Principles of Atomic Structure

Before we begin our study of organic chemistry, we must review some basic principles. Many of these concepts of atomic and molecular structure are crucial to your understanding of the structure and bonding of organic compounds. 

Each element is distinguished by the number of protons in the nucleus (the atomic number). The number of neutrons is usually similar to the number of protons, although the number of neutrons may vary. Atoms with the same number of protons but different numbers of neutrons are called isotopes. For example, the most common kind of carbon atom has six protons and six neutrons in its nucleus. Its mass number (the sum of the protons and neutrons) is 12, and we write its symbol as C. About 1% of carbon atoms have seven neutrons the mass number is 13, written C. A very small fraction of carbon atoms have eight neutrons and a mass number of 14. The C isotope is radioactive, with a half-life (the time it takes for half of the nuclei to decay) of 5730 years. The predictable decay of is used to determine the age of organic materials up to about 50,000 years old. 

Basic atomic structure. An atom has a dense, positively charged nucleus surrounded by a cloud of electrons. 

An element s chemical properties are determined by the number of protons in the nucleus and the corresponding number of electrons around the nucleus. The electrons form bonds and determine the structure of the resulting molecules. Because they are small and light, electrons show properties of both particles and waves in many ways, the electrons in atoms and molecules behave more like waves than like particles. 

Electrons that are bound to nuclei are found in orbitals. The Heisenberg uncertainty principle states that we can never determine exactly where the electron is nevertheless, we can determine the electron density, the probability of finding the electron in a particular part of the orbital. An orbital, then, is an allowed energy state for an electron, with an associated probability function that defines the distribution of electron density in space. 

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What Do We Need to Know Already The information in this chapter is organized around the principles of atomic structure and specifically the periodic table (Chapter 1). However, the chapter draws on all the preceding chapters, because it uses those principles to account for the properties of the elements. 

Explain each of the following observations using principles of atomic structure... 

The chapter will assume some prior knowledge of the principles of atomic structure, including quantum numbers, wavefunctions, principle shells and subshells and the radial distribution function, which indicates the probability of finding an electron as a function of distance from the nucleus. 

As a research tool, X-rays also advanced the study of the elements. Moseley s work from 1913 on X-ray spectra had shown that the order of the elements in the periodic table was the result not simply of chance but of some fundamental principle of atomic structure. It confirmed the ordering of some problematic elements and revealed that there was a missing element in the rare-earth series between neodymium and samarium. Element 61, promethium, was officially added to the periodic table in 1949. 

This chapter starts with a short explanation of the basic principles of atomic structure and the nature of the chemical bond. Afterwards, the three main groups of materials, metals, ceramics, and polymers, are discussed. The most important characteristics of their interatomic bonds are covered, and the microscopic structure of the different groups is also treated. 

We ve worked out a model of the interactions among electrons and atomic nuclei that allows us to predict the properties of single atoms. The next step is to add more atomic nuclei in order to make molecules. The Coulomb force will continue to govern the interactions of all the particles we are working with, so up to a point we will see that the physics is only an extension of the principles we ve just used to describe atoms. However, the addition of more atomic nuclei fundamentally changes the nature of the degrees of freedom that our particles can use to store and transfer energy. The principles of atomic structure will get us started, but then we will soon encounter the rich complexity of function and application that makes molecular structure the foundation of chemistry. 

Before estabiishing the connection between atomic orbitals and the periodic table, we must first describe two additionai features of atomic structure the Pauli exclusion principle and the aufbau principle. 

One important aspect not discussed above is the change in atomic structure at a surface. Contrary to the schematic picture of the Si(lll) surface shown in Fig. 14.6, a solid surface is usually not just the end of a perfect crystal. Surfaces reconstruct in response to the changes in the electronic distribution caused by the surface itself. Again, all these changes occur selfconsistently, and in principle, if the total energy for various configurations of atomic structures at a surface could be evaluated, the shifts in the positions of the atoms and the electronic structures of the surface could be determined theoretically. This approach will be discussed in the next section, but the first calculations for reconstructed surfaces were done using experimental determinations of the atomic positions. 

When Bohr published his first paper on the topic in 1921, the physicists who read it were convinced that his results were based on undisclosed calculations. They didn t see how so complex a theory could be worked out without making use of some mathematical foundation. But they were wrong. Bohr often proceeded intuitively, using whatever principle seemed most appropriate, as he considered one or another of the elements. Given his methods, it isn t surprising that Bohr made some faulty assignments. Nevertheless, his picture of atomic structure is basically the same as the one used by chemists and physicists today. 

Principles of skeletal structure formation of Raney catalysts are discussed, first from the perspective of phase transformation by chemical leaching. Some ideas are then proposed for making new Raney catalysts. Rapid solidification and mechanical alloying (MA) are described as potential processes for preparing particulate precursors. A rotating-water-atomization (RWA) process developed by the author and co-workers is shown as an example of rapid solidification. 

The common long form of the periodic chart (Fig. 211) may be considered a graphic portrayal of the rules of atomic structure given previously. The arrangement of the atoms follows naturally from the aufbau principle The various groups oT the chart may be classified as follows ... 

On the basis of contemporary electronic theory of atomic structure we con classify the different types or valence. The guiding principle is that the atoms tend to assume an inert gas electronic structure of eight electrons in the outer shell (ill the ease of hydrogen it is two). To do this, the atom either luses to, gains from, or shares with other atoms, electrons. This process leads to molecule formation. The following are Ihe principal types of valences and their electronic interpretation. 

The problems that are connected with the solution of the electronic structures of molecules are in principle the same as those which occur in the treatment of atomic structures. The single-electron orbitals for molecules are called molecular orbitals, and systems with more than one electron are built up by filling the molecular orbitals with electrons, paying proper attention to the Pauli principle. Thus, we always require that the total wave function be antisymmetric. 

Following the development of quantum theory by Heisenberg [1] and Schrodinger [2] and a few further discoveries, the basic principles of the structure of atoms and molecules were described around 1930. Unfortunately, the complexity of the Schrodinger equation increases dramatically with the number of electrons involved in a system, and thus for a long time the hydrogen and helium atoms and simple molecules as H2 were the only species whose properties could really be calculated from these first principles. In 1929, Dirac [3] wrote ... 

The possibility that reacting species prefer to react along those paths in which they undergo the least modification has always been intuitively attractive. At one time or another, so-called principles of minimum structural change or deformation, configurational change, and minimum atomic and electronic motion have been invoked (Wheland, 1960 Hine, 1966). To account for Michael s rule of favored anti 1,2-addition, Pfeiffer formulated acetylenes as tram-heat structures in 1904 Frankland (1912) suggested that anti elimination is favored by an inherent tendency to centric symmetry. The more conscious applications of PLM by Muller after 1886, are probably misapplications of the principle, since they were usually concerned with complex pyrolytic reactions above 1000° (Muller and Peytral, 1924). 

Fedorov A, Shi W, Kicska GA, Fedorov E, Tyler PC, Furneaux RH, Hanson JC, Gainsford GJ, Larese JZ, Schramm VL, Almo SC (2001) Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis. Biochemistry 40 853-860... 

Inorganic Covalent Heterocycles Containing Transition Metals. There are numerous inorganic (carbon-free) rings containing transition metal atoms. We will present only a few selected examples, to illustrate the principles of their structures and formation. 

The nature of the chemical bond and the principles of molecular structure were formu lated along time ago to systematize an immense body of chemical knowledge. With the advent of quanmm mechanics, it became possible to actually derive the concepts of chemical bonding from more fundamental laws governing matter on the atomic scale. Remarkably, many of the empirical concepts developed by chemists have remained valid when reexpressed in terms of quantum-mechanical principles. 

Many applications in chemistry require us to interpret—and even predict—the results of measurements where we have only limited information about the system and the process involved. In such cases the best we can do is identify the possible outcomes of the experiment and assign a probability to each of them. Two examples illustrate the issues we face. In discussions of atomic structure, we would like to know the position of an electron relative to the nucleus. The principles of quantum mechanics tell us we can never know the exact location or trajectory of an electron the most information we can have is the probability of finding an electron at each point in space around the nucleus. In discussing the behavior of a macroscopic amount of helium gas confined at a particular volume, pressure, and temperature we would like to know the speed with which an atom is moving in the container. We do not have experimental means to tag a particular atom. 

Heisenberg, Werner P. (1901-1976). A native of Germany, Heisenberg received his doctorate from the University of Munich in 1923, after which he was closely associated for several years with Niels Bohr in Copenhagen. He was awarded the Nobel Prize in physics in 1932 for his brilliant work in quantum mechanics. In 1946, he became director of the Max Planck Institute. His notable contributions to theoretical physics, best known of which was the uncertainty principle, imparted new impetus to nuclear physics and made possible a better understanding of atomic structure and chemical bonding. 

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