Orbitals visualizing

The JME Editor is a Java program which allows one to draw, edit, and display molecules and reactions directly within a web page and may also be used as an application in a stand-alone mode. The editor was originally developed for use in an in-house web-based chemoinformatics system but because of many requests it was released to the public. The JME currently is probably the most popular molecule entry system written in Java. Internet sites that use the JME applet include several structure databases, property prediction services, various chemoinformatics tools (such as for generation of 3D structures or molecular orbital visualization), and interactive sites focused on chemistry education [209]. 

The three quantum numbers may be said to control the size (n), shape (/), and orientation (m) of the orbital tfw Most important for orbital visualization are the angular shapes labeled by the azimuthal quantum number / s-type (spherical, / = 0), p-type ( dumbbell, / = 1), d-type ( cloverleaf, / = 2), and so forth. The shapes and orientations of basic s-type, p-type, and d-type hydrogenic orbitals are conventionally visualized as shown in Figs. 1.1 and 1.2. Figure 1.1 depicts a surface of each orbital, corresponding to a chosen electron density near the outer fringes of the orbital. However, a wave-like object intrinsically lacks any definite boundary, and surface plots obviously cannot depict the interesting variations of orbital amplitude under the surface. Such variations are better represented by radial or contour... 

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). 

Besides molecular orbitals, other molecular properties, such as electrostatic potentials or spin density, can be represented by isovalue surfaces. Normally, these scalar properties are mapped onto different surfaces see above). This type of high-dimensional visualization permits fast and easy identification of the relevant molecular regions. 

For many reasons, including the Woodward-IIoffm an rules that describe the likelihood of reaction based on arguments about the shapes of orbitals, it is desirable to be able to visualize molecular orbitals. 

Once the job is completed, the UniChem GUI can be used to visualize results. It can be used to visualize common three-dimensional properties, such as electron density, orbital densities, electrostatic potentials, and spin density. It supports both the visualization of three-dimensional surfaces and colorized or contoured two-dimensional planes. There is a lot of control over colors, rendering quality, and the like. The final image can be printed or saved in several file formats. 

The macmolplt graphics package is designed for displaying the output of GAMESS calculations. It can display molecular structures, including an animation of reaction-path trajectories. It also may be used to visualize properties, such as the electron density, orbitals, and electrostatic potential in two or three dimensions. 

Wave functions can be visualized as the total electron density, orbital densities, electrostatic potential, atomic densities, or the Laplacian of the electron density. The program computes the data from the basis functions and molecular orbital coefficients. Thus, it does not need a large amount of disk space to store data, but the computation can be time-consuming. Molden can also compute electrostatic charges from the wave function. Several visualization modes are available, including contour plots, three-dimensional isosurfaces, and data slices. 

The total electron density contributed by all the electrons in any molecule is a property that can be visualized and it is possible to imagine an experiment in which it could be observed. It is when we try to break down this electron density into a contribution from each electron that problems arise. The methods employing hybrid orbitals or equivalent orbitals are useful in certain circumsfances such as in rationalizing properties of a localized part of fhe molecule. Flowever, fhe promotion of an electron from one orbifal fo anofher, in an electronic transition, or the complete removal of it, in an ionization process, both obey symmetry selection mles. For this reason the orbitals used to describe the difference befween eifher fwo electronic states of the molecule or an electronic state of the molecule and an electronic state of the positive ion must be MOs which belong to symmetry species of the point group to which the molecule belongs. Such orbitals are called symmetry orbitals and are the only type we shall consider here. 

Two successful and widespread appHcations of visualization techniques in the field of chemistry are the visualization of molecular orbitals and the visualization of molecules in molecular mechanics studies. 

It is now possible to "see" the spatial nature of molecular orbitals (10). This information has always been available in the voluminous output from quantum mechanics programs, but it can be discerned much more rapidly when presented in visual form. Chemical reactivity is often governed by the nature of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). Spectroscopic phenomena usually depend on the HOMO and higher energy unoccupied states, all of which can be displayed and examined in detail. 

When discassing molecular orbitals, three dimensional visualization software mar be very instructive. 

In the PPP model, each first-row atom such as carbon and nitrogen contributes a single basis functiqn to the n system. Just as in Huckel theory, the orbitals x, m e not rigorously defined but we can visualize them as 2p j atomic orbitals. Each first-row atom contributes a certain number of ar-electrons—in the pyridine case, one electron per atom just as in Huckel 7r-electron theory. 

The KS-LCAO orbitals may be visualized by all the popular methods, or one may just focus on the Mulliken population analysis indices (Figure 13.5). 

The reason for the weak mixing of and cr orbitals in propylene is that there is a weak pseudo vertical symmetry plane in the molecule. It is the plane which would have existed if the carbon skeleton were linear, with 110 central hydrogen atom. One can also visualize its existence by joining the two local vertical symmetry planes of the CH2 and CH3 groups. 

For molecular systems with up to thirty valence electrons, an amplitude of =t0.1 a.u. was chosen for the contour level. For systems with more than thirty valence electrons it was necessary to reduce this value to 0.08 a.u. to maintain the orbital size at a comfortable visual level. The molecular orbitals were normalized to an occupancy... 

The total molecular energy is invariant to all transformations involving basis orbitals, just as any physical event is invariant under any transformation of coordinates. But just as the proper choice of coordinates helps in visualizing physical events, so the choice of the proper orbital basis is helpful in visualizing molecular properties. 

Molecular modeling helps students understand physical and chemical properties by providing a way to visualize the three-dimensional arrangement of atoms. This model set uses polyhedra to represent atoms, and plastic connectors to represent bonds (scaled to correct bond length). Plastic plates representing orbital lobes are included for indicating lone pairs of electrons, radicals, and multiple bonds—a feature unique to this set. 

The Lewis symbol for nitrogen, for example, represents the valence electron configuration 2s22pA.12p>112p 1 (see 1), with two electrons paired in a 2s-orbital and three unpaired electrons in different 2p-orbitals. The Lewis symbol is a visual summary of the valence-shell electron configuration of an atom and allows us to see what happens to the electrons when an ion forms. 

To picture the spatial distribution of an electron around a nucleus, we must try to visualize a three-dimensional wave. Scientists have coined a name for these three-dimensional waves that characterize electrons they are called orbitals. The word comes from orbit, which describes the path that a planet follows when it moves about the sun. An orbit, however, consists of a specific path, typically a circle or an ellipse. In contrast, an orbital is a three-dimensional volume for example, a sphere or an hourglass. The shape of a particular orbital shows how an atomic or a molecular electron fills three-dimensional space. Just as energy is quantized, orbitals have specific shapes and orientations. We describe the details of orbitals in Section 7-1. 

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. 

To visualize bond formation by an outer atom other than hydrogen, recall the bond formation in HF. One valence p orbital from the fluorine atom overlaps strongly with the hydrogen 1 S orbital to form the bond. We can describe bond formation for any outer atom except H through overlap of one of its valence p orbitals with the appropriate hybrid orbital of the inner atom. An example is dichloromethane, CH2 CI2, which appears in Figure 10-11. We describe the C—H bonds by 5 -I S overlap, and we describe the C—Cl bonds by 5 - 3 p... 

In triethylaluminum, each A1—C bond can be visualized as an. y p hybrid on aluminum overlapping with an S p hybrid on a carbon atom. Figure 10-13 shows this bonding representation, with three equivalent A1—C bonds and the unused 3 p orbital on the aluminum atom. 

The ligands of a tetrahedral complex occupy the comers of a tetrahedron rather than the comers of a square. The symmetry relationships between the d orbitals and these ligands are not easy to visualize, but the splitting pattern of the d orbitals can be determined using geometry. The result is the opposite of the pattern found in octahedral... 

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