In doing so, we found that the atom size seen in TEM images shows a strong correlation to the atomic number ( Z), particularly if we consider the shot noise in digital images. 1 B) more confusing than revealing, and we became convinced of a need for new atomic radii that better represent the experimental images (compare Fig. Here, we found the CPK atomic radii ( Fig. 1 A) that forms in the synthesis of a crystal of a metal–organic framework (MOF MOF-5) ( 12) was impossible without reducing the number of initial guess structures down to several hundred from a total of 4,096 isomers and their rotamers as to the 2-iodo-1,4-phenylene bridges ( Fig. For example, structure assignment of the AR-TEM images of a rotating zinc cluster ( Fig. The difficulty is particularly important when we deal with unknown structures that are mobile and lack structural periodicity. 1), and this discrepancy contributed to reducing the popularity of AR-TEM in molecular science. However, experimental TEM images often differ greatly from what chemists expect using their favorite molecular models ( Fig. With the advent of atomic-resolution transmission electron microscopy (AR-TEM) achieving sub-Ångstrom image resolution and submillisecond time resolution ( 5– 8), an era of “cinematic molecular science” has arrived, where chemists can visually study the time evolution of molecular motions and reactions at atomistic precision ( 9– 11). The atomic radii chosen in these models reflect the electronic properties of atoms and molecules. Shannon’s ionic model ( 4) is useful for inorganic chemistry. Representing the van der Waals isosurface, a Corey–Pauling–Koltun (CPK) model was developed to illustrate the molecular surface for analysis of intermolecular interactions ( 3). Whereas wire and ball-and-stick models are primitive, showing only bond lengths, bond angles, and torsional angles, chemists have implemented further information into molecular models.
Here, the choice of the radii of the spheres, in addition to coloring, is the most crucial visual identifier of atoms and atomic ions, and a variety of useful constructions of radii, either empirical or quantum mechanical ( 1, 2), have been proposed in accord with chemical intuition. The world of atoms and molecules invisible to human eyes has been illuminated by the development of three-dimensional models in which atoms represented by spheres are connected to each other with appropriate spatial disposition. The molecular models will stimulate the imaginations of chemists planning to use AR-TEM for their research. Two parameter sets were developed for TEM images recorded under high-noise (ZC HN) and low-noise (ZC LN) conditions. We propose Z-correlated (ZC) atomic radii for modeling AR-TEM images of single molecules and ultrathin crystals with which we can develop a good estimate of the molecular structure from the TEM image much more easily than with conventional molecular models. We found a good correlation between the atomic number ( Z) and the atomic size seen in TEM images when we consider shot noise in digital images. The difference arises from the fundamental design of the molecular models that represent atomic connectivity and/or the electronic properties of molecules rather than the nuclear charge of atoms and electrostatic potentials that are felt by the e-beam in TEM imaging. However, the appearance of experimental TEM images often differs greatly from that of conventional molecular models, and the images are difficult to decipher unless we know in advance the structure of the specimen molecules. With the advent of atomic resolution transmission electron microscopy (AR-TEM) achieving sub-Ångstrom image resolution and submillisecond time resolution, an era of cinematic molecular science where chemists can visually study the time evolution of molecular motions and reactions at atomistic precision has arrived.