Hybridization states, geometry

Organic molecules are generally composed of covalent bonded atoms with several well-defined hybridization states tending to have well-understood preferred geometries. This makes them an ideal case for molecular mechanics parameterization. Likewise, organic molecules are the ideal case for semiempirical parameterization. 

The atoms in niethylketene (C3H4O) are connected in the order and according to the geometry shown. (You can view this model in more detail on Learning By Modeling.) Determine the hybridization state of each carbon and write a Lewis structure for this neutral molecule. 

To truly understand the geometry of bonds, we need to understand the geometry of these three different hybridization states. The hybridization state of an atom describes the type of hybridized atomic orbitals (ip, sp, or sp) that contain the valence electrons. Each hybridized orbital can be used either to form a bond with another atom or to hold a lone pair. 

If you can determine the hybridization state of any atom, you will be able to easily determine the geometry of that atom. Let s do another example. 

Now that we know how to determine hybridization states, we need to know the geometry of each of the three hybridization states. One simple theory explains it all. This theory is called the valence shell electron pair repulsion theory (VSEPR). Stated simply, all orbitals containing electrons in the outermost shell (the valence shell) want to get as far apart from each other as possible. This one simple idea is all you need to predict the geometry around an atom. First, let s apply the theory to the three types of hybridized orbitals. 

That s it. There are only six different types of geometry that we need to know. First we determine the hybridization state. Then, nsing the number of lone pairs, we can figure out which of the six different types of geometry we are dealing with. Let s try it out on a problem. 

PROBLEMS Identify the hybridization state and geometry of each atom in the following compounds. Do not worry about the geometry of atoms connected to only one other atom. For example, do not worry about the geometry of any hydrogen atoms or about the geometry of the oxygen atoms in problems 4.12,4.13,4.15, and 4.17. 

PROBLEMS Identify the hybridization state and geometry of each nitrogen atom and each oxygen atom in the following compounds. 

The carbon atom undergoes a change in its geometry and its hybridization state during the reaction. 

Exercise 6-5 Examine the following structures and predict the most likely geometry, using concepts of orbital hybridization. State whether the molecule should be planar or nonplanar, and list the approximate values expected for the bond angles. ... 

Ab initio calculations at the MP2/6-31+ G level have been performed for gas-phase El elimination reactions of CH3CH2X (X = NH3"1", Br, Cl, F, SH) promoted by NH . OH-, F-, PH2. SH-, and Cl- in order to determine how changes in transition-state geometry, from reactant-like to product-like, influence kinetic isotope effects.9 Secondary isotope effects (a-H) on leaving group departure are correlated with the hybridization at C7 in the transition state, whereas there is no such correlation between secondary (/5-H) isotope effects and the transition state hybridization at C/ . The primary deuterium isotope effect is influenced markedly by the nucleophilic atom concerned but approach to a broad maximum for a symmetric transition structure can be discerned when due allowance is made for the element effect. 

PROBLEMS For each compound below, identify the hybridization state and geometry for every atom in the compound. 

In the case of PDB ligands, only part of the graph information is defined in the PDB file format sepcification bond types and atom hybridization states are missing and will later be derived from the three-dimensional arrangement of connected atoms. Connectivity information, however, is already present and can be used to seperate cyclic from non-cyclic molecule parts. Especially for planar rings, this separation is a prerequisite for geometry interpretation, because of... 

Figure 11. Contour map of hybrids 4>i-5 used for the VB structure Iq obtained by analyzing the CASSCF wavefunction at the transition state geometry for the electrophilic attachment of chlorine to ethylene in aqueous solution.

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