Electron density representation

The usual way chemistry handles electrons is through a quantum-mechanical treatment in the frozen-nuclei approximation, often incorrectly referred to as the Born-Oppenheimer approximation. A description of the electrons involves either a wavefunction ( traditional quantum chemistry) or an electron density representation (density functional theory, DFT). Relativistic quantum chemistry has remained a specialist field and in most calculations of practical... 

In more recent years, additional progress and new computational methodologies in macromolecular quantum chemistry have placed further emphasis on studies in transferability. Motivated by studies on molecular similarity [69-115] and electron density representations of molecular shapes [116-130], the transferability, adjustability, and additivity of local density fragments have been analyzed within the framework of an Additive Fuzzy Density Fragmentation (AFDF) approach [114, 131, 132], This AFDF approach, motivated by the early charge assignment approach of Mulliken [1, 2], is the basis of the first technique for the computation of ab initio quality electron densities of macromolecules such as proteins [133-141],... 

In representations of electron densities, the presence or lack of boundaries plays a crucial role. A quantum mechanically valid electron density distribution of a molecule cannot have boundaries, nevertheless, artificial electron density representations with actual boundaries provide useful tools of analysis. For these reasons, among the manifold representations of molecular electron densities, manifolds with boundaries play a special role. 

The linear size dependence of the AFDF family of methods is an advantage that can be exploited in the rapid generation of macromolecular electron density representations which are of better quality than those obtained by locally spherical distributions in the usual structure refinement process. The proposed approach, a quantum crystallographic application of the AFDF method (QCR-AFDF) is outlined below. 

X-ray diffraction structural modeling based on a continuous electron density representation and textural analyses by the combined XRD-adsorption method were applied for to quantify distinctions in the wall structure of the MCM-41 and SBA-15 types of mesostructured materials. 

When we square the wave function of the crfs MO, we get the electron density representation which we saw earlier, in Figure 9.32. Notice once again that we lose the phase information when we look at the electron density. 

Molecular orbitals were one of the first molecular features that could be visualized with simple graphical hardware. The reason for this early representation is found in the complex theory of quantum chemistry. Basically, a structure is more attractive and easier to understand when orbitals are displayed, rather than numerical orbital coefficients. The molecular orbitals, calculated by semi-empirical or ab initio quantum mechanical methods, are represented by isosurfaces, corresponding to the electron density surfeces Figure 2-125a). 

Both space-filling and electron density models yield similar molecular volumes, and both show the obvious differences in overall size. Because the electron density surfaces provide no discernible boundaries between atoms (and employ no colors to highlight these boundaries), the surfaces may appear to be less informative than space-filling models in helping to decide to what extent a particular atom is exposed . This weakness raises an important point, however. Electrons are associated with a molecule as a whole and not with individual atoms. The space-filling representation of a molecule in terms of discernible atoms does not reflect reality, but rather is an artifact of the model. The electron density surface is more accurate in that it shows a single electron cloud for the entire molecule. 

For a preliminary survey of the electron density, it is usual to make a pictorial representation as we did in previous chapters. Whilst such diagrams do not carry much information, they do provide a theoretical measure which can be compared to the results of X-ray diffraction studies. A whole volume of the Transactions of the American Chemical Society (1972) was devoted to the Symposium Experimental and Theoretical Studies of Electron Densities . 

We can distinguish between static theories, which in essence give a description of the electron density, and dynamic theories, where an attempt is marie to measure the response of a molecule to (e.g.) an approaching N02" " ion. In recent years, the electrostatic potential has been used to give a simple representation of the more important features of molecular reactivity. It can be calculated quite easily at points in space ... 

The raw output of a molecular structure calculation is a list of the coefficients of the atomic orbitals in each LCAO (linear combination of atomic orbitals) molecular orbital and the energies of the orbitals. The software commonly calculates dipole moments too. Various graphical representations are used to simplify the interpretation of the coefficients. Thus, a typical graphical representation of a molecular orbital uses stylized shapes (spheres for s-orbitals, for instance) to represent the basis set and then scales their size to indicate the value of the coefficient in the LCAO. Different signs of the wavefunctions are typically represented by different colors. The total electron density at any point (the sum of the squares of the occupied wavefunctions evaluated at that point) is commonly represented by an isodensity surface, a surface of constant total electron density. 

A methyl group may be shown in a structural representation as CH3 or Me, and similar pseudo-elemental symbols are used for ethyl, propyl and butyl side chains. It is cortrmon to represent a phenyl group as either Ph or as a hexagon with a circle irtscribed within it. This circle is meant to represent electron density that lies above and beneath the main plane of the molecule. However, when faced with... 

The treatment presented so far is quite general and formally exact. It combines the eikonal representation for nuclear motions and the time-dependent density matrix in an approach which could be named as the Eik/TDDM approach. The following section reviews how the formalism can be implemented in the eikonal approximation of short wavelengths for the nuclear motions, and for specific choices of electronic states leading to the TDHF equations for the one-electron density matrix, and to extensions of TDHF. 

A formulation of electronic rearrangement in quantum molecular dynamics has been based on the Liouville-von Neumann equation for the density matrix. Introducing an eikonal representation, it naturally leads to a general treatment where Hamiltonian equations for nuclear motions are coupled to the electronic density matrix equations, in a formally exact theory. Expectation values of molecular operators can be obtained from integrations over initial conditions. 

We need ways to visualize electrons as particle-waves delocalized in three-dimensional space. Orbital pictures provide maps of how an electron wave Is distributed In space. There are several ways to represent these three-dimensional maps. Each one shows some important orbital features, but none shows all of them. We use three different representations plots of electron density, pictures of electron density, and pictures of electron contour surfaces. 

Orbital density pictures are probably the most comprehensive views we can draw, but they require much time and care. An electron contour drawing provides a simplified orbital picture. In this representation, we draw a contour surface that encloses almost all the electron density. Commonly, almost all means 90%. Thus, the electron density is high inside the contour surface but very low outside the surface. Figure 7-19c shows a contour drawing of the 2s orbital. 

The quantum number / — 1 corresponds to a p orbital. A p electron can have any of three values for Jitt/, so for each value of tt there are three different p orbitals. The p orbitals, which are not spherical, can be shown in various ways. The most convenient representation shows the three orbitals with identical shapes but pointing in three different directions. Figure 7-22 shows electron contour drawings of the 2p orbitals. Each p orbital has high electron density in one particular direction, perpendicular to the other two orbitals, with the nucleus at the center of the system. The three different orbitals can be represented so that each has its electron density concentrated on both sides of the nucleus along a preferred axis. We can write subscripts on the orbitals to distinguish the three distinct orientations Px, Py, and Pz Each p orbital also has a nodal plane that passes through the nucleus. The nodal plane for the p orbital is the J z plane, for the Py orbital the nodal plane is the X Z plane, and for the Pz orbital it is the Jt plane. 

Figure 2-1. Representations of the electron density of the water molecule (a) relief map showing values of p(r) projected onto the plane, which contains the nuclei (large values near the oxygen atom are cut out) (b) three dimensional molecular shape represented by an envelope of constant electron density (0.001 a.u.). 

As a typical example we illustrate in Figure 2-1 the electron density of the water molecule in two different representations. In complete analogy, p(x) extends the electron density to the spin-dependent probability of finding any of the N electrons within the volume element dr, and having a spin defined by the spin coordinate s. 

Levy, M., 1979, Universal Variational Functionals of Electron Densities, First Order Density Matrices, and Natural Spin Orbitals and Solution of the v-Representability Problem , Proc. Natl. Acad. Sci. USA, 16, 6062. 

From the early advances in the quantum-chemical description of molecular electron densities [1-9] to modem approaches to the fundamental connections between experimental electron density analysis, such as crystallography [10-13] and density functional theories of electron densities [14-43], patterns of electron densities based on the theory of catastrophes and related methods [44-52], and to advances in combining theoretical and experimental conditions on electron densities [53-68], local approximations have played an important role. Considering either the formal charges in atomic regions or the representation of local electron densities in the structure refinement process, some degree of approximate transferability of at least some of the local structural features has been assumed. 

---