Calculation of Atomic Properties

In the calculation of atomic properties it is convenient to introduce atomic units which are defined so that all the relevant parameters for the ground state of H have magnitude one. The atomic units most useful for our purposes are given in Table 2.1.2 An extensive list is given by Bethe and Salpeter.2 Throughout the book atomic units will be used for all calculations, with conversions to other units to facilitate comparisons to experiment. 

One approach for dealing with this problem is to solve the equation numerically. That is, a computer is used to find the numerical values of the wave functions at each point in space that produce the lowest overall energy for the atom. Although this approach allows accurate calculation of atomic properties, it suffers from two major disadvantages It is prohibitively time-consuming for any but the simplest of atoms, and the results are very difficult to interpret physically. 

Resonances in Electron Atom and Molecule Scattering, D. E. Golden The Accurate Calculation of Atomic Properties by Numerical Methods, Brian C. Webster, Michael J. Jamieson, and Ronald E. Stewart (e, 2e) Collisions, Erich Weigold and Ian E. McCarthy... 

R. Ahlberg and O. Goscinski On the Optimization of Local Linear Response Calculations of Atomic Properties J. Phys. B 8, 2149 (1975). 

Borschevsky, A., Pershina, V., Eliav, E., Kaldor, U. Benchmark calculations of atomic properties of elements 113-122. Presentation at the TAN2011 Conference, Sochi, 5-11 Sept 2011. (http //tanl 1. jinr.ru/Final Programme-TANll.htm)... 

The chirality code of a molecule is based on atomic properties and on the 3D structure. Examples of atomic properties arc partial atomic charges and polarizabilities, which are easily accessible by fast empirical methods contained in the PETRA package. Other atomic properties, calculated by other methods, can in principle be used. It is convenient, however, if the chosen atomic property discriminates as much as possible between non-equivalent atoms. 3D molecular structures are easily generated by the GORINA software package (see Section 2.13), but other sources of 3D structures can be used as well. 

Photo 5 (left) Linus Pauling with Arnold Sommerfeld (on left). Sommerfeld, well-known professor of theoretical physics in the University of Munich, Germany, was an expert on an early form of quantum mechanics, the Bohr-Sommerfeld atomic model. The picture was taken on the occasion of Sommerfeld s visit to Caltech in 1928. Pauling studied quantum mechanics with Sommerfeld in 1926—1927, which is where Pauling got his start in the application of quantum mechanics to chemical bonding (Chapter 1) and to the calculation of molecular properties (Chapter 8). 

Kello, V. and Sadlej, A.J. (1996) Standardized basis sets for high-level-correlated relativistic calculations of atomic and molecular electric properties in the spin-averaged Douglas-Kroll (nopair) approximation 1. Groups Ib and 11b. Theoretica Chimica Acta, 94, 93-104. 

The reliability of molecular mechanics calculations hinges entirely on the validity and range of applicability of the force field. The parameterisation of these functions (the force field) represents the chemistry of the species involved. Many force fields have been developed and the one used in any application usually depends on the molecular mechanics package being used. The force field itself can be validated against experimental and ab initio results. Because of the relative speed of molecular mechanics calculations, it is possible to consider routine calculations of a large number of atoms, certainly tens of thousands, which makes the method amenable to calculations on polymers. To remove surface effects, calculations of bulk properties are normally carried out employing 3D periodic boundaries. In this way it is possible to perform calculations on both amorphous and crystalline systems. 

From these early beginnings, computer studies have developed into sophisticated tools for the understanding of defects in solids. There are two principal methods used in routine investigations atomistic simulation and quantum mechanics. In simulation, the properties of a solid are calculated using theories such as classical electrostatics, which are applied to arrays of atoms. On the other hand, the calculation of the properties of a solid via quantum mechanics essentially involves solving the Schrodinger equation for the electrons in the material. 

The calculation of the properties of a solid via quantum mechanics essentially involves solving the Schrodinger equation for the collection of atoms that makes up the material. The Schrodinger equation operates upon electron wave functions, and so in quantum mechanical theories it is the electron that is the subject of the calculations. Unfortunately, it is not possible to solve this equation exactly for real solids, and various approximations have to be employed. Moreover, the calculations are very demanding, and so quantum evaluations in the past have been restricted to systems with rather few atoms, so as to limit the extent of the approximations made and the computation time. As computers increase in capacity, these limitations are becoming superseded. 

We then turn to the question of how to eliminate the spin-orbit interaction in four-component relativistic calculations. This allows the assessment of spin-orbit effects on molecular properties within the framework of a single theory. In a previous publication [13], we have shown how the spin-orbit interaction can be eliminated in four-component relativistic calculations of spectroscopic properties by deleting the quaternion imaginary parts of matrix representations of the quaternion modified Dirac equation. We show in this chapter how the application of the same procedure to second-order electric properties takes out spin-forbidden transitions in the spectrum of the mercury atom. Second-order magnetic properties require more care since the straightforward application of the above procedure will extinguish all spin interactions. After careful analysis on how to proceed we... 

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. 

The Molecular Surface (MS) first introduced by Richards (19) was chosen as the 3D space where the MLP will be calculated. MS specifically refers to a molecular envelope accessible by a solvent molecule. Unlike the solvent accessible surface (20), which is defined by the center of a spherical probe as it is rolled over a molecule, the MS (19), or Connolly surface (21) is traced by the inwardfacing surface of the spherical probe (Fig. 2). The MS consists of three types of faces, namely contact, saddle, and concave reentrant, where the spherical probe touches molecule atoms at one, two, or three points, simultaneously. Calculation of molecular properties on the MS and integration of a function over the MS require a numerical representation of the MS as a manifold S(Mk, nk, dsk), where Mk, nk, dsk are, respectively, the coordinates, the normal vector, and the area of a small element of the MS. Among the published computational methods for a triangulated MS (22,23), the method proposed by Connolly (21,24) was used because it provides a numerical presentation of the MS as a collection of dot coordinates and outward normal vectors. In order to build the 3D-logP descriptor independent from the calculation parameters of the MS, the precision of the MS area computation was first estimated as a function of the point density and the probe radius parameters. When varying... 

As mentioned before, when the population parameters have been defined with respect to local atomic coordinate systems, the moments must be transferred to a common coordinate system for the calculation of molecular properties. The matrix D will have to be modified accordingly. Analogous to Eq. (7.41), the elements of D are given by... 

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. 

The P,T-parity nonconservation parameters and hyperfine constants have been calculated for the particular heavy-atom molecules which are of primary interest for modern experiments to search for PNC effects. It is found that a high level of accounting for electron correlations is necessary for reliable calculation of these properties with the required accuracy. The applied two-step (GRECP/NOCR) scheme of calculation of the properties described by the operators heavily concentrated in atomic cores and on nuclei has proved to be a very efficient way to take account of these correlations with moderate efforts. The results of the two-step calculations for hyperfine constants differ by less than 10% from the corresponding exper-... 

Born, M. and Lande, A. (1918). [The absolute calculation of crystal properties with the aid of the Bohr atom model]. Sitsungsber. Preuss. Akad. Wissen. Berlin 45, 1048-68 (in German). 

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