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Organic Chemistry

What is Organic Chemistry?

A Crystal Clear Chemistry Tutorial

Organic chemistry sounds as though it should be the study of molecules from living beings, and that's what it used to be. Now, however, we call that molecular biology and biochemistry. Instead, organic chemistry has now come to mean the study of molecules containing carbon. Why carbon? Because molcules from living beings contain lots of carbon, and towards the end of the 19th century, we started to realize that that's what made biological molecules so interesting in terms of their reactivities. Thus, organic chemistry is now the study of of all molecules containing carbon, from proteins, DNA, oils, and other large biological molecules to graphite, diamonds, and plastics. Still, we must ask, why is carbon so interesting?

Why Carbon?

Carbon is interesting because it can form four strong, stable bonds to a wide variety of elements, including hydrogen, oxygen, nitrogen, sulfur, phosphorous, and many halogens, metals, and metalloids. Carbon can also form very stable double and triple bonds to itself and to some other elements, such as nitrogen and oxygen. This allows for a huge variety of 3D structures involving carbon to exist, and more are being discovered every year.

Carbon's electronegativity is almost exactly in the middle between the lowest and the highest electronegativity elements (Carbon has electronegativity 2.5, while Flourine has about 4 and Cesium has about 1). Because of this, carbon can form many different kinds of polar bonds (see the tutorial about Bonding for more on polarity and electronegativity), both where carbon is more positively charged and where carbon is negatively charged. This makes many different kinds of reactions with carbon possible, from mild reactivity exhibited at the biological level to complicated rearrangements made possible by reactive metals and acids or bases.

Finally, carbon is also fairly abundantly available, making it an ideal, cheap material for a wide variety of materials, including biological molecules, plastics, dyes, medicines, and many other consumer products. The unique variety of 3D structures, the wide variety of bonds, and the relative inexpensiveness of carbon compared to most other elements makes it a fascinating and rich object of study for organic chemists around the world.

How Does Organic Chemistry Relate to Other Sciences?

Organic chemistry is intricately related to many different fields of science, from physics and biology to astronomy and geology. In the figure below, we've made a tree-chart showing some of the relationships between organic chemistry and other major fields of science; this is by no means a full chart of all of chemistry, physics, or biology, and it doesn't even do justice to all the sciences that are affected by organic chemistry, but these are the most common fields.

Biochemistry and molecular biology are two very similar fields that study molecules in living systems, such as DNA, RNA, proteins, enzymes, and so on. Most of this field is focused on the interactions of macromolecules, that is, very big biological molecules. Topics such as the transcription of DNA, chemical signaling between different cells, and enzymes and proteins involved in growth are all examples of research areas in biochemistry and molecular biology.

A very closely related field is bioorganics, which has a more chemical bent to the study of biological molecules. Here, the emphasis is on making molecules that can affect or mimic biological systems, or to use biological molecules to do things that biology does not. For instance, David Liu at Harvard harnesses DNA molecules to "program" chemical reactions to occur in a specific sequence. Another example is the creation of "receptor" systems, where researchers attempt to synthesize artificial receptors that will recognize or detect certain molecules, similarly to how biological receptors detect specific chemical signals. This field is less about investigating biology and more about doing organic chemistry that is "inspired" by biology.

A field that is at the intersection of bioorganics and biochemistry is chemical biology, which is a relatively new field inspired by the pharmaceuticals industry. This field tries to use molecules made through chemistry to probe biological systems and explore how living systems work. Many drugs from the pharmaceuticals industry were made without knowing how they worked, and by using these molecules to probe living systems, fascinating new research was spawned in biology. Chemical biology is an attempt to take this method and make it more systematic, and the field is still in its infancy. There are both high hopes and high levels of skepticism surrounding this field. This field is closely related to pharmacology and medicinal chemistry, both of which are more oriented towards finding drugs that can have some beneficial effect against diseases.

Organometallics is the combination of organic chemistry and inorganic chemistry. Since organic chemistry is the study of molecules based on carbon atoms, inorganic chemistry is essentially the study of molecules based on everything else; "everything else" makes this a very large field of research! Organometallics is, as the name suggests, the study of how organic molecules interact with metals. A very big subset of this field is organometallic catalysis, which tries to create new catalysts that will perform certain kinds of reactions very well, making them extremely useful in industrial manufacturing and synthesis.

Bioinorganics is analogous to bioorganics, except that it studies organometallic chemistry that is inspired by biological systems. Originally, this area of research was spawned by the study of molecules in living systems, such as hemoglobin and chlorophyll, that used metals as an essential part of their biological function. Much research continues in that area, but one new area is in biomimetic chemistry, which tries to create catalysts that are inspired by or imitate biological catalysts such as enzymes. Some of this research is oriented towards finding out whether life on earth could have started by the production of RNA, DNA, sugar, and so on by inorganic mineral catalysts deep in the oceans.

Physical organic chemistry is the study of the physics involved in organic chemistry. Much of this field attempts to quantify and systematize some ideas and notions that organic chemists understand qualitatively, such as the hydrophobic effect, kinetics, solvent effects, acidity and basicity, and so on. One relatively new field that has come about from physical organic chemistry is the study of large biological molecules, which has resulted in the field known as single-molecule biophysics. Biological systems often have molecules that act similarly to large machines, such as motors, ratchets, and gates, and the study of how these molecules act, from a physical point of view, is the object of this field. The study of biological molecules is related to the field of nanotechnology, as much knowledge and inspiration can be gained from studying the best nanomachines in existance so far, which are made every day in living systems.

Organic electronics is closely related to physical organic chemistry and organometallics, particularly the aspect of organometallics known as materials science. Organic electronics studies ways in which one can create carbon-based electronics and circuits, which could lead the way to inexpensive computers made entirely of plastic, which can also be used in medical technologies and instruments, as they would be non-toxic and biologically non-reactive.

As you can see, organic chemistry influences many different fields of science, making it an essential part of many different kinds of science at the molecular level. It is intricately connected to biology, as it has been since the very beginning, but it is also very closely connected to physics and inorganic chemistry. Organic chemistry is also by no means limited to the fields mentioned above. There are several other fields here that are very important for our lives, safety, and industry, and many of these fields have resulted in the goods that are essential for our lives, from dyes and adhesives to plastics and new coatings and materials. Organic chemistry studies life, improves life, and is inspired by life, and it is a fascinating field of research.