Electron density in hydrogen

Savariault, J. M., and Lehmann, M. S. Experimental determination of the deformation electron density in hydrogen peroxide by combination of X-ray and neutron diffraction measurements. J. Amer. Chem. Soc. 102,1298-1303 (1980,1... 

O. Galvez, P. C. Gomez, and L. F. Pacios, Variation with the intermolecular distance of properties dependent on the electron density in hydrogen bond dimers, J. Chem. Phys. 115, 11166-11184(2001). 

E. Espinosa, M. Souhassou, M. Lachekar and C. Lecomte, Topological analysis of the electron density in hydrogen bonds, Acta Cryst. B55, 563-572 (1999). 

Figure 2.4 uses electrostatic potential maps to show this build-up of electron density in the region between two hydrogen atoms as they approach each other closely enough for their orbitals to overlap. 

The size and shape of an electron cloud is described by the electron density (the number of electrons per unit volume). Consider a graph of electron density in the hydrogen atom as a function of distance from the nucleus. 

Now consider the alkynes, hydrocarbons with carbon-carbon triple bonds. The Lewis structure of the linear molecule ethyne (acetylene) is H—O C- H. To describe the bonding in a linear molecule, we need a hybridization scheme that produces two equivalent orbitals at 180° from each other this is sp hybridization. Each C atom has one electron in each of its two sp hybrid orbitals and one electron in each of its two perpendicular unhybridized 2p-orbitals (43). The electrons in the sp hybrid orbitals on the two carbon atoms pair and form a carbon—carbon tr-bond. The electrons in the remaining sp hybrid orbitals pair with hydrogen Ls-elec-trons to form two carbon—hydrogen o-bonds. The electrons in the two perpendicular sets of 2/z-orbitals pair with a side-by-side overlap, forming two ir-honds at 90° to each other. As in the N2 molecule, the electron density in the o-bonds forms a cylinder about the C—C bond axis. The resulting bonding pattern is shown in Fig. 3.23. 

Methane has four pairs of valence electrons, each shared in a chemical bond between the carbon atom and one of the hydrogen atoms. The electron density in each C—H bond is concentrated between the two nuclei. At the same time, methane s four pairs of bonding electrons repel one another. Electron-electron repulsion in methane is minimized by keeping the four C—bonds as far apart as possible. 

The S+ hydrogen atom seeks out the electron density in the double bond. The curly arrow El represents the movement of a pair of electrons. 

Structures of actual enzyme-substrate complexes are generally difficult to determine, because the reaction occurs too quickly, but techniques now available occasionally enable study of these complexes [53]. Protein X-ray crystallography has several limitations, for example, it often gives little or no information about the positions of protons (because of the low electron density of hydrogen atoms) in a particular protein. This can cause prob-... 

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. 

A mechanism which has been offered to explain these and other data is shown in the following scheme (s. p. 176). The initial step corresponds to the metallation of a metal-hydrogen bond. The rate of metallation of a haloalkene (which is essentially an electrophilic attack by the metal on the bond) depends on the electron density in the C—H bond. Obviously electron-withdrawing substituents such as halogen atoms would be expected to reduce the rate of metallation. We can rationalize the data for the reactions on platinum (100) by assuming that a halogen atom directly attached to the carbon of a C-H bond reduces the rate of metallation to a negligible value. 

The good correlation (Fig. 2) observed between the relative rates and the chemical shifts of the protons in position 2 of the protonated pjn idines indicates that the major factor controlling both the relative shielding of the hydrogen nuclei in the position meta to the substituent and the chemical reactivity is the electron density in position 2 of the unperturbed ground-state molecule. 

The binding of substrates via hydrogen bonds (either as hydrogen bond acceptor or as donor) is necessarily associated with changes in electron densities. In catalytic systems, the resulting polarization leads to an activation of the reactants. 

Interactions between two hydrogen atoms separated by a distance of less than 2.4 A can be formulated as dihydrogen bonds if they correspond to criteria based on the topology of the electron density in the H- H directions The pc values should be small, and the V pc values should be small and positive. 

---