Stick atomic

When Dalton invented the idea of atoms as participants in chemical reactions, he had the problem of how to stick atomic models together. He instmcted his friend, Peter Ewart, to prepare a set of wooden balls, drill holes into the balls and insert wooden pegs to hold the model in place. These models appeared around 1810, about the same time that Wollaston was postulating the structuring of atoms into regular shapes to form molecules, the word first... 

Holscher, H., Schirmeisen, A., and Schwarz, U.D. (2008) Principles of atomic friction from sticking atoms to superlubric sliding. Philos. Trans. 

Most fiindamental surface science investigations employ single-crystal samples cut along a low-index plane. The single-crystal surface is prepared to be nearly atomically flat. The surface may also be modified in vacuum. For example, it may be exposed to a gas that adsorbs (sticks) to the surface, or a film can be grown onto a sample by evaporation of material. In addition to single-crystal surfaces, many researchers have investigated vicinal, i.e. stepped, surfaces as well as the surfaces of polycrystalline and disordered materials. 

Wlien a surface is exposed to a gas, the molecules can adsorb, or stick, to the surface. Adsorption is an extremely important process, as it is the first step in any surface chemical reaction. Some of die aspects of adsorption that surface science is concerned with include the mechanisms and kinetics of adsorption, the atomic bonding sites of adsorbates and the chemical reactions that occur with adsorbed molecules. 

The coverage of adsorbates on a given substrate is usually reported in monolayers (ML). Most often, 1 ML is defined as the number of atoms in the outemiost atomic layer of the umeconstmcted, i.e. bulk-tenuinated, substrate. Sometimes, however, 1 ML is defined as the maximum iiumber of adsorbate atoms that can stick to a particular surface, which is temied the saturation coverage. The saturation coverage can be much smaller... 

L exposure would produce 1 ML of adsorbates if the sticking coefficient were unity. Note that a quantitative calculation of the exposure per surface atom depends on the molecular weight of the gas molecules and on the actual density of surface atoms, but the approximations inlierent in the definition of tire Langmuir are often inconsequential. 

Atom abstraction occurs when a dissociation reaction occurs on a surface in which one of the dissociation products sticks to the surface, while another is emitted. If the chemisorption reaction is particularly exothennic, the excess energy generated by chemical bond fomiation can be chaimelled into the kinetic energy of the desorbed dissociation fragment. An example of atom abstraction involves the reaction of molecular halogens with Si surfaces [27, 28]. In this case, one halogen atom chemisorbs while the other atom is ejected from the surface. 

The first two of these we can readily approach with the knowledge gained from the studies of trappmg and sticking of rare-gas atoms, but the long timescales involved in the third process may perhaps more usefiilly be addressed by kinetics and transition state theory [35]. 

The addition of potassium to Fe single crystals also enliances the activity for ammonia synthesis. Figure A3.10.19 shows the effect of surface potassium concentration on the N2 sticking coefficient. There is nearly a 300-fold increase in the sticking coefficient as the potassium concentration reaches -1.5 x 10 K atoms cm ... 

Sticking, for simplicity, with a simple atomic system, the kinetic energy may be written... 

The capped sticks model can be seen as a variation of the wire frame model, where the structure is represented by thicker cylindrical bonds (figure 2-123b). The atoms are shi unk to the diameter of the cylinder and ai e used only for smoothing or closing the ends of the tubes. With its thicker bonds, the capped sticks model conveys an improved 3D impression of a molecule when compared with the wire frame model. 

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

When we graph the positions of all six atoms in the x, y plane, the approximate nature of the input file is evident. Anyone who has used simple ball and stick molecular models will see that the carbon atoms in Fig. 4-4 are too close together and the entire molecule is compressed in the -direction. 

One precaution is that, especially with congested molecules, these potential energy loci should not be taken too literally because rotated atoms or groups (within the model) can stick during rotation, then suddenly snap into place , giving a potential energy discontinuity that has no counterpart in the real molecule. 

WebLab Viewer gives a very-high-quality display suitable for publication and presentation. Molecules can be displayed as lines, sticks, ball and stick, CPK, and polyhedrons. In addition, different atoms within the same structure may be displayed in different ways. Text can be added to the display as well as labeling parts of the structure in a variety of ways. The user has control over colors, radii, and display quality. The program can also replicate a unit cell to display a crystal structure. Several types of molecular surfaces can be displayed. 

The earliest ball and stick models were exactly that wooden balls in which holes were drilled to ac commodate dowels that connected the atoms Plastic versions including relatively inexpensive student sets became available in the 1960s and proved to be a valuable learning aid Precisely scaled stainless steel framework and plastic space filling models although relatively expensive were standard equipment in most research laboratories... 

FIGURE 1 6 Molecular models of methane (CH4) (a) Framework (tube) models show the bonds connecting the atoms but not the atoms themselves (b) Ball and stick (ball and spoke) models show the atoms as balls and the bonds as rods (c) Space filling models portray overall molecular size the radius of each sphere approximates the van der Waals radius of the atom (d) An electrostatic potential map of methane... 

Ball and stick model (Section 1 10) Type of molecular model in which balls representing atoms are connected by sticks representing bonds Similar to ball and spoke models of Learning By Modeling... 

Acyclic Compounds. Different conformations of acyclic compounds are best viewed by construction of ball-and-stick molecules or by use of Newman projections (see Fig. 1.2). Both types of representations are shown for ethane. Atoms or groups that are attached at opposite ends of a single bond should be viewed along the bond axis. If two atoms or groups attached at opposite ends of the bond appear one directly behind the other, these atoms or groups are described as eclipsed. That portion of the molecule is described as being in the eclipsed conformation. If not eclipsed, the atoms... 

Panel 1.1 The 20 different amino acids that occur in proteins. Only side chains are shown, except for the first amino acid, alanine, where all atoms are shown. The bond from the side chain to Ca is red. A ball-and stick model, the chemical formula, the full name, and the three-letter and one-letter codes are given for each amino acid. 

All pictorial representations of molecules are simplified versions of our current model of real molecules, which are quantum mechanical, probabilistic collections of atoms as both particles and waves. These are difficult to illustrate. Therefore we use different types of simplified representations, including space-filling models ball-and-stick models, where atoms are spheres and bonds are sticks and models that illustrate surface properties. The most detailed representation is the ball-and-stick model. However, a model of a protein structure where all atoms are displayed is confusing because of the sheer amount of information present (Figure 2.9a). 

Figure S.22 Chemical formula for sialic acid (a-5-n-acetylneuramlnlc acid) drawn In approximately the same orientation as the ball and stick models in Figure 5.24. Ri and Rz which are H atoms in sialic acid, denote substituents introduced to design tightly bound inhibitors. These are large and hydrophobic as shown in Figure 5.24.

In most cases surface reactions proceed according to well-established elementary steps, as schematized in Fig. 1. The first one comprises trapping, sticking, and adsorption. Gaseous reactants atoms and/or molecules are trapped by the potential well of the surface. This rather weak interaction is commonly considered as a physisorbed precursor state. Subsequently, species are promoted to the chemisorbed state, that is, a much stronger... 

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