the AF secular temperature is T AF 138 mK instead of 115 mK. This is also the value that should appear in the abstract.

Gas-phase multiply charged proteins have been sympathetically cooled to translational temperatures below 1 K by Coulomb interaction with laser-cooled barium ions in a linear ion trap. In one case, an ensemble of 53 cytochrome c molecules ͑mass Ӎ12 390 amu, charge +17e͒ was cooled by Ӎ160 laser-cooled barium ions to less than 0.75 K. Storage times of more than 20 min have been observed and could easily be extended to more than an hour. The technique is applicable to a wide variety of complex molecules.

Using the positively charged aniline ion ͑C 6 H 5 NH 2 + ͒ as a test molecule, we demonstrate that it is possible to study consecutive photodissociation of complex molecular ions at the single molecule level in an ion trap. When a single C 6 H 5 NH 2 + ion is exposed to laser light at 397 nm and 294 nm, direct or consecutive photodissociation leads to the production of a range of smaller polyatomic molecular ions such as C 5 H 6 + and C 3 H 3 + . The applied method is very versatile and can, e.g., be used in combination with free electron lasers or synchrotron radiation sources.