Covalent bonds formation

The second important type of primary bond is the covalent bond. Whereas ionic bonds involve electron transfer to produce oppositely charged species, covalent bonds arise as a result of electron sharing. In principle, the 

To illustrate, consider the simplest possible molecule, namely, the HJ molecule, which has one electron but two nuclei. This molecule is chosen in order to avoid the complications arising from electron-electron repulsions already alluded to earlier. 

The procedure is similar to that used to solve for the electronic wave function of the H atom [i.e. the wave functions have to satisfy Eq. (2.1)] except that the potential energy term has to account for the presence of two positively charged nuclei rather than one. The Schrodinger equation for the HT molecule thus reads 

The solution for the H2 molecule is quite similar, except that now an extra potential energy term for the repulsion between the two electrons 

The atoms are held at the distance that separates them, which can either be calculated or obtained experimentally, and the molecular orbitals of HF are calculated. The calculations are nontrivial and beyond the scope of this book the result, however, is shown schematically in Fig. 2.Sb. The total number of electrons that have to be accommodated in the molecular orbitals is eight (seven from F and one from H). Placing two in each orbital fills the first four orbitals and results in an energy for the molecule that is lower (more negative) than that of the sum of the two noninteracting atoms, which in turn renders the HF molecule more stable relative to the isolated atoms. 

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This topic has been dealt with in depth previously, and it should be particularly noted that in each type of hydrolysis the initial electrostatic attraction of the water molecule is followed by covalent bond formation and (in contrast to hydration) the water molecule is broken up. 

The Lewis bases that react with electrophiles are called nucleophiles ( nucleus seek ers ) They have an unshared electron pair that they can use m covalent bond formation The nucleophile m Step 3 of Figure 4 6 is chloride ion... 

Many biological processes involve an associa tion between two species in a step prior to some subsequent transformation This asso ciation can take many forms It can be a weak associ ation of the attractive van der Waals type or a stronger interaction such as a hydrogen bond It can be an electrostatic attraction between a positively charged atom of one molecule and a negatively charged atom of another Covalent bond formation between two species of complementary chemical re activity represents an extreme kind of association It often occurs in biological processes in which aide hydes or ketones react with amines via imine inter mediates... 

This class of inhibitors usually acts irreversibly by permanently blocking the active site of an enzyme upon covalent bond formation with an amino acid residue. Very tight-binding, noncovalent inhibitors often also act in an irreversible fashion with half-Hves of the enzyme-inhibitor complex on the order of days or weeks. At these limits, distinction between covalent and noncovalent becomes functionally irrelevant. The mode of inactivation of this class of inhibitors can be divided into two phases the inhibitors first bind to the enzyme in a noncovalent fashion, and then undergo subsequent covalent bond formation. 

The efficiency of inactivation by covalent bond formation vs release of the reactive species into solution has been described by its partition ratio. The most efficient inactivators have catalytic partition ratios of 0, in which case each inhibitor molecule leads to inactivation of the enzyme. To this date, many of these inhibitors have been designed, and alternative names like suicide substrate, Trojan Horse inactivator, enzyme induced inactivator, inhibitor, and latent inactivator have been used for this class of inhibitors. A number of comprehensive reviews are available (26—32). 

A/-(2,3-Epoxypropyl)-A/-amidinoglycine [70363-44-9] (21) was shown to be an affinity label of creatine kinase. Its mechanism of covalent bond formation is outlined as follows ... 

Coupling to a mineral surface requires the presence of active hydroxyls on the substrate. The coupling reaction is a multi-step process that proceeds from a state of physisorption through hydrogen bond formation to actual covalent bond formation through condensation of surface hydroxyls with silanols ... 

Blasius and coworkers have offered a somewhat different approach to systems of this general type. In the first of these, shown in Eq. (6.20), he utilizes a hydroxymethyl-substituted 15-crown-5 residue as the nucleophile. This essentially similar to the Mon-tanari method. The second approach is a variant also, but more different in the sense that covalent bond formation is effected by a Friedel-Crafts alkylation. In the reaction... 

FIGURE 1.6 Covalent bond formation by e pair sharing. 

FIGURE 16.9 Examples of covalent bond formation between enzyme and substrate. In each case, a nucleophilic center (X ) on an enzyme attacks an electrophilic center on a substrate. 

A 1 1 mixture of thiols (7 and 2), on treatment with oxygen in the presence of a catalytic amount of Et3N, gives one unsymmetrical (4) and two symmetrical disulfides (3 and 5) (Eq. 4). As a measure of the degree of the recognition between 7 and 2 in the oxidation, the selectivity (r) is employed which is represented by the logarithmic ratio of the yield of 4 to twice that of 3 (Eq. 5). The r is so defined as to become zero when oxidation yields the three disulfides in a 1 2 1 ratio. In the present case, the recognition process is followed by covalent bond formation. 

Molecular orbital (MO) theory describes covalent bond formation as arising from a mathematical combination of atomic orbitals (wave functions) on different atoms to form molecular orbitals, so called because they belong to the entire molecule rather than to an individual atom. Just as an atomic orbital, whether un hybridized or hybridized, describes a region of space around an atom where an electron is likely to be found, so a molecular orbital describes a region of space in a molecule where electrons are most likely to be found. 

Molecular orbital (MO) theory (Section 1.11) A description of covalent bond formation as resulting from a mathematical combination of atomic orbitals (wave functions) to form molecular orbitals. 

Our rule about covalent bond formation can be applied quite simply through an orbital representation ... 

In covalent bond formation, atoms go as far as possible toward completing their octets by sharing electron pairs. 

The basic requirement for cellulose dissolution is that the solvent is capable of interacting with the hydroxyl groups of the AGU, so as to eliminate, at least partially, the strong inter-molecular hydrogen-bonding between the polymer chains. There are two basic schemes for cellulose dissolution (i) Where it results from physical interactions between cellulose and the solvent (ii) where it is achieved via a chemical reaction, leading to covalent bond formation derivatizing solvents . Both routes are addressed in details below. 

The electron affinity of the carbocations as measured by red is a useful index for the stability of the carbocations. It is of great interest to correlate the occurrence of three principal reactions between a carbocation and a carbanion, i.e. covalent bond formation (36), single-electron transfer (37) and salt formation (38), with the magnitude of the E ed for the carbocations. 

Fig. 8 Reactions of various carbocations with Kuhn s anion [2 ] as compared with their reduction potentials (peak potentials measured vs. Ag/Ag in acetonitrile by cyclic voltammetry cf. Tables 1 and 8 and Okamoto et al., 1983). SALT, salt formation COV, covalent bond formation ET, single-electron transfer. 

As the cation becomes progressively more reluctant to be reduced than [53 ], covalent bond formation is observed instead of electron transfer. Further stabilization of the cation causes formation of an ionic bond, i.e. salt formation. Thus, the course of the reaction is controlled by the electron affinity of the carbocation. However, the change from single-electron transfer to salt formation is not straightforward. As has been discussed in previous sections, steric effects are another important factor in controlling the formation of hydrocarbon salts. The significant difference in the reduction potential at which a covalent bond is switched to an ionic one -around -0.8 V for tropylium ion series and —1.6 V in the case of l-aryl-2,3-dicyclopropylcyclopropenylium ion series - may be attributed to steric factors. 

Lanthanides form soluble complexes with many inorganic and organic substances however, the nature of the bonding in these complexes has not been completely determined. There is evidence for either ionic or covalent bond formation or a combination of both. Lanthanides are complexed by inorganic ions, but not as readily as are the transition elements. The inorganic complexes are not as important... 

NU(C) base atoms (5) The stereoselectivity of the BPDEs during intercalative covalent binding in kinked DNA and (6) The possible reorientation of the complex to yield an externally bound adduct. The energetics for each of these processes will be presented to identify the important steps that influence the binding of specific isomers. It will be shown that the orientation of each diastereoisomer of BPDE about specific base atoms in kinked receptor sites in the duplex DNA during covalent bond formation is the determining factor in stereoselectivity. 

The most stable base sequences (67 7M are the pyrimidine(p) purine ones TpA, TpG and CpG. For binding to N2(G), N6(a), 06(g) and NH(c) these lead to 5% 5% Y and 3 type binding for receptor sites. The 3 and 5 type binding for (pu) and (py) base atoms, respectively, require the use of receptor sites which are less stable. These binding orientations are less likely to occur if the intercalation process precedes covalent bond formation. 

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