Density molecular orbital

In either picture, the bond order of the central bond should be > 1 and that of the other carbon-carbon bonds < 2, although neither predicts that the three bonds have equal electron density. Molecular orbital bond orders of 1.894 and 1.447 have been calculated. ... 

On the basis that the transition state for the addition step is as pictured above, it would be expected that the preferential orientation of the entering nucleophile would follow the order of the ground-state 7r-electron densities. Molecular orbital calculations of the w-electron densities at the various nuclear carbon atoms in the ground-state of 3-picoline for several different values of the nitrogen and methyl group... 

These similarity indices are related to a correlation function between two 3D functions. The idea is simple. Let us consider two functions f(r) and g(r), which are one-electron molecular properties for two different molecules, measured at a point r. These functions can be total electron densities, molecular orbitals, electrostatic potentials, or other relevant properties. The correlation coefficient C for two such functions is... 

The first point to remark is that methods that are to be incorporated in MD, and thus require frequent updates, must be both accurate and efficient. It is likely that only semi-empirical and density functional (DFT) methods are suitable for embedding. Semi-empirical methods include MO (molecular orbital) [90] and valence-bond methods [89], both being dependent on suitable parametrizations that can be validated by high-level ab initio QM. The quality of DFT has improved recently by refinements of the exchange density functional to such an extent that its accuracy rivals that of the best ab initio calculations [91]. DFT is quite suitable for embedding into a classical environment [92]. Therefore DFT is expected to have the best potential for future incorporation in embedded QM/MD. 

Depending on the application, models of molecular surfaces arc used to express molecular orbitals, clcaronic densities, van dor Waals radii, or other forms of display. An important definition of a molecular surface was laid down by Richards [182] with the solvent-accessible envelope. Normally the representation is a cloud of points, reticules (meshes or chicken-wire), or solid envelopes. The transparency of solid surfaces may also be indicated (Figure 2-116). 

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. 

Figure 2-125. Different isovalue-based surfaces of phenylalanine a) isoelectronic density b) molecular orbitals (HOMO-LUMO) c) isopotential surface and d) isosurface of the electron cryo-microscopic volume of the ribosome of Escherichia coii.

IlyperCl hem can display molecular orbitals and the electron density ol each molecular orbital as contour plots, showing the nodal structure and electron distribution in the molecular orbitals. 

If you define a density matrix R by summing over all occupied molecular orbitals ... 

The Total Electron Density Distribution and Molecular Orbitals... 

Jj u e e. press the molecular orbital ipj as a linear combination of basis functions, then the electrojT density at a point r is given as ... 

I he electron density distribution of individual molecular orbitals may also be determined and plotted. The highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) are often of particular interest as these are the orbitals most cimimonly involved in chemical reactions. As an illustration, the HOMO and LUMO for Jonnamide are displayed in Figures 2.12 and 2.13 (colour plate section) as surface pictures. 

Highest occupied molecular orbital Intermediate neglect of differential overlap Linear combination of atomic orbitals Local density approximation Local spin density functional theory Lowest unoccupied molecular orbital Many-body perturbation theory Modified INDO version 3 Modified neglect of diatomic overlap Molecular orbital Moller-Plesset... 

The origins of the Finnis-Sinclair potential [Finnis and Sinclair 1984] lie in the density of states and the moments theorem. Recall that the density of states D(E) (see Section 3.8.5) describes the distribution of electronic states in the system. D(E) gives the number of states between E and E - - 8E. Such a distribution can be described in terms of its moments. The moments are usually defined relative to the energy of the atomic orbital from which the molecular orbitals are formed. The mth moment, fi", is given by ... 

The simplest molecular orbital method to use, and the one involving the most drastic approximations and assumptions, is the Huckel method. One str ength of the Huckel method is that it provides a semiquantitative theoretical treatment of ground-state energies, bond orders, electron densities, and free valences that appeals to the pictorial sense of molecular structure and reactive affinity that most chemists use in their everyday work. Although one rarely sees Huckel calculations in the resear ch literature anymore, they introduce the reader to many of the concepts and much of the nomenclature used in more rigorous molecular orbital calculations. 

A basis set is a set of functions used to describe the shape of the orbitals in an atom. Molecular orbitals and entire wave functions are created by taking linear combinations of basis functions and angular functions. Most semiempirical methods use a predehned basis set. When ah initio or density functional theory calculations are done, a basis set must be specihed. Although it is possible to create a basis set from scratch, most calculations are done using existing basis sets. The type of calculation performed and basis set chosen are the two biggest factors in determining the accuracy of results. This chapter discusses these standard basis sets and how to choose an appropriate one. 

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. 

Once you have calculated an ab initio or a semi-empirical wave function via a single point calculation, geometry optimization, molecular dynamics or vibrations, you can plot the electrostatic potential surrounding the molecule, the total electronic density, the spin density, one or more molecular orbitals /i, and the electron densities of individual orbitals You can examine orbital energies and select orbitals for plotting from an orbital energy level diagram. 

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