プログラム学習・有機化学 Organic chemistry Programmed Study

1.1 Isomerism, isomers

A compound, whether it is organic or inorganic, always has its specific molecular formula. Reverse is, however, not always true. Thus a molecular formula can sometimes point out more than one compound. Molecules with the identical molecular formula and different structures are isomers, and such a phenomena is called isomerism.
The isomerism can be divided into some classes depending on how far those isomers are resembled each other. In order to understand the isomerism, it is necessary to determine and describe exactly the molecular structure of each molecule. The molecular formula provides the number and the type of atoms within a molecule.

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It is a rational formula that specifies the group which the compound belongs to by showing functional units which are the source of the properties of a compound (functional group). Connecting one atom and another by required numbers of bonds lead to structural formula. It can completely describe molecular structures as far as the sequence of bonds is concerned.

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It is not necessary to draw bonds corresponding to their actual lengths, even though bond lengths of C-C, C-O and C-H bonds in structural formula 2~5 are different each other. Actual bond angles between bonds are not also reflected in structural formula. For example, the real bond angle for <HOH of water H₂O has been experimentally determined as about 104°. However, the structural formula of water is usually drawn as 6 or 7. Thus, the dimension and direction of bonds in structural formula may not precisely reflect the actual molecular structures.

▶go to S1.1 molecular formula, rational formula, structural formula

1.2 Factors to determine molecular structures

Even in the structural formulas 2~5, these can not reflect the real structure of those molecules, since those formulas drawn on a sheet of paper can describe only the order of atoms in molecules.

Then, what kind of parameters could define a molecular structure? It can be defined by only atomic distance r AB for diatomic molecules, and for triatomic molecules, it can be defined by three parameters ­ two atomic distances r AB, r AC and bond angle ­BAC. Both an atomic distance and a bond angle are the specific parameters of atoms that form the bonds, and they have own values which can be predicted by the chemical bond theory.

For tetra atomic molecules, three atomic distances r AB, r BC, r CD and two bond angles ­ABC, ­BCD cannot be enough to define the geometry of a molecule. Even though these parameters would be determined, the geometry could not be defined until it is determined that whether those four atoms placed on the identical plane or not. If these are not on the identical plane, it must be decided which atom is away from the plane.

The geometry of 10 can finally be defined by the sixth parameter ­ dihedral angle f. A dihedral angle is defined as an angle between the plane 1 including atom ABC and the plane 2 including BCD. It is necessary to introduce a new parameter dihedral angle, which is driven from neither the atomic distance nor the bond angle, to determine the structure of tetraatomic molecule. This fact suggests us two following things.

Figure 1.1 Dihedral angle

1) Molecules are three-dimensional, and are not always arranged on the two-dimensional sheet of a paper.
2) Molecular structures are not defined by atoms or by types of bonding in the molecules.

Needless to say, bond angles play the main role in determining molecular structures. Therefore atomic orbitals of a carbon atom, which is the factor controlling bond angles in organic compound, will be learned in the next section.

1.3 Atomic orbitals of carbon atoms; hybridization

The electron configuration of a carbon atom in its ground state is 1s²2s²2p². Reasoning from the electron configuration and the direction of atomic orbital, the bonding electrons are only two 2p electrons that occupy the 2p orbital because 2s electrons are not involved in the bond formation because these form a unshared electron pair. Thus, hydride of carbon would be expected to be CH₂, and its bond angle should be 90°, which is the angle between two 2p electrons. (Figure 1.2 )

Figure 1.2 Hypothetical hydride of carbon; CH₂

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However, studies about methane and its substituted species (e.g. chloroform CH₃Cl) reveal that each of those four hydrogen atoms in methane is identical. The fact means that a carbon must use four identical atomic orbitals with four unpaired electrons, but not an s orbital and three p orbitals. It can be explained in term of hybridization that means mixing an s orbital and three p orbitals to make up four equivalent new orbitals, and the resulting orbital is called sp³hybridized orbital.

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One may wonder that it is impossible to decide which of those expected structures 11~13 can be the true structure of methane without some direct observations. However, if substituted methanes should have the same structure as methane, it is possible to deduce the structure of methane from the numbers of the isomers of substituted methanes.

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Since some investigations reveal that only one compound exists as methylene chloride, the tetrahedron should be acceptable as the structure of methane. Atomic orbitals of an sp³hybridized carbon atom that forms tetrahedral structure is shown in Fig 1.4. Methane is made up by four bonds which is formed by the overlap of each sp³orbitals of a carbon atom with a 1s orbital of a hydrogen atom. Therefore, direction of those atomic orbitals determines the geometry of a molecule.

In addition, chemistry about a molecule that is formed by substituting three hydrogen of methane with each different atoms or groups (hereafter referred to as "ligand") such as a comparatively simple molecule bromochlorofluoromethane CHBrClF provides a more critical evidence for the tetrahedral structure of methane.

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Here we have learned the pair of isomers 14 and 15. 14 and 15 are differed in their three-dimensional arrangement of atoms, even though they seem to be similar on the two-dimensional plane. Generally, isomers, though identical in their structural formula, differ in the arrangement of those atoms in space are called stereoisomers. Though there are some classes of stereoisomers, a pair of nonidentical images such as a right hand and a left hand or a real image and its mirror image is called a pair of enantio isomers or simply a pair of enantiomers. Though the terms antipode and mirror image isomer are also used, the term enantiomer will be exclusively employed in this textbook. 14 and 15 are differed in their steric configuration around carbon atom.

Next, we will discuss on the relations between stereoisomers including enantiomers. While it is clear that they are isomers with different structure, is there any difference in their property or chemical reactivity? Stereochemistry is one of a branch of science that involves the study about physical and chemical properties of various compounds especially associated with its three-dimensional structures. Chemistry could not make any progress without stereochemistry. Stereochemistry is an essential part of chemistry. Then, is it necessary to separate the study of stereochemistry from the study of chemistry?

There is a good reason for stereochemistry to be recognized as an important and independent field of chemistry. First of all, physical and chemical properties of stereoisomers are sometimes different so much that it is possible to obtain much information about the relation between molecular structure and properties. Next, a definite and considerably elaborate procedure is necessary to represent information about three-dimensional structure of a molecule on a two-dimensional sheet of paper and then to reproduce original three-dimensional information from it.

1.4 Multiple bonds

Carbon atom is not always connected to four different atoms. Carbon atoms involved in double or triple bonds combine three or two another atoms, respectively. First of all, we will consider carbon atoms that form a double bond. A carbon atom with the electron configuration 2s¹2p_x¹2p _y¹2p_z¹ can form three hybridized orbitals of equal energy from three atomic orbitals, 2s and two of 2p orbitals. One of the 2p orbital (e.g. 2pz orbital) is remained unaffected. This hybridized orbital is called sp²hybridized orbital from its constitution. All of the sp²-hybridized orbitals are on the same plane including the carbon atom, and the remaining 2p orbital is perpendicular to the plane. Fig 1.4 (b) shows the atomic orbital of sp² hybridized carbon atom.

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Skeleton of ethylene is formed when sp² hybridized orbitals of each of two carbon atoms overlap to form a s bond. Overlap can take place when two p orbitals are placed parallel and the result is the formation of a p bond. Therefore, a double bond is made up from a s bond and a p bond. Ethylene C ₂H₄ is completed when hydrogen atoms attached to each of the residual sp² hybridized orbitals.

Figure 1.4 Hybridized atomic orbitals of carbon (p orbitals are omitted).

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If carbon atom forms triple bond, it can be connected to only two other atoms. In this case, the carbon in 2s¹2p _x¹2p_y¹2p _z¹ electron configuration forms two equivalent sp hybridized orbitals (Fig 1.4(c)) from a 2s and one of 2p orbitals, and two 2p orbitals are left over. The sp hybridized orbitals are in the opposite direction. In other words, the angle between each of two sp hybridized orbitals is 180°. In acetylene C₂H₂, a s bond is formed by the overlap of sp hybridized orbitals from each sp hybridized carbon, and two p bonds are also formed by the overlap of two pairs of p orbitals, and hydrogen atoms are bonded to the remaining two sp hybridized orbitals.

Figure 1.5 The structure of basic organic compounds.

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▶go to S1.2 hybridization of carbon atom

1.5 Molecular models and geometry of molecule

As is clear from the figures in the previous sections, it is not easy to represent the arrangement of atoms that make up molecules onto the two-dimensional plane of a paper even for considerably simple molecules such as methane, ethane and acetylene.

Therefore, since latter half of 19th century, when the importance of stereochemistry was began to be recognized, various molecular models have been devised and some of them have been commercially available to assist chemists. However, previously the molecular models had been used only for research, not for education, because stereochemistry was the limited field of science where only a part of chemists were likely to be interested in. In the 20th century, increased recognition for the stereochemistry especially for chemists studying organic chemistry brought the molecular models into the tool of education.

Figure 1.6 illustrates typical molecular models. Each of them is a model of ethane.

(a) Space filling model (e.g. Stuart model, Courtaulds model) represents spread of electronic cloud. However, they fail to represent atoms inside a molecule clearly. It is not always easy to understand the arrangement of atoms in a complex molecule till one would have some experiences. On the other hand,

(b) skeletal model represents a molecule only with sticks in proportion to the bond length. The utility of this type of model is that it is easier to have a good idea on the bond angles, bond lengths and the shape of whole molecule, which is not so clear in the space filling model.

(c) Stick and ball model can be considered as a variation of (b).

The location of an atom (or rather the location of atomic nucleus) is shown by a ball with several holes. Sticks of appropriate length represent the bonds. The angle of each hole on the ball is fitted to correspond to bond angles, and the length of each sticks are also made proportional to corresponding bond lengths. The utility of this model, which it is often easy to understand chemical structure of a molecule since the balls are colored by elements that they symbolize, can make it to be the most suitable one for education.

Figure 1.6 Various molecular models

HGS model is a domestic product, and it is easily available everywhere, and a set for students of modest price is also available. It would be worth obtaining a molecular model, because it is necessary for learning stereochemistry.

HGS model consists in balls (in fact polyhedron) with four holes for sp³hybridized carbon atoms, balls with five holes (two for p orbitals) for sp²hybridized carbon atoms, multipurpose balls with many holes including those for sp hybridization, and plastic rods with various lengths. The balls are color-coded for differentiation. There are balls with many holes to be used to construct complex molecules.

▶go to S1.3 Variety of molecular models

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There are two methods to represent multiple bonds by molecular models. In the first method, a multiple bond is represented by means of a bond with a bond length or a bond angle from those of the single bond. Dreiding model is one of the examples. Another method is to represent the multiple bond between atoms directly by some ways. HGS model is of the first method so that it is set balls and sticks suitable to this way, but the model is also ready to the second way. For example, ethylene molecule can be represented by connecting two balls for an sp³ hybridized carbon by two curved bonds (Fig 1.7(a)). As for acetylene, three curved bonds can be applied.

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In HGS model, the third method to solute the problem is provided. A double bond can be made up by using balls with five holes and hydrogen atoms and plates for p orbitals (fig 1.7 (b)). Since a molecule will be most stable when two pairs of p orbitals come to overlap most effectively, the most stable structure of ethylene can be achieved by fastening those plates.

(a) the model with bent bonds (b) the model with plates for p orbital

Figure 1.7 Molecular model of ethylene by HGS molecular model

There is some similarity between the problem how to represent a double bond in molecular model and the problem how to represent a C-C single bond. When you build up a molecular model of ethane, geometry of two methyl groups is not fixed, whatever model is chosen. In molecular models, one of the methyl groups can be allowed to rotate while holding the other methyl group. Thus, the shape of whole molecule is changed continuously. However, even if the shape would be changed, bond angles and bond lengths are not changed. What is changing is the distance between hydrogen atoms of those two methyl groups.

Suppose you choose one of the hydrogen atoms of each methyl groups and name these H_A and H_B, respectively. It is clear that the distance between H_A and H_B is changing by the rotation of the methyl groups, and this can be described by the change of dihedral angle defined by four atoms H_A-C-C-H_B (Fig.1.8 a, b).

Figure 1.8 The shape of ethane and the dihedral angle

Then, does the change that is taken place in molecular models correspond to the actual phenomenon? Or is it only the result of imperfection with models? It have been widely recognized that such a free rotation around a carbon­carbon single bond is possible more than a handled years ago. By the middle of 20th century, further understanding has been developed and such a rotation is not completely free but restricted to some degree ­ restricted rotation.

How are structure, character and reactivity of a molecule influenced by the rotation? This is also an interesting issue with stereochemistry.

1.6 Nomenclature of stereochemistry

The nomenclature of compounds should have an important role because one or more molecules are present for single molecular formula. First of all, a name must specify only one compound (though two or more name is possible for one compound). Secondly, the structure of a compound should be deduced from its name unambiguously. After the age of Lavoisier, chemists made much effort to devise reasonable and universal and simple rules for nomenclature of compounds. As a result, even beginners can easily understand and use the nomenclatures especially for considerably simple compounds. For example, C₄H<sub">9OH 2~5 is named as follows.

The first nomenclature (A) is traditional or trivial one which have been used since 19 th century, while the second nomenclature (B) is more regular or systematic one. Once you understand its general rules, the latter may be more useful.

Structural isomers, which have the same molecular formula but differ in the order in which the atoms are arranged in space, also require a nomenclature system by which one name will correspond to only one compound. It should also be possible to reconstitute the structure from the name. Although the nomenclature based on stereochemistry of a molecule ­ stereochemical nomenclature -- is much newer than nomenclature for compounds, they shared their ways to develop. This means that stereochemical nomenclature for certain group of compounds (e.g. alkenes or oxime etc.) was established first, and subsequently systematic nomenclature which could be applied to every group of compounds was devised.

Although the systematic nomenclature will become the standard, the former system still plays some role. Indeed, both nomenclatures are actually used, and necessity of past literatures written with old-fashioned nomenclature still exists. Therefore, we will learn both nomenclatures in this textbook.

Sequence rule

The systematic nomenclature is based on the sequence rule. The sequence rule decides the priority sequence among ligands. The stereochemistry of a compound is described by the order ranked according to the sequence rule and several additional rules about each compounds.

Now, let us take a look at the compound 19 and rank the ligands that are bonded to the atom X in order of priority.

1. Generally, the greater the atomic number, the higher the priority.
2. In the case of isotopes, the mass number is used to determine their relative priority.
3. First of all, the priority depends on the atoms that directly attached to the atom X. 
4. In the case of a tie (i.e. A, A), the ligands that are attached to each of the atoms (i.e. B, C, D, and B, C, E, respectively) must be considered.
5. Even if there are still tie atoms remaining, the procedure must be repeated till the priority is determined.
6. If an atom is doubly or triply bonded to another atom, the priority system treats it as if it were bonded to two or three of those atoms.

Thus, in A-B double bond, the atom A is considered to be bonded to two of atom B, the atom B is to be bonded to two of atom A, and the sequence rules (1)~(5) are to be applied.

These atoms (A) or (B) are called replica atoms.

▶go to S1.4 Sequence rules

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The priority order of common ligands is listed in ▶S1.5.. It may be worth warning that the order can be easily changed by substitution. For example, methyl group is ranked lower than ethyl group in the list, however fluoromethyl CH₂F-has higher priority than ethyl.

▶go to S1.5 Priority of representative ligands (lower to higher)