Atomic and molecular structure

Because so much of the chemistry of atoms and molecules is related to their structures, the study of descriptive chemistry begins with a consideration of these topics. The reasons for this are simple and straightforward. For example, many of the chemical characteristics of nitrogen are attributable to the structure of the N2 molecule, N = N . The triple bond in the N2 molecule is very strong, and that bond strength is responsible for many chemical properties of nitrogen (such as it being a relatively unreactive gas). Likewise, to understand the basis for the enormous difference in the chemical behavior of SF4 and SF6 it is necessary to understand the difference between the structures of these molecules, which can be shown as 

Moreover, to understand why SF6 exists as a stable compound whereas SC16 does not, we need to know something about the properties of the S, F, and Cl atoms. As another illustration, it may be asked why the P043- ion is quite stable but N043 is not. Throughout this descriptive chemistry book, reference will be made in many instances to differences in chemical behavior that are based on atomic and molecular properties. Certainly not all chemical characteristics are predictable from an understanding of atomic and molecular structure. However, structural principles are useful in so many cases (for both comprehension of facts and prediction of properties) that a study of atomic and molecular structure is essential. 

What follows is a nonmathematical treatment of the aspects of atomic and molecular structure that provides an adequate basis for understanding much of the chemistry presented later in this book. Much of this chapter should be a review of principles learned in earlier chemistry courses, which is intentional. More theoretical treatments of these topics can be found in the suggested readings at the end of this chapter. 

FIGURE 1.7 Probability of electrora positiora for the hydrogera Is orbital. (Tharaks to Prof Peter Kraowles for this figure.) 

FIGURE 1.8 Probability of the electron position for the hydrogen 2s orbital. (Thanks to Prof Peter Knowles for this figure.) 

FIGURE 1.11 Probabilities for Is, 2s, 3s, and 4s orbitals. (Thanks to Prof Peter Knowles forthis figure.) 

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

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

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... 

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... 

Chemistry is the science of the combination of atoms, and physics is the science of the forces between atoms. Simply stated, chemistry deals with matter and its transformations, and physics deals witli energy and its transformations. These transformations may be temporaiy, such as a change in phase, or seemingly penmnent, such as a change in the form of matter resulting from a chemical reaction. The study of atomic and molecular structure deals witli tliese transformations, and can be used to make a preliminary identification of a healtli liazard. 

Tsaparlis, G. (1997). Atomic and molecular structure in chemical education - A critical analysis from various perspectives of science education. Journal of Chemical Education, 74, 922-925. 

Gray, Harry B. Chemical Bonds An Introduction to Atomic and Molecular Structure. Menlo Park, Calif W.A. Benjamin, Inc., 1973. 

Gray, H.B. (1995). Chemical Bonds - An Introduction to the Atomic and Molecular Structure. 

Although Einstein made use of the assumption that light behaves as a particle, there is no denying the validity of the experiments that show that light behaves as a wave. Actually, light has characteristics of both waves and particles, the so-called particle-wave duality. Whether it behaves as a wave or a particle depends on the type of experiment to which it is being subjected. In the study of atomic and molecular structure, it necessary to use both concepts to explain the results of experiments. 

The science of spectroscopy has become the most powerful tool available for the determination of atomic and molecular structures and can be applied on a wide range of samples. 

Working first with Polanyi, Weissenberg, and Brill, and later as the leader of the Textile Chemistry Section, Mark successively published papers on the crystal structures of hexamethylenetetramine, pentaerythritol, zinc salts, tin, urea, tin salts, triphenylmethane, bismuth, graphite, sulfur, oxalic acid, acetaldehyde, ammonia, ethane, diborane, carbon dioxide, and some aluminum silicates. Each paper showed his and the laboratory s increasing sophistication in the technique of X-ray diffraction. Their work over the period broadened to include contributions to the theories of atomic and molecular structure and X-ray scattering theory. A number of his papers were particularly notable including his work with Polanyi on the structure of white tin ( 3, 4 ), E. Wigner on the structure of rhombic sulfur (5), and E. Pohland on the low temperature crystal structure of ammonia and carbon dioxide (6, 7). The Mark-Szilard effect, a classical component of X-ray physics, was a result of his collaboration with Leo Szilard (8). And his work with E. A. Hauser (9, 10, 11) on rubber and J. R. 

Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, et al. 1993. General atomic and molecular structure system. J Comput Chem 14 1347-1363. 

Chemistry is an experimental science, and to rationalize our observations we gradually develop and invoke a number of rules and principles. Theories may have to change as scientific data increase, and as old principles cease to explain the facts. All of the foregoing description of atomic and molecular orbitals is a hypothesis for atomic and molecular structure supported by experimental data. So far, the description meets most of our needs and provides a good rationalization of chemical behaviour. However, it falls short in certain ways, and we have to invoke a further modification to explain the facts. Here are three observations based upon sound experimental evidence, which are not accommodated by the above description of bonding ... 

The relationship between alternative separable solutions of the Coulomb problem in momentum space is exploited in order to obtain hydrogenic orbitals which are of interest for Sturmian expansions of use in atomic and molecular structure calculations and for the description of atoms in fields. In view of their usefulness in problems where a direction in space is privileged, as when atoms are in an electric or magnetic field, we refer to these sets as to the Stark and Zeeman bases, as an alternative to the usual spherical basis, set. Fock s projection onto the surface of a sphere in the four dimensional hyperspace allows us to establish the connections of the momentum space wave functions with hyperspherical harmonics. Its generalization to higher spaces permits to build up multielectronic and multicenter orbitals. 

The first topic has an important role in the interpretation and calculation of atomic and molecular structures and properties. It is needless to stress the importance of electronic correlation effects, a central topic of research in quantum chemistry. The relativistic formulations are of great importance not only from a formal viewpoint, but also for the increasing number of studies on atoms with high Z values in molecules and materials. Valence theory deserves special attention since it improves the electronic description of molecular systems and reactions with the point of view used by most laboratory chemists. Nuclear motion constitutes a broad research field of great importance to account for the internal molecular dynamics and spectroscopic properties. 

Siegbahn, K., Nordling, C., Fahlman, A., Nordberg, R., Hamrin, K., Hedman, J., Johansson, G., Bergmark, T., Karlson, S.-E., Lindgren, I., and Lindberg, B., ESCA, Atomic and Molecular Structure Studied by Means of Electron Spectroscopy, Almqvist and Wiksell Uppsala (1967). 

In summary, the dynamical interactions among electrons give rise to instantaneous spatial correlations that must be handled to arrive at an accurate picture of atomic and molecular structure. The simple, single-configuration picture provided by the mean-field model is a useful starting point, but improvements are often needed. 

Modern many-body methods have become sufficiently refined that the major source of error in most ab initio calculations of molecular properties is today associated with truncation of one-particle basis sets e.g. [1]- [4]) that is, with the accuracy with which the algebraic approximation is implemented. The importance of generating systematic sequences of basis sets capable of controlling basis set truncation error has been emphasized repeatedly in the literature (see [4] and references therein). The study of the convergence of atomic and molecular structure calculations with respect to basis set extension is highly desirable. It allows examination of the convergence of calculations with respect to basis set size and the estimation of the results that would be obtained from complete basis set calculations. 

PROGRESS WITH BERTHA A RELATIVISTIC ATOMIC AND MOLECULAR STRUCTURE PACKAGE... 

I. P. Grant and H. M. Quiney, Progress with BERTHA A relativistic atomic and molecular structure package, this Volume. 

D. M. P. Mingos, Essential Trends in Inorganic Chemistry, Oxford University Press, Oxford, 1998. A new look at trends in physical and chemical properties of the elements and their compounds. This is a general text that would cover the material of most university courses in inorganic chemistry apart from some specialized topics, but is recommended here for the sections on atomic and molecular structure. 

This book has evolved from the author s previous attempts to give a general description of the ideas which are used to describe atomic and molecular structure, and fulsome thanks go to Ellis Horwood, the publisher of some of my books, for his generous permission to use some of the material in the present volume. 

Quantum mechanics, including atomic and molecular structure... 

Elementary quantum-chemical theories of atomic and molecular structure [including atomic orbitals (AO) and molecular orbitals (MO)] are part of the... 

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