Rotation About Single Bonds Conformations

Over the past 25 years, numerous species-specific examples of such deception among plants have been discovered. The deception is so effective that reproductive success in the insect is compromised, with the potentially disastrous consequence to the plant of losing its population of insect pollinators. Fortunately, after being swindled once or twice, individual insects seem to recognize the deception and look for more suitable mates. 

In Summary Straight-chain alkanes have regular structures. Their melting points, boiling 

We have considered how intermolecular forces can affect the physical properties of molecules. These forces act between molecules. In this section, we shall examine how the forces present within molecules (i.e., intramolecular forces) make some geometric arrangements of the atoms energetically more favorable than others. Later chapters will show how molecular geometry affects chemical reactivity. 

If we build a molecular model of ethane, we can see that the two methyl gronps are readily rotated with respect to each other. The energy required to move the hydrogen atoms past each other, the barrier to rotation, is only 2.9 kcal moF (12.1 kJ moF ). This valne turns out to be so low that chemists speak of free rotation of the methyl gronps. In general, there is free rotation about all single bonds at room temperature. 

The many forms of ethane (and, as we shall see, substituted analogs) created by such rotations are called conformations (also called conformers). All of them rapidly inter-convert at room temperature. The study of their thermodynamic and kinetic behavior is conformational analysis. 

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Conformational analysis (Section 3 1) Study of the conforma tions available to a molecule their relative stability and the role they play in defining the properties of the molecule Conformations (Section 3 1) Nonidentical representations of a molecule generated by rotation about single bonds Conformers (Section 3 1) Different conformations of a single molecule... 

Rotation about Single Bonds Conformations CHAPTER 2... 

Structures A B and C represent different conformations of hydrogen peroxide Conformations are different spatial arrangements of a molecule that are generated by rotation about single bonds Although we can t tell from simply looking at these struc tures we now know from experimental studies that C is the most stable conformation... 

Determine whether the two structures in each of the following pairs represent constitutional isomers different conformations of the same compound or stereoisomers that cannot be inter converted by rotation about single bonds... 

Conformational Isomers. A molecule in a conformation into which its atoms return spontaneously after small displacements is termed a conformer. Different arrangements of atoms that can be converted into one another by rotation about single bonds are called conformational isomers (see Fig. 1.1). A pair of conformational isomers can be but do not have to be mirror images of each other. When they are not mirror images, they are called diastereomers. 

To understand the function of a protein at the molecular level, it is important to know its three-dimensional stmcture. The diversity in protein stmcture, as in many other macromolecules, results from the flexibiUty of rotation about single bonds between atoms. Each peptide unit is planar, ie, oJ = 180°, and has two rotational degrees of freedom, specified by the torsion angles ( ) and /, along the polypeptide backbone. The number of torsion angles associated with the side chains, R, varies from residue to residue. The allowed conformations of a protein are those that avoid atomic coUisions between nonbonded atoms. 

One of the frmdamental structural facets of organic chemistry, which has been explained most satisfactorily in MO terms, is the existence of a small barrier to rotation about single bonds. In ethane, for example, it is known that the staggered conformation is about 3kcal/mol more stable than the ecl sed conformation so that the eclipsed conformation represents a transition state for transformation of one staggered conformation into another by rotation. 

In addition to constitution and configuration, there is a third important level of structure, that of conformation. Conformations are discrete molecular arrangements that differ in spatial arrangement as a result of facile rotations about single bonds. Usually, conformers are in thermal equilibrium and cannot be separated. The subject of conformational interconversion will be discussed in detail in Chapter 3. A special case of stereoisomerism arises when rotation about single bonds is sufficiently restricted by steric or other factors that- the different conformations can be separated. The term atropisomer is applied to stereoisomers that result fk m restricted bond rotation. ... 

Conformations (Section 3.1) Nonidentical representations of a molecule generated by rotation about single bonds. 

Rotation about single bonds and conformational changes can be studied. Amides constitute a classic example. Because of the partial double bond character of the carbon-nitrogen bond as a consequence of the contribution of 2 to the electronic structure, there is an energy barrier to rotation about this bond. 

The conformations of H2NS02F and HC(S02F)3 as a result of rotation about single bonds are shown in Figure 8 by projection formulas. The S—C bond length in the latter is 1.831(5) A. 

Conformational analysis the analysis of the energy changes that a molecule undergoes as groups rotate about single bonds. 

Conformational isomers, or conformers, interconvert easily by rotation about single bonds. Configurational isomers interconvert only with difficulty and, if they do, usually require bond breaking. We shall study these in turn. 

With a double bond, rotation would destroy the tt bond that arises from overlap of p orbitals consequently, there is a very large barrier to rotation. It is of the order of 263 kJmol , which is very much higher than any of the barriers to rotation about single bonds that we have seen for conformational isomerism. Accordingly, cis and trans isomers do not interconvert under normal conditions. Ring systems can also lead to geometric isomerism, and cis and trans isomers... 

It is clear that this representation of c/5 -dimethyl-cyclohexane shows a plane of symmetry, and we can deduce it to be a meso compound. No such plane of symmetry is present in the representation of fran -dimethylcyclohexane. Why does this approach work Simply because the transformation of planar cyclohexane (with echpsed bonds) into a non-planar form (with staggered bonds) is a conformational change achieved by rotation about single bonds. The fact that cyclohexane is non-planar means we may have to invoke the conformational mobihty to get the three-dimensional picture. 

Protein chains are not the sprawling, ill-defined structures that might be expected from a single polypeptide chain. Most proteins are compact molecules, and the relative positions of atoms in the molecule contribute significantly to its biological role. A particularly important contributor to the shape of proteins is provided by the peptide bond itself. Drawn in its simplest form, one might expect free rotation about single bonds, with a variety of conformations possible (see Section 3.3.1). However,... 

Special cases of these involving transition states for rotation about single bonds, inversion of pyramidal nitrogen and phosphorus centers and ring inversion in cyclohexane, have been discussed in the previous chapter. The only difference is that these conformational processes are typically well described in terms of a simple motion, e.g., rotation about a single bond, whereas the motion involved in a chemical reaction is likely to be more complex. 

The energy difference AF between gauche and trans conformers, resulting from rotation about single bonds of the chain backbone in trans-1,4-polybutadiene, c/s-1,4-polybutadiene and 1,5-hexadiene, is evaluated from IR measurements on the bands characteristic of bending vibration of CH2 groups. Consideration of the experimental results, on the basis of the RIS model, leads to the conclusion that a value of 0.4 to 0.8 kJ mol-1 is the best estimate of AF. 

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