Atomic perspective

In this chapter, we present the atomic perspective of matter, as expressed by atomic theory and the principies of atomic stmcture. We describe the buiiding biocks of atoms eiectrons, protons, and neutrons. Then we show how these interact to form aii the chemicai eiements and expiain which combinations are stabie. Next we describe how atomic masses are reiated to these buiiding biocks. We end the chapter by introducing ions, atoms that have either iost or gained eiectrons. Eurther appiications of radioactive atoms in medicine are found within the chapter. 

In the discussions to follow, the concept of the interfadal region will be presented from a molecular (or atomic) perspective and from the viewpoint of the thermodynamics involved. In this way one can obtain an idea of the situations and events occurring at interfaces and have at hand a set of basic mathematical tools for understanding the processes involved and to aid in manipulating the events to best advantage. The concepts presented are intended to be primarily qualitative in nature and do not necessarily represent reality in every detail. Similarly, the mathematical tools will be, for the most part, the basic elements necessary for accomplishing the purpose, with little or no derivation presented. More elaborate and sophisticated treatments of the subjects will be referenced but left for the more adventurous reader to pursue as needed. 

Half-Reactions Building a Galvanic Cell Terminolo for Galvanic Cells Atomic Perspective on Galvanic Cells... 

Tiana D, Francisco E, Blanco MA, Macchi P, Sironi A, Pendas AM (2010) Bonding in classical and non-classical transition metal carbonyls the interacting quantum atoms perspective. J Chem Theory Comput 6 1064-1074... 

From an atomic perspective, plastic deformation corresponds to the breaking of bonds with original atom neighbors and then the re-forming of bonds with new neighbors as large numbers of atoms or molecules move relative to one another upon removal of the stress, they do not return to their original positions. The mechanism of this deformation is different for crystalline and amorphous materials. For crystalline solids, deformation is accomplished by means of a process called slip, which involves the motion of dislocations as discussed in Section 7.2. Plastic deformation in noncrystalline solids (as well as liquids) occurs by a viscous flow mechanism, which is outlined in Section 12.10. 

Describe edge and screw dislocation motion from an atomic perspective. 

Describe the phenomenon of grain growth from both macroscopic and atomic perspectives. 

Briefly explain the phenomenon of thermal expansion from an atomic perspective using a... 

From an atomic perspective, thermal expansion is reflected by an increase in the average distance between the atoms. This phenomenon can best be understood by consulting the potential energy-versus-interatomic spacing curve for a solid material introduced previously (Figure 2.10b) and reproduced in Figure 19.3a. The curve is in... 

The following two sections will focus on epitaxial growth from a surface science perspective with the aim of revealing the fundamentals of tliin-film growth. As will be discussed below, surface science studies of thin-film deposition have contributed greatly to an atomic-level understanding of nucleation and growth. 

As an example for an efficient yet quite accurate approximation, in the first part of our contribution we describe a combination of a structure adapted multipole method with a multiple time step scheme (FAMUSAMM — fast multistep structure adapted multipole method) and evaluate its performance. In the second part we present, as a recent application of this method, an MD study of a ligand-receptor unbinding process enforced by single molecule atomic force microscopy. Through comparison of computed unbinding forces with experimental data we evaluate the quality of the simulations. The third part sketches, as a perspective, one way to drastically extend accessible time scales if one restricts oneself to the study of conformational transitions, which arc ubiquitous in proteins and are the elementary steps of many functional conformational motions. 

To put the errors in comparative models into perspective, we list the differences among strucmres of the same protein that have been detennined experimentally (Fig. 9). The 1 A accuracy of main chain atom positions corresponds to X-ray structures defined at a low resolution of about 2.5 A and with an / -factor of about 25% [192], as well as to medium resolution NMR structures determined from 10 interproton distance restraints per residue [193]. Similarly, differences between the highly refined X-ray and NMR structures of the same protein also tend to be about 1 A [193]. Changes in the environment... 

EXAFS is a nondestructive, element-specific spectroscopic technique with application to all elements from lithium to uranium. It is employed as a direct probe of the atomic environment of an X-ray absorbing element and provides chemical bonding information. Although EXAFS is primarily used to determine the local structure of bulk solids (e.g., crystalline and amorphous materials), solid surfaces, and interfaces, its use is not limited to the solid state. As a structural tool, EXAFS complements the familiar X-ray diffraction technique, which is applicable only to crystalline solids. EXAFS provides an atomic-scale perspective about the X-ray absorbing element in terms of the numbers, types, and interatomic distances of neighboring atoms. 

More complete interpretations of Diels-Alder regioselectivity have been developed. MO results can be analyzed from an electrostatic perspective by calculating potentials at the various atoms in the diene and dienophile. These results give a more quantitatively accurate estimate of the substituent effects. Diels-Alder regioselectivity can also be accounted for in terms of HSAB theory (see Section 1.2.3). The expectation would be that the most polarizable (softest) atoms would lead to bond formation and that regioselectivity would reflect the best mateh between the diene and dienophile termini. These ideas have been applied using 3-2IG computations. The results are in agreement with the ortho rule for normal-electron-demand Diels-Alder reactions. ... 

From a quantum mechanical perspective, an atom or molecule would be considered to have no permanent dipole moment if the probability of finding electrons is symmetric about the nucleus. For example the probability of finding the electron in the ground state of hydrogen is constant with respect to its solid... 

Erickson, J., Zimmermann, E., Southwick, J. and Kiibler. K., Adhes. Age, Nov. (1995). Charlesby, R., Atomic Radiation and Polymers. Pergamon Press, New York, I960, p. 467. Pappas, S.P., Radiation curing a personal perspective. In Pappas, S.P. (Ed.), Radiation Curing Science and Technology. Plenum Press, New York, 1992, p. I. 

Among the newer probes now being developed, spectroscopic observations of crystals in the elastic-plastic regime hold promise for limited development of atomic level physical descriptions of local defects [91S02]. It is yet to be determined how generally this probe can be applied to solids. The electrochemical probe appears to have considerable potential to describe shock-compressed matter from a radically different perspective. 

---