Notes for Chapter 1

Chem 243

Notes for Chapter 1

Carbon Compounds and Chemical Bonds

Though there is much review material in the early chapters, this should be considered important because it will be the foundation for the remainder of the course. You can always refer back to fundamental concepts to make increasingly complex systems easier to comprehend, so make a strong effort to do all the problems you can, including those that are not explicitly assigned, and it will make the rest of the textbook more understandable.

An inordinate amount of memorization is not required to understand organic chemistry. Understanding of the structural theory of organic chemistry will provide you with the skills you need to gain a good working knowledge of the subject. This theory suggests that the properties (chemical and physical) of an organic molecule, are determined largely by its structure. This allows you to look at the structure of a new molecule and estimate some of the important properties and how it will behave under certain conditions.

Of course, there are some things that it will be useful to remember to make the course easier. The valence of various elements will help you in many of the problems you will encounter. In particular, carbon has a valence of 4, meaning that it can form up to four bonds to other atoms. Bonds can be single double or triple, but must total four. This applies to "ground state" molecules. Other species, such as transition states, can have five bonds to a carbon, but they are not stable and cannot be isolated. We will also encounter cations and anions of carbon which will be involved in many reactions.

The structural theory takes into account several important concepts, the "octet rule", electronegativity, and molecular orbital theory. Understanding these concepts are fundamental for a good understanding of organic chemistry. From these concepts you can build a structure of a molecule and from that structure, gain insights into how that molecule will react with other molecules and what kind of physical properties it might have. The physical properties in which we will be most interested, are melting and boiling points, solubility in various kinds of solvents, and interaction with various wavelengths of electromagnetic radiation.

Once you know the way atoms are bonded to each other, and know the geometry of those bonds, you can examine the relative electronegativity of the atoms and estimate the polarity (dipole moment) of the molecule or a part of the molecule. Since the dipole moment is just a description of the separation of positive and negative charges, you now get an idea of how the molecule will interact with other molecules. The attraction of unlike charges and repulsion of like charges tells you what molecules will approach each other. This is the first step in understanding how reactions occur.

You can understand a great deal of organic chemistry if you know the structures of molecules and the distribution of electrical charges on that molecule. So concentrate on knowing the structures and electronegativities of atoms and molecules.

You should know how to write Lewis structures, (though they look simplistic, they can provide you with important information about electron distribution, though little about geometry), and be able to locate any formal charges on their proper atoms.

Quantum mechanics gives us a description of molecular orbitals. The geometries of these orbitals determine the three dimensional structure of molecules, so this is an important concept to study.

Besides the geometry of a molecule, the orbitals give us insights into the chemical reactions and how they occur. Chemical reactions involve breaking and forming of chemical bonds and this involves changes in molecular orbitals.

We will be interested in hydrogen and the atoms in the second row of the periodic table, and a few metals, halogens, phosphorus, sulfur and a few other elements, so don't worry about memorizing a lot of material.

Multiple Bonds

Lewis structures can represent single, double and triple bonds, but molecular orbitals give us a deeper understanding of how the electrons are distributed and how tightly they are held to the nuclei. This knowledge is important for understanding chemical reactions.

The Chemical Bond

This is the central concept in chemistry. If there were no bonds, there would be no chemistry and you wouldn't have to take this course. of course, we would then all be nothing but an atomic gas and the universe would be quite boring.

A chemical bond is the force that holds two atoms together. It consists of a pair of electrons being shared by two atoms. This means that there will be a high concentration of electrons between two bonded atoms. You need to think about these electrons as a pair rather than two individual electrons. As individuals, you could think they would then repel each other (like charges) and force the atoms apart. As an electron pair, they occupy a molecular orbital and attract each positive nucleus,while insulating the repulsive positive charges of the two atomic nuclei from each other. This is the covalent bond. There are various types of covalent bonds, mainly sigma and pi for our purposes, and how the electrons are distributed will determine chemical and physical properties. The more strongly held the electrons aare to the two nuclei, the stronger the bond. Weaker bonds are more easily broken and thus more chemically reactive. Bond strengths also determine molecular vibration frequencies which we will study in Chapter 2.

As we will see, a particular bond can be effected by a number of factors of the molecules structure. This can increase or decrese the electron density of the bond, and have implications on physical and chemical properties.

Always consider the chemical bond to be a shared pair of electrons and then determine how strongly those electrons are held based on the hybridization of the molecular orbitals.

Hybridization

We learn the shapes of atomic orbitals, specifically the s orbitals which are spherical and centered on the atomic nucleus and the p orbitals which have lobes on either side of the nucleus. So when orbitals on different atoms overlap, you might expect the molecular orbitals formed to be composed of s and p orbitals. Well, quantum mechanics, which describes the orbitals, allows the energy levels of the orbitals to be perturbed and result in a "mixing" of different orbitals. This mixing results in new orbitals with geometries determined by the component atomic orbitals. The hybrid orbitals formed are the ones that will be of interest to us in organic chemistry. The sp3, sp2 and sp orbitals give us the great variety of organic molecule geometries. Also, they have different electron distributions, giving the molecules a wide range of chemical and physical properties. you should understand the nature of hybrid orbitals and the geometries and electron distributions of orbitals that result. This will help you understand organic chemistry without the need for all that mindless memorization.

Isomers

Several molecules can have the same empirical formula. They have the same number and types of atoms, but they are connected in a different way. This is the reason for the vast number of organic compounds. Using the structural theory helps bring order to mass of information.

You will need to know how many ways a given set of atoms can be connected within the rules of chemistry and physics. Practice this a lot since you will need to do this throughout the course. There are various types of isomers which will be introduced throughout the course.

Representations of Molecules.

A large part of the early learning of organic chemistry might seem boring or useless because you need to learn the spoken and written language of the subject before you can get into the real chemistry.

We have molecular formulas which only tell you how many atoms of each element are present. Lewis structures tell you about the number and location of valence electrons in the molecule and can also show the location of charges.

Next, there are structures which are of several types. In the bond-line structures, a single line represents a shared electron pair. You can write the structure with each atom explicitly depicted or you can condense the structure by writing some parts of molecules, or groups, in a shorthand manner. You can even write a molecule as a series of lines without any letters or numbers. When you learn the meaning of each type of structure, you will be able to know, unambiguously, what the structure of the molecule is. You will also be able to translate this 2-dimensional symbol into a 3-dimensional model which is the ultimate goal of all these formula types. There are andiron or sawhorse structures and wedge structures which give you good information about 3-dimensional structures. Using the software that comes with the textbook, you can also see the ball and stick models and the space-filling models which show the positions of nuclei and the distribution of electrons in the molecule, so practice converting the 2-dimensional symbols into 3-dimensional models. An inexpensive set of molecular models will be very valuable to you in organic chemistry.

Remember that all these depictions are only symbols and that the symbol used is selected to convey certain information, so Lewis structures may look like simpleminded structures like you saw in 7th grade chemistry, but if you are only intending to show the atoms and their valence electrons, it is an economical method of doing this. Practice the problems on structures thoroughly because you will need to be proficient in this for the entire course.

Later, we will be learning how to assign names to all the molecules. This will be done in a systematic way so that you can eventually be able to build a 3-dimensional structure from the name alone. The sooner you develop these skills, the more you can get out of the course and the best way to learn this is by practice, practice, practice! It's even easier to learn than cuneoform.