Atoms and atomic structure

Table 1.1 presents some of the advantages and disadvantages of different ways of defining the notion of an element. Clearly a parallel list could be drawn up for compounds. The most useful approach to take will depend to some extent on the class and in particular on how much relevant prior knowledge students bring to the lesson. Ideas based on notions of atoms, or subatomic particles, can clearly only be introduced after students have learnt about atoms and atomic structure, respectively. 

These effects were recorded in Greece around 2500 years ago and not long afterwards Democritus proposed an atomic structure for all matter. The magnetic compass seems to have taken another 1500 years to appear and magnetic theory a further half century. 

A 1.2.2 QUANTUM THEORY OF ATOMIC AND MOLECULAR STRUCTURE AND MOTION... 

Surfaces are found to exliibit properties that are different from those of the bulk material. In the bulk, each atom is bonded to other atoms m all tliree dimensions. In fact, it is this infinite periodicity in tliree dimensions that gives rise to the power of condensed matter physics. At a surface, however, the tliree-dimensional periodicity is broken. This causes the surface atoms to respond to this change in their local enviromnent by adjusting tiieir geometric and electronic structures. The physics and chemistry of clean surfaces is discussed in section Al.7.2. 

Much surface work is concerned with the local atomic structure associated with a single domain. Some surfaces are essentially bulk-temiinated, i.e. the atomic positions are basically unchanged from those of the bulk as if the atomic bonds in the crystal were simply cut. More coimnon, however, are deviations from the bulk atomic structure. These structural adjustments can be classified as either relaxations or reconstructions. To illustrate the various classifications of surface structures, figure A1.7.3(a ) shows a side-view of a bulk-temiinated surface, figure A1.7.3(b) shows an oscillatory relaxation and figure A1.7.3(c) shows a reconstructed surface. 

Most metal surfaces have the same atomic structure as in the bulk, except that the interlayer spaciugs of the outenuost few atomic layers differ from the bulk values. In other words, entire atomic layers are shifted as a whole in a direction perpendicular to the surface. This is called relaxation, and it can be either inward or outward. Relaxation is usually reported as a percentage of the value of the bulk interlayer spacing. Relaxation does not affect the two-dimensional surface unit cell synuuetry, so surfaces that are purely relaxed have (1 x 1) synuuetry. 

At a surface, not only can the atomic structure differ from the bulk, but electronic energy levels are present that do not exist in the bulk band structure. These are referred to as surface states . If the states are occupied, they can easily be measured with photoelectron spectroscopy (described in section A 1.7.5.1 and section Bl.25.2). If the states are unoccupied, a teclmique such as inverse photoemission or x-ray absorption is required [22, 23]. Also, note that STM has been used to measure surface states by monitoring the tunnelling current as a fiinction of the bias voltage [24] (see section BT20). This is sometimes called scamiing tuimelling spectroscopy (STS). 

AFM measures the spatial distribution of the forces between an ultrafme tip and the sample. This distribution of these forces is also highly correlated with the atomic structure. STM is able to image many semiconductor and metal surfaces with atomic resolution. AFM is necessary for insulating materials, however, as electron conduction is required for STM in order to achieve tiumelling. Note that there are many modes of operation for these instruments, and many variations in use. In addition, there are other types of scaiming probe microscopies under development. 

Herzberg G 1937 Atomic Spectra and Atomic Structure (New York Prentice-Hall)... 

Magnussen O M, Hotios J, Beitei G, Koib D M and Behm R J 1991 Atomic structure of ordered copper adiayers on singie-crystaiiine goid eiectrodes J. Vac. Sc/. Technol. B 9 969... 

Hegenbart G and Mussig Th 1992 Atomic force microscopy studies of atomic structures on AgBr(111) surfaces Surf. Sc/. Lett. 275 L655... 

The atomic structure of a surface is usually not a simple tennination of the bulk structure. A classification exists based on the relation of surface to bulk stnicture. A bulk truncated surface has a structure identical to that of the bulk. A relaxed surface has the synnnetry of the bulk stnicture but different interatomic spacings. With respect to the first and second layers, lateral relaxation refers to shifts in layer registry and vertical relaxation refers to shifts in layer spacings. A reconstructed surface has a synnnetry different from that of the bulk synnnetry. The methods of stnictural analysis will be delineated below. 

Aono M and Souda R 1985 Quantitative surface atomic structure analysis by low energy ion scattering spectroscopy Japan. J. Appl. Phys. Part 1 24 1249-62... 

Figure B2.5.12 shows the energy-level scheme of the fine structure and hyperfme structure levels of iodine. The corresponding absorption spectrum shows six sharp hyperfme structure transitions. The experimental resolution is sufficient to detennine the Doppler line shape associated with the velocity distribution of the I atoms produced in the reaction. In this way, one can detennine either the temperature in an oven—as shown in Figure B2.5.12 —or the primary translational energy distribution of I atoms produced in photolysis, equation B2.5.35.

Vop D, Kruger P, Mazur A and Pollmann J 1999 Atomic and electronic structure of WSe from ah initio theory bulk crystal and thin film systems Phys. Rev. B 60 14 311... 

Reinhardt W P 1982 Complex coordinates in the theory of atomic and molecular structure and dynamics Ann. Rev. Phys. Chem. 35 223... 

Koinuma M and Uosaki K 1996 Atomic structure of bare p-GaAs(IOO) and electrodeposited Cu on p-GaAs (100) surfaces in H2SO4 solutions An AFM study J. Eiectroanai. Chem. 409 45-50... 

What are the principal differences in physical and chemical properties between any one metal from Group I and any one metal from Group IV and any one transition metal How far can you explain these differences in terms of their different atomic structures ... 

The structure of nitrogen dioxide contains an unpaired (odd) electron and the molecule is consequently paramagnetic. The odd electron is not localised on any atom and the structure can be best represented as a resonance hybrid of the structures ... 

Fig. 1. Structure adapted hierarchical description of Coulomb interactions in biological macromolecules. Filled circles (level 0) represent atoms, structural units (li vel 1) are surrounded by a single-line border, and clusters (level 2) are surrounded by a double-line border.

The PDB contains 20 254 experimentally determined 3D structures (November, 2002) of macromolecules (nucleic adds, proteins, and viruses). In addition, it contains data on complexes of proteins with small-molecule ligands. Besides information on the structure, e.g., sequence details (primary and secondary structure information, etc.), atomic coordinates, crystallization conditions, structure factors. 

Many molecules are obtained and used in a crystalline form, the nature of which can have e significant impact on their properties and behaviour. Moreover, it is sometimes possible foi a given material to exist in more than one crystalline form, depending upon the conditions under which it was prepared. This is the phenomenon of polymorphism. This can be important because the various polymorphs may themselves have different properties. It is Iberefore of interest to be able to predict the three-dimensional atomic structure(s) that a gi en molecule may adopt, for those cases where it is difficult to obtain experimental data and also where one might wish to prioritise molecules not yet synthesised. 

Birktoft J J and D M Blow 1972. The structure of Crystalline Alpha-Chymotrypsin V. The Atomic Structure of Tosyl-Alpha-Qiymotrypsin at 2 Angstroms Resolution. Journal of Molecular Biology 68 187-240. 

The Hydrogenic atom problem forms the basis of much of our thinking about atomic structure. To solve the corresponding Schrodinger equation requires separation of the r, 0, and (j) variables... 

For the kind of potentials that arise in atomic and molecular structure, the Hamiltonian H is a Hermitian operator that is bounded from below (i.e., it has a lowest eigenvalue). Because it is Hermitian, it possesses a complete set of orthonormal eigenfunctions ( /j Any function spin variables on which H operates and obeys the same boundary conditions that the ( /j obey can be expanded in this complete set... 

The development of the structural theory of the atom was the result of advances made by physics. In the 1920s, the physical chemist Langmuir (Nobel Prize in chemistry 1932) wrote, The problem of the structure of atoms has been attacked mainly by physicists who have given little consideration to the chemical properties which must be explained by a theory of atomic structure. The vast store of knowledge of chemical properties and relationship, such as summarized by the Periodic Table, should serve as a better foundation for a theory of atomic structure than the relativity meager experimental data along purely physical lines. ... 

The mobility of the proton in position 2 of a quaternized molecule and the kinetics of exchange with deuterium has been studied extensively (18-20) it is increased in a basic medium (21-23). The rate of exchange is close to that obtained with the base itself, and the protonated form is supposed to be the active intermediate (236, 664). The remarkable lability of 2-H has been ascribed to a number of factors, including a possible stabilizing resonance effect with contributions of both carbene and ylid structure. This latter may result from the interaction of a d orbital at the sulfur atom with the cr orbital out of the ring at C-2 (21). 

In Chapter 1 we saw that a major achievement of the first half of the twentieth cen tury was the picture of atomic and molecular structure revealed by quantum mechan ICS In this the last chapter we examine the major achievement of the second half of that century—a molecular view of genetics based on the structure and biochemistry of nucleic acids... 

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