Molecular structures three-electron atoms

The ball and wire display is used for model building Although it is convenient for this purpose other model displays show three dimensional molecular structure more clearly and may be preferred The space filling display is unique m that it portrays a molecule as a set of atom centered spheres The individual sphere radii are taken from experi mental data and roughly correspond to the size of atomic electron clouds Thus the space filling display attempts to show how much space a molecule takes up... 

Optimize these three molecules at the Hartree-Fock level, using the LANL2DZ basis set, LANL2DZ is a double-zeta basis set containing effective core potential (ECP) representations of electrons near the nuclei for post-third row atoms. Compare the Cr(CO)5 results with those we obtained in Chapter 3. Then compare the structures of the three systems to one another, and characterize the effect of changing the central atom on the overall molecular structure. 

The Lewis dot formula predicts 4 regions of high electron density around the central N atom, a tetrahedral electronic geometry and a pyramidal molecular geometry. The N atom has sp3 hybridization (Sections 8-8 and 28-14). The three-dimensional structure is shown below. 

The Lewis structure of NC13 has three Cl atoms bonded to N and one lone pair attached N. These four electron groups around N produce a tetrahedral electron-group geometry. The fact that one of the electron groups is a lone pair means that the molecular geometry trigonal pyramidal. 

These definitions apply to any atomic system, molecule or crystal. Fig. 7.3 a illustrates their application to the charge distribution of the guanine-cytosine base-pair. Fig. 7.3 b shows the molecular structure defined by the bond paths and the associated CPs that clearly and uniquely define the three hydrogen bonds that link the two bases. Fig. 7.3 c shows the atomic boundaries and bond paths overlaid on the electron density in the plane of the nuclei. All properties of the atoms can be determined, enabling one, for example, to determine separately the energy of formation of each of the three hydrogen bonds. 

The molecular geometry, which allows optimal p orbital interaction to yield a three-electron bond, presumes an orientation of p orbitals belonging to each sulfur atom along the S S axis. This is the case of the chair-boat conformer of the 1,5-dithiacyclooctane cation-radical, the first structure in Scheme 3.22.In the 1,3-dithiacyclopentane cation-radical, the sulfurp orbitals are aligned almost perpendicular to the ring plane, and this prevents stabilization by the transannular interaction between the two sulfur atoms in the cycle. This unreal structure (the second structure in brackets in Scheme 3.22) cannot exist. However, the cation-radical of bis(2-methyl-1,3-dithianyl)methanol (the third structure in Scheme 3.22) was predicted to exist Li and Kutateladze (2003) calculated this structure as the most stable because it differs by a special orbital pattern from the structure in brackets. 

Qualitatively, the resonance picture is often used to describe the structure of molecules, but quantitative valence-bond calculations become much more difficult as the structures become more complicated (e.g., naphthalene, pyridine, etc.). Therefore the molecular-orbital method is used much more often for the solution of wave equations.5 If we look at benzene by this method (qualitatively), we see that each carbon atom, being connected to three other atoms, uses sp1 orbitals to form a bonds, so that all 12 atoms are in one plane. Each carbon has a p orbital (containing one electron) remaining and each of these can overlap equally with the two adjacent p orbitals. This overlap of six orbitals (see Figure 2.1) produces six new orbitals, three of which (shown) are bonding. These three (called it orbitals) all occupy approximately the same space.6 One of the three is of lower energy than... 

Bismuth is the fifth member of the nitrogen family of elements and, like its congeners, possesses five electrons in its outermost shell, 6s 6p. In many compounds, the bismuth atom utilizes only the three 6p electrons in bond formation and retains the two 6x electrons as an inert pair. Compounds are also known where bismuth is bonded to four, five, or six other atoms. Many bismuth compounds do not have simple molecular structures and exist in the solid state as polymeric chains or sheets. 

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