Sp3-nitrogen atom

In principle, the sp2 nitrogen atom of the C=N double bond of N-substituted imines (or of imidines) is a better nucleophile (and a better base193) than the sp3 nitrogen atom... 

For a nice flow sheet to derive proper SYBYL atom types, see the SYBYL manual or http //www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom types.html. Specific attention should be paid to the protonation states of heteroatoms (for example, a protonated sp3 nitrogen atom has atom type N.4, and a deprotonated carboxylate oxygen atom has atom type 0.co2). 

A typical bimodal character of the distribution appears for bond lengths D2, D3 and D7 (Figure 16b,c,g). In the case of D2 and D3 the two frequency maxima at about 1.39 A and 1.46-1.47 A correspond to N—C bond lengths for the sp2 and sp3 nitrogen atom hybridization, respectively. The bimodal D7 distribution shows frequency maxima at... 

Fig. 23 (a) Lehn s spherical cryptand, 13, and (b) calculated structure (MM+) of 13, in which each sp3 nitrogen atom points its lone pair inside the cavity, (c) The six oxygen atoms are placed at the comers of an octahedron, and the four nitrogen atoms at the comers of a tetrahedron. The tetrahedron is inserted into the octahedron. Hydrogen atoms have been omitted for clarity... 

Like the carbon atom in methane and the nitrogen atom in methylamine, the oxygen atom in methanol (methyl alcohol) and many other organic molecules can also be described as sp3-hybridized. The C-O-H bond angle in methanol is 108.5°, very close to the 109.5° tetrahedral angle. Two of the four sp3 hybrid... 

For substituted anilines (Thompson and Williams, 1977) and for 1-naphthylamine and a series of derivatives thereof (Castro et al., 1986a), k2 and the ratio Ar 2/Ar3 have been determined for nucleophilic catalysis with Cl-, Br-, SCN-, and SC(NH2)2. The values of k2 correspond fairly well to those found for the diazotization of aniline, but those of Ar 2/Ar3 increase markedly in the above sequence (Table 3-1). As k3 is expected to be independent of the presence of Cl- or Br- and to show little dependence on that of SCN- or thiourea, the increase in k 2/k3 for this series must be due mainly to 2. Indeed, the value of log(Ar 2/Ar3) shows a linear correlation with Pearson s nucleophilicity parameter n (Pearson et al., 1968). This parameter is based on nucleophilic substitution of iodine (as I-) in methyl iodide by various nucleophiles. The three investigations on nucleophilic catalysis of diazotization demonstrate that Pearson s criteria for bimolecular nucleophilic substitution at sp3 carbon atoms are also applicable to substitution at nitrogen atoms. 

The bond angles in PH3, AsH3, and SbH3 are interesting in view of the fact that in NH3, the bond angle is about equal to that expected for sp3 hybridization on the nitrogen atom with a small decrease... 

The carbonylation of the sp3 C-H bond adjacent to a nitrogen atom is also possible by means of chelation-assisted C-H bond activation.121 The carbonylation reaction of A-(2-pyridyl)pyrrolidine occurs at the a-position of the pyrrolidine ring by using [RhCl(cod)]2 as a catalyst and 2-propanol as a solvent. Cyclic amines exhibit a high reactivity (up to 84%) (Equation (93)), while acyclic amines show relatively low reactivity (18%). The use of Ru3(CO)i2 as a catalyst does not result in a carbonylation reaction, but instead the addition of the sp3 C-H bond across the olefin bond to give an alkylation product, as mentioned before (Section 10.05.4). 

Figure 7 Formation of sp3 hybrid orbitals in the nitrogen atom.

The MM2 force field3 is probably the most extensively parameterized and intensively used force field to date. It reproduces a variety of molecular properties such as geometry, dipole moments, conformational energies, barriers to rotation and heats of formation. Of particular importance for calculations of amines is that MM2 treats lone pairs on sp3 nitrogens (and oxygens) as pseudo atoms with a special atom type and parameters. A closely related force field, MM2 7, was derived from MM2 by Osawa and Jaime. MM2 uses the same potential functions as MM2, but employs a different set of parameters in an attempt to better reproduce barriers to rotation about single C—C bonds. 

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