Molecular plane, contour plot

You can use the semi-empirical and ab initio Orbitals dialog box in HyperChem to request a contour plot of any molecular orbital. When requested, the orbital is contoured for a plane that is parallel to the screen and which is specified by a subset selection and a plane offset, as described above. The index of the orbital and its orbital energy (in electron volts, eV) appears in the status line. 

Figure 6.4 Contour plot of the electron density in the molecular plane of SCI2. The outer contour line corresponds to 0.001 au and the next contour lines correspond to values increasing according to the pattern 2 X 10", 4 X 10", 8X10" where n varies from —3 to 2.

Figure 6.11 (a) Contour plot of p for the molecular plane of the ethene molecule, (b) The gradient vector field of the electron density for the same plane. All the gradient paths shown originate at infinity and terminate at one of the six nuclei. 

Figure 6.17 Contour map of p in the interatomic surface associated with the CC bond critical point in ethene. The plane of the plot is perpendicular to the molecular plane. The C and two H nuclei are projected onto the plane of the plot to indicate the orientation of the molecule. We see that electronic charge is preferentially accumulated in the direction perpendicular to the molecular plane, giving an elliptical shape to the electron density in this plane.

Figure 8.23 Contour plots of L for the oxygen atom in (CHj O (a) in the molecular plane and (b) perpendicular to the molecular plane, and for the oxygen atom in (SiHj O (c) in the molecular plane and (d) perpendicular to the molecular plane through the oxygen.

Fig. 12 (see p. 88 ) exhibits contour diagrams for localized 7r-MO s in benzene. The contours drawn in this and all subsequent figures represent values of the MO s in a plane which is parallel to the molecular plane and contains the maxima of all (2pz) atomic orbitals. Since the latter are chosen to have the orbital exponent 1.61789 in atomic units, the contour plot plane is the plane z =... 

Fig. 10. Molecular and electronic structure of cation 74. (a) Perspective view on the cation 74. (b) Coordination sphere of the Pb atom, selected interatomic distances (pm) and angles (deg) Pb-(center CC, C7), 281.7 Pb-(center C6 CT), 280.7 Pbl-C2, 227(2) Pbl-C2 221.1(15) Pbl-C8, 231.0(19) C6-C7, 133(2) CC-CT 132(2) (center C6, C7)-Pb-(center C6, C7 163.6. (c) Contour plots of the Laplacian distribution [V p(r)] in the plane containing the atoms Pb, C6 and C7. Solid and dotted lines designate regions of local charge concentration and depletion, respectively. The bond paths are indicated by the solid back lines, bond critical points are marked with a black square. (Reprinted with permission from Ref. 53. Copyright 2003, Wiely-VCH.)...

Figure 14. Contour plot of the electron density at one time step during the zero-voltage molecular dynamics run. The circles indicate the simultaneous positions of those water molecules with the oxygen atom within 3 a.u. of the plane of the contour plot. From Ref. 52, by permission.

Fig. 3. Spin-coupled orbital (fq in benzene — throughout this review we present contour plots of the square modulus of the orbitals,

Fig. 1. Molecular electrostatic potential contour plot (values in au) for a portion of the benzene molecule in the molecular plane. Carbon nuclei are located at C and D with the hydrogen nuclei at C and >. Saddlepoint-like structures are seen at the points P and F. (Reproduced from [9] copyright-American Institute of Physics)...

Fig. 3. The contour plot of the NDDO AM 1 MEP of the benzene molecule 1.75 A above the molecular plane (kJ/mol)...

Fig. 5. A contour plot representing a two-dimensional slice of the molecular electrostatic potential for vinyl sulfone in the plane of the molecule with a sample uniform cubic grid superimposed grid points would be placed at the intersections of the perpendicular lines. (Reproduced from [71] copyright-John Wiley Sons)...

Fig. 5.1. Contour plots of the ground-state molecular charge distribution of LiF, LiO, and LiH. The intersection of the interatomic surface with the plane shown in the diagram is indicated...

FIGURE 45. Isocontour spin density plot in the molecular plane of phenoxyl radical. Contour levels are spaced by 0.0005 a.u. 

Figure la is a plot of the electron density and its associated gradient vector field of a planar molecule BF3 in the molecular plane. The figure illustrates how the zero-flux surfaces partition the molecular space into disjoint mononuclear regions, namely atomic basins, and how such surfaces differ from an arbitrary surface for which Vp(r) n(r) f 0. The left half of Fig. la is a contour plot of the electron density p(r), the contours increase in value as they approach the nuclei. Each contour line is a line with a constant value of the electron density. 

Figure 4. a and b) Displays of the electron density p(r) contours in the molecular plane of anthracene and phenanthrene, respectively. The density increases from the outermost 0.001 au contour in the order 2 x 10", 4 x 10 , and 8 x 10" au with n starting at —3 and increasing in steps of unity. The intersections of the interatomic zero-flux surfaces with the planes of the figures and the bond paths are superimposed on the plots, (c) A display of the gradient vector field of phenanthrene in the same orientation and plane as in b). The gradient vector Vp(r) field clearly shows the shape of each atomic basin and its bounding zero-flux surface. 

Fig. 3. Contour plots (in the plane z = 1 bohr) of the position-space electron density for the occupied n-orbitals for trans-C2oH22- Red (/ iO and green (broken) contours denote regions in which the wavefunction has opposite phases. The labels mark the positions of the nuclei (projected onto the plane z = 1). Orbital rr, has the highest binding energy and orbital n o is the least strongly bound. Note also the orientation of the axes (the x-axis points along the chain and the z-axis perpendicular to the molecular plane), as well as the marked distances d and h to which reference is made in the text...

This potential is illustrated as a contour plot in the molecular plane in Fig. 4a, whereas Fig. 4b corresponds to a plane perpendicular to the molecule, rotated 90° from the first. The red contours indicate regions of negative potential (attractive to a positive charge) and blue represents positive. The red and blue contours occur in the vicinity of the O and H atoms, respectively, as expected, based on their respective electronegativities. It is reiterated that this potential is a function of the full electron density and has no dependence on any arbitrary assignment of charges to atoms or other sites. 

Figure 4 Molecular electrostatic potential of water molecule, represented as a contour plot with intervals of 0.025 au. Red contours indicate regions of negative potential and blue represents positive, (a-b) Potential generated from full electron density, in and perpendicular to the molecular plane, respectively (c d) potential generated from point charges situated at three atomic positions (e-f) potential generated from point charges and dipoles situated at three atomic positions. (See color plate at end of chapter.)...

The electron density distribution is a four-dimensional function (the number of elearons at a given point (x,y,z)), which is difficult to visually represent. Figures 1 and 2, respectively, show a three-dimensional isoelectronic surface of benzene and a contour plot of the elearon density p(r) in the molecular plane of benzene. Both representations show only gross features of the density. In particular, the total electron density distribution is dominated by the core electrons and appears simply as an aggregate of slightly distorted spheres... 

Figure 2 Contour plot of the electron density in the molecular plane of benzene.

Figure 1. Contour plot of the electron density distribution in the BF3 molecule. The lines connecting the nuclei are the bond paths along which the electron density is greater than along any other line connecting the two nuclei. The curved lines between the atoms are the lines along which the interatomic (zero-flux) surfaces cut the molecular plane.

Figure 7.18 Contour line plots of the Laplacian Tj p[r) of the electron density of (a) Ru(ZnH),Q, (b) Rh(ZnH)g, (c) Pd(ZnH)g, and (d) Pd(CdH)g. Solid lines connecting the atoms represent the bond paths. Solid lines that separate the atomic basins indicate the zero-flux surfaces crossing the molecular plane.

Fig. 15 (a) Molecular structure of [F2Si OC(Ph)=NNMe2 2] (6) (c) Faplacian distributions along the Si N, Si-O and Si-F bond paths Contour plots of the Faplacian distribution in the O-Si-F (b) and N-Si-N (d) plane. Charge concentration depicted in blue, depletion in red lines... 

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