Organic chemistry/Alkanes and cycloalkanes

Introduction

Tryptophan

In this course you should learn how to draw structural formulas correctly and how to represent even complicated connections clearly without leaving out important information or adding unnecessary information to the formula. You can see a good example of a structural formula on the right. The skeletal formula of tryptophan is shown there. Tryptophan is an essential amino acid that we eat every day and that is essential for our bodies to survive. We'll come back to tryptophan at the end. If you don't understand every detail in this structural formula now, that's not a problem. At the end of the course, you will be able to paint such a formula with ease. But one by one.

Valence stroke formulas

Butane in a full molecular repersentation

Butane, in skeletal repersentation

Let's start with a simple example: butane. Butane is a hydrocarbon, more precisely an alkane. Hydrocarbons all have in common that they only consist of, as the name suggests, carbon and hydrogen.

Each carbon atom is tetravalent, i.e. each carbon atom has one single bond (an electron pair connected) with four other atoms. You can see this clearly in the following illustration:

For example, a hydrogen atom is bonded to the second carbon atom in positions 1 and 3 and a carbon atom in positions 2 and 4. Another way of representation would be the following abbreviated notation:

The hydrogen atoms are summarized here for each carbon atom.

A common chemical folly that beginners fall for often is the mistaken conception that all C atoms are in a line; that does not correspond to reality. One could also think that the entire butane molecule lies in one plane and that all bonds are at a 90 ° angle to each other. This is also not the case in reality.

Skeletal formulas

The actual spatial structure of molecules can be determined by examining organic compounds using X-ray structure analysis. You then get this 3D structure:

Methane

And as you can see, butane isn't linear, it's angled. And the H atoms shown here in white do not simply protrude from the C atoms above and below, but are arranged at an angle.

The tetrahedron angle: The black carbon atom in the middle is bound to four white carbon or hydrogen atoms at an angle of approx. 109.5°, forming A tetrahedron

Both the zigzag carbon atoms and the angled forward and backward hydrogen atoms have a very specific angle to each other, which is approximately 109.5 °. This angle is called a tetrahedron angle because the atoms are arranged like the corners in a tetrahedron, a body with four triangular sides. In the middle of this tetrahedron there is also an atom, namely a carbon atom, which is bonded to all the atoms in the corners. One carbon atom in the middle, four attached hydrogen or carbon atoms in the corners of the tetrahedron. Here you can again see the four-bonded structure of the C-atom.

Even if you cannot paint a three-dimensional structure on paper, you should represent a hydrocarbon chain such as butane in the 2D representation on the paper as a zigzag. That comes closest to the real structure and looks like this:

Unfortunately, this representation still has one catch: It is quite confusing. The whole structural formula is overloaded with the element symbols C and H and you don't see at first glance how long the chain actually is and what really depends on the C atoms. Sometimes it is an H atom, sometimes it is a CH₃ group ( methyl group ) To finally get to the skeletal formula , all H atoms and the bonds to the H atoms are simply left out. The letter C is also omitted everywhere. Only the bonds between the carbon atoms remain.

This makes the structural formula much clearer. You can quickly see that it is a chain made up of four carbon atoms (the carbon atoms are linked by three bonds). And this notation has another advantage. You will notice this when you draw the molecule yourself on a piece of paper. It goes faster! Draw a zigzag line and you have a finished butane molecule on the paper. You just add the H atoms by always keeping in mind that the C atom is four-bonded. If two other bonds go from the carbon atom in the skeletal formula to two other carbon atoms, then two more hydrogen atoms must be bonded to this carbon atom. You just have to mentally fill every carbon atom with hydrogen atoms up to four bonds.

Functional groups

In the case of butane, this is perhaps still quite clear if you don't use the skeleton notation, but in the case of large molecules with functional groups , it is important to see at first glance which functional group is where. But that doesn't mean you shouldn't use the skeletal formulas for small, simple molecules like butane.

Lactic acid

For example, look at this lactic acid valence formula:

And now we again leave out all H atoms and the associated bonds and the Cs as well.

That looks a lot clearer. But you might have noticed that we left the two H atoms on the two OH groups. This is because there are two functional groups, on the left the OH group (a hydroxyl group ) and on the right the COOH group (a carboxyl group ), the carbon atom with the double bond to the O belongs to the functional group. One could assume that oxygen, as an element from the sixth main group of the periodic table, is double-bonded and one simply counts the missing H in order, according to the octet rule, to eight outer electrons(2 electron pairs for the 2 bonds make 4 electrons plus 2 free electron pairs on the oxygen atom, which are not shown here = 8 outer electrons), but functional groups are extremely important for chemical reactions. Often there is an H atom or an extra H atom attached to it. That is why you avoid misunderstandings and paint the hydrogen atom, if it is bound to the O, to it.

Most of the chemical reactions take place on the functional groups. The hydrocarbon framework usually only plays a subordinate role. The C and H atoms can be thought of as the skeleton or skeleton of the molecule, the backbone of the functional groups. And here you can see why you should also paint skeletal or scaffolding formulas. They emphasize the important functional groups and let the unreactive scaffold move into the background. With the representation you can see more quickly what is important in a chemical reaction.

Tryptophan

tryptophan also

Let us now come to our example mentioned at the beginning, tryptophan. Check out the valence line formula and the skeletal formula. Here you can see immediately that one should definitely not write out C and H atoms. The valence line formula is completely confusing, you don't even recognize the six- or five-membered ring right away. Likewise, the nitrogen is completely lost as part of a functional group in the five-membered ring. Let's take another look at the skeletal formula:

Since the element nitrogen is in the fifth main group of the periodic table, it is trivalent in the uncharged state. In order for it to have eight outer electrons on its electron octet, it forms three single bonds (3 electron pairs = 6 electrons). With a lone pair of electrons on the nitrogen atom, not shown here, there are actually eight outer electrons. Nevertheless, one draws the H atom in all non-C atoms (these atoms are called heteroatoms in organic chemistry ), since it often happens here in reactions that an H is lost or an additional one comes up. The same applies as for the oxygen mentioned above. So there are no misunderstandings when it comes to the question of whether the hydrogen atom is implicitly involved or not. 3D structure of tryptophan And you might have noticed something else: The bond to the right NH 2 group ( amino group ) on the alkyl residue (the “zigzag residue”) is painted as a wedge. A colored wedge means that the group is facing forward, i.e. in your direction out of the screen. In the valence line formula you can also see the H atom pointing backwards. This is indicated by a dashed wedge. If you cannot imagine this spatially yet, take a look at the 3D structure of tryptophan on the right-hand side. In the right part of the molecule you can see the nitrogen atom painted in blue with the two hydrogen atoms attached to it, which is looking in your direction. The single white hydrogen atom that is bound to the same carbon atom as the NH 2-Group, on the other hand, points backwards away from you. In the above type of representation with wedges, one also speaks of wedge line formulas .

Summary

You should keep the following points in mind:

Note: The Cs in alkanes or alkyl radicals are not arranged in a row, but in a zigzag. All four radicals on such a carbon atom are arranged in a tetrahedral angle. This is approx. 109.5 °. Always paint structural formulas realistically, clearly, and in a time-saving manner. Therefore, always use skeleton or wedge line formulas. Always draw molecular chains in a zigzag shape. Leave out all H atoms and their bonds, unless there is a good reason not to do so, for example if the H atom is bound to a heteroatom or if you want to highlight it on a C atom because it is chemical Reaction is involved. Leave out all Cs. Here, too, there can be exceptions if you want to emphasize the carbon atom due to a chemical reaction. Dashed and colored wedges show the spatial orientation of the residues on a carbon atom. Functional groups are of great importance for the properties and the reaction behavior of a substance. The hydrocarbon skeleton often only plays a subordinate role in reactions.

You have now mastered something extremely important. What you have learned in this course is the basis for all things organic chemistry that you will learn in school, in your studies or in your life as a chemist. The most important means of communication in organic chemistry are clear and understandable structural formulas. In the organic area of Wikiversity, too, you will always have to rely on skeletal or wedge line formulas. But not only do we follow the rules above. You too should always make sure that you paint structural formulas correctly. Before you ever write a C or an H again, think twice about whether this is really necessary in your case.