Carbonyl oxygen description

In order for the transferability of parameters to be a good description of the molecule, force fields use atom types. This means that a sp carbon will be described by different parameters than a. sp - carbon, and so on. Usually, atoms in aromatic rings are treated differently from sp atoms. Some force fields even parameterize atoms for specific functional groups. For example, the carbonyl oxygen in a carboxylic acid may be described by different parameters than the carbonyl oxygen in a ketone. 

The General References and two other reviews (17,25) provide extensive descriptions of the chemistry of maleic anhydride and its derivatives. The broad industrial appHcations for this chemistry derive from the reactivity of the double bond in conjugation with the two carbonyl oxygens. 

The linker between helix and strand (H-L3-E) has one major sub-cluster. The first residue is mostly Gly and the second is hydrophobic with significant population of Ala residues, liie side chain of the centi linker residue points outwards but the carbonyl oxygen of L2 points inside the space between the packed helices (Figure 7), nu g this different from those observed in H-L3-H or E-L3-E linkers. The linker E-L3-H that links strands and helices has two major clusters and descriptions of backbone conformations are listed in Table n. The third linker residue L3 of the first sub-cluster has x, of g conformation. For the second sub-cluster, L2 has main chain conformation and g side chain conformationand L3 has extended backbone conformation and g side chain conformation. 

The simplest way to create a local ordered structure within a polypeptide chain made up of amide linkages would be to form hydrogen bonds between residues which are close to one another in the amino acid sequence. As seen from Figure 3.9, this would involve either the second, third, fourth, or fifth NH group from the C=0 of the first amino acid residue. In the 2.2y ribbon description, 2.2 refers to the number of residues per turn and the subscript 7 to the number of atoms between the main chain carbonyl oxygen and the amide... 

Rather, a carbon-metallated strnctnre retaining a strong metal-oxygen bond, as in 11, seemed a more accurate description. The dative bond between the carbonyl oxygen and metal center resnlts in a lower bond order for the carbonyl, which is reflected in a carbonyl stretch at snbstantially lower wave numbers. 

Extensive studies of AChE have resulted in the purification and amino acid sequencing of the enzyme from several sources as well as the description of its quaternary structure from x-ray crystallographic and molecular modeling studies (38). To understand the mode of action of AChEls, it is necessary to examine the mechanism by which AChE catalyzes hydrolysis of acetylcholine. This enzymatically controlled hydrolysis parallels the two chemical mechanisms for hydrolysis of esters. The first mechanism is acid-catalyzed hydrolysis, in which the initial step involves protonation of the carbonyl oxygen. The transition state is formed by the attack of a molecule of water at the electrophilic carbonyl carbon atom. Collapse of the transition state affords the carboxylic acid and the alcohol (Fig. 12.11). The second mechanism, base-catalyzed hydrolysis, involves the nucleophilic attack ... 

Questions about the gross mechanism that remain to be answered are whether the proton in the reactive protonated ester is on the carbonyl oxygen or on the ether oxygen, whether the attacking water molecule first adds or substitutes directly, and whether or not the transition state is highly polar. These questions are similar to those discussed earlier in connection with the hydrolysis of 8-propiolactone, and the possible transition states are similar to those in Table 7. Again, of course, the representations are of extreme transition states, and the true one may be intermediate. A decision in favor of one of these representations is to be taken as an abbreviated statement, the fuller description being that the particular transition state chosen is nearer the true one than any other. 

The description of diorganotin complexes with penicillamine enantiomers and 3-thiopropanoic add in the solid state was undertaken. The 3-thiopropanoic acid complexes derivatives contain both trigonal bipyramidal and tetrahedral structures about the tin. These structures are maintained initially after solution. Again, cyclic formation with chelation occurring with the carbonyl oxygen of the carboxylic group occurs [66]. 

To model reactions in. solution, other workers have included the effects of counterions on the potential eneigy surface. For example, LiNHi has been used to model the synthetically important reactions of lithium amides with carbon acids such as aldehydes and acetylenes. When carbonyls are involved (i.e., aldehydes), precoordination of the carbonyl oxygen to the metal ion plays an important role and must be incorporated for a realistic description of the condensed phase system. To date, efforts to model counterion effects generally have neglected solvent and it appears that a QM/MM or related approach could be valuable for future studies of ion-paired proton transfers. 

In terms of an atomic-orbital description, the carbonyl bond can be represented as shown in Figure 16-1. The carbon is. sp2-hybridized so that its [Pg.674]

Figure 16-1 Atomic-orbital description of the carbonyl group. The a bonds to carbon are coplanar, at angles near to 120° the two pairs of unshared electrons on oxygen are shown as occupying orbitals n.

Further analysis of the microwave spectra provides a precise description of the bond lengths and angles (Table 7). The C2C3 bond is unusually long and relatively weak as shown by the reactivity of substituted cyclopropanones in cycloaddition reactions (see Section 4.4). The carbon-oxygen bond is somewhat shorter than the average carbonyl group and this feature is reflected in the infrared properties of cyclopropanones outlined below. 

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