Introduction to Organic Chemistry

Organic Molecules: Signatures of Life

What are organic compounds and why has an entire branch of chemistry been devoted to studying them? Organic molecules are compounds of carbon that, for the past 200 years, have been recognized by chemists as signatures of life.

If you had to determine whether life existed on another planet, what would you look for? When the Viking probe landed on Mars in 1976 , scientists included instruments to detect the presence of organic compounds. This robot lander, however, found no evidence for life.

A Viking Lander on display at the Smithsonian's National Air & Space Museum. Two of these craft landed on Mars in 1976. Click on thumbnail for a full image.

(Smithsonian Photo #80-3070 by Dane A. Penland. Copyright 1993 Smithsonian Institution. Do not reproduce without permission.)

In August 1996 newspaper headlines reported that possible evidence of life on Mars was discovered in a meteorite. The evidence for life was the presence of organic compounds called polycyclic aromatic hydrocarbons (PAHs) and microscopic shapes that resemble fossilized bacteria found on earth. The meteorite, Allan Hills 84001 (AH 84001), is believed to have crystallized from molten rock on Mars 4.5 billion years ago. About 15 million years ago asteroid impact on Mars blasted AH 84001 into space. It fell in Antarctica about 13,000 years ago where it was discovered in 1984. In fractures in the meteorite, scientists found the organic compounds called polycyclic aromatic hydrocarbons, PAHs, that were determined to be indigenous to the rock and not the result of contamination. Whether or not this evidence will stand up to further investigation, this case demonstrates that organic compounds are the molecules of life.

For a time it was believed that organic compounds did not follow the chemical principles that applied to inorganic compounds. A Theory of Vitalism developed which claimed that organic compounds were produced in living systems by a vital force and were fundamentally different from inorganic compounds.

In the formative stage of the science of chemistry, chemical substances were divided into inorganic compounds which were derived from minerals or the atmosphere and organic compounds obtained from plants or animals.

The theory of vitalism was overthrown in 1828 when Frederick Wöhler heated the inorganic salt ammonium cyanate and obtained urea, an organic compound produced in the kidneys of many animals. 

Both urea and ammonium cyanate have the same chemical formula (CH₆N₂0), but since they have different properties, they are distinct substances called isomers. The synthesis of urea was the first laboratory preparation of an organic compound.

This discovery led to the unification of chemistry around basic chemical principles. All compounds are composed of elements and behave in predictable ways whether they occur in nature or are made in a laboratory.

As improved methods of chemical analysis were developed, it was found that organic compounds always contained the element carbon, and organic chemistry became the chemistry of carbon compounds.

In the 1950's Stanley L. Miller and Harold Urey obtained a mixture of organic molecules which act as building blocks of living organisms by passed electrical sparks through an atmosphere of water, ammonia, nitrogen, and methane.  This famous experiment was designed to replicate conditions that might have existed on earth before life evolved. In such experiments amino acids and the bases found in DNA and RNA were formed.

The search for the possible existence of life on other planets led scientists to search for organic compounds in space. Using spectroscopic methods, scientists found the presence of simple organic molecules such as methane, formaldehyde, and hydrogen cyanide in outer space.

Forms of Carbon

To study the possible formation of clusters of carbon atoms in space, Richard Smalley of Rice University and Harry Kroto vaporized graphite by a laser in 1984 and obtained a molecule with the formula C₆₀. They deduced that the sixty carbon atoms had to be arranged in a sphere and named this new form of carbon buckminsterfullerene. For this work the 1996 Nobel Prize in Chemistry was awarded to  Richard Smalley, Sir Harold Kroto, and Robert Curl, Jr . 

The preparation of gram quantities of C₆₀ needed for laboratory study was accomplished in 1990 by Wolfgang Kratschmer and Donald Huffman.

Buckminsterfullerene became the third form of matter made entirely from carbon atoms. These materials with vastly different properties differ only in the way in which the carbon atoms bond to each other. This interrelationship between the structure and properties of organic compounds is one of the most significant discoveries of science.

In diamond each carbon atom is connected to four other carbon atoms. This three-dimensional arrangement is based on the tetrahedron The arrangement of carbon atoms in diamond make it the hardest known natural substance. 

Carbon may also be found in nature as the soft graphite familiar to us in pencil lead. In graphite, each carbon atom is bonded to only three other carbon atoms in planar sheets. These sheets stack on top of each other and easily slide apart. That is why graphite in pencil "lead" rubs off on paper and in powdered form is used for lubricating locks. 

Graphite In the Chime animation note that the atoms in the center of each sheet are bonded to three other carbon atoms.

Carbon Atoms: Building Blocks of Organic Molecules

Atoms are the building blocks for molecules. Most of the mass of an atom is concentrated in a positively charged nucleus composed of protons and neutrons. Negatively charged electrons are distributed at relatively large distances from the nucleus and are delocalized in space.

One of the great discoveries of the Twentieth Century is that electrons behave like waves and we can only talk about the probability of finding an electron at a certain point. We are relegated to speaking of electron densities instead of precise positions of electrons.

The carbon atom consists of a nucleus of six protons and six neutrons surrounded at a relatively large distance by six electrons. The following diagram, based on the Bohr atomic model, is a useful model for visualization and electron bookkeeping, but does not represent current theories about the electron distribution in atoms. As we proceed in our investigation of organic chemistry we will see several theories and models for chemical bonding and reactions. Usually, the simplest model that fits the facts under study will be used at the expense of a more complete, but less intuitive theory. 

The number of protons in the carbon atom is called its atomic number and determines the position of carbon in the periodic table. Since protons have a positive charge, neutral atoms must contain the same number of negatively charged electrons.

The mass number of carbon is 12 and is the sum of the number of protons and neutrons in the nucleus. This nuclear arrangement, designated ¹²C, is the dominant type found in naturally occurring organic molecules. However, there are two other forms of carbon with the same number of protons (same atomic number) but different numbers of neutrons (different mass numbers. Atoms with the same atomic number but different mass numbers are called isotopes. Carbon has three isotopes ¹²C, ¹³C and ¹⁴C as shown in the following table. Carbon14 is radioactive and is the isotope that allows radiocarbon dating of ancient samples of organic material and is used as a tracer in research.

The ratio of of C¹² to C¹³ varies in organic molecules depending on the process of their formation. For example, the carbon isotope ratio was used to show that carbonate granules in the meteorite AH84001 did not come from its stay in the Antarctic. 

In a carbon atom the 6 electrons are arranged in two shells designated by the principal quantum number (n). Two electrons fill the first electron shell of an atom. The second shell can hold a maximum of 8 electrons. For any atom the maximum number of electrons that can occupy any shell is shown in the following table. 

At the level of electrons, matter behaves with unique properties described by quantum mechanics. Electrons can behave as both particles and waves. The dots and orbits that we used to describe the carbon atoms are strictly a bookkeeping device and do not present a true picture the atom. A carbon atom is not like a miniture solar system. Quantum mechanics descrbes electrons by mathematical wave functions. These equations can be plotted and the density of these plots gives another representation of the electrons in the carbon atom. Each principal shell (n) is further divided into n kinds of orbitals. An orbital can hold a maximum of two electrons. The first shell (n=1) has only 1 kind of orbital (designated s). The second shell (n=2) has two kinds of orbitals (s and p). There are 1 s and 3 p orbitals in the second shell. Since each orbital can hold two electrons, there is a maximum capacity of 8 electrons in the second shell. The table below shows the distribution of orbitals in the first four electron shells. Each electron has a unique identity defined by four values called  quantum numbers which define the energy of the electron. 

Shapes of atomic orbitals

Since orbitals are mathematical wave functions they can be distributed over all of space; however, the probability of finding electron density is greatest at specific distances from the nucleus. It is like the ambiguity of trying to define exactly where Mt. Everest begins. We may not be able to mark a beginning of the mountain but we can certainly determine its highest point with reasonable accuracy.

S orbitals are spherical in shape and are uniformly distributed about the nucleus. Orbitals in the first shell (1s) are closer to the nucleus and are of lower energy than 2s orbitals and so on.

The three p orbitals have lobes and are distributed at right angles from each other. They are often designated as p_x, p_y, and p_z to indicate their orientation in three-dimensional coordinates.

The relative energy of the atomic orbitals for the first 4 shells is shown below. The general trend is that energy of the orbitals increases with the shell number. Notice that the 4s orbital is lower in energy than the 3d orbital.

We can describe the distribution of electrons in an atom by specifying the orbitals which they occupy. The electron distribution may be determined using the aufbau (building) principle which states that electrons occupy the lowest energy orbitals possible. This principle gives rise to the following electron filling order. This is a general principle and applies to many, but not all, atoms. Exceptions are found especially among the transition elements.

For the 6 electrons in the carbon atom, two electrons occupy the 1s orbital. The next two electrons enter the 2s orbital, filling it. The remaining two electrons are found in the 2p orbitals. A shorthand notation for the electron configuration of carbon is:

What about the two electrons in the 2p orbitals? We have seen that there are three p orbitals that are equal in energy but are orientated in different directions in space. The lowest energy arrangement is found when electrons enter different p orbitals before they pair in the same orbital. The Pauli Exclusion Principle states that no two electrons in an atom can have exactly the same set of quantum numbers. Electrons that are paired in the same orbital have a different property called spin. We will come back to this point when we discuss chemical bonding.

Although the periodic table was first organized in the 1860's based on observable chemical and physical properties, by the 1930's it was recognized that the arrangement of electrons in the elements was the fundamental feature behind the table. The number of a period in the table gives the number of the highest occupied electron shell. For example, elements in the third period have their outermost electrons in the third electron shell. Elements in the same group have the same number of electrons in their outermost shells, with a few exceptions for the transition elements and for the element helium which has only two valence electrons. For the main group elements (those with Roman numerals followed with an A) the Roman numeral gives the number of valence electrons. For example, elements in Group IA have only 1 electron in the outermost shell, those in Group II have two electron in the outermost shell, those in Group IIIA have three electrons, etc.

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