Organic chemistry and the periodic table

Pfizer s atorvastatin (Lipitor) cholesterol-lowering drug 

We cannot maintain our present high density of population in the developed world, nor deal with malnutrition in the developing world unless we preserve our food supply from attacks by insects and fungi and from competition by weeds. The world market for agrochemicals produced by multinationals such as Bayer CropScience and Syngenta is over 10bn per annum divided between herbicides, fungicides, and insecticides. 

All the compounds we have shown you are built up on hydrocarbon (carbon and hydrogen) skeletons. Most have oxygen and/or nitrogen as well some have sulfur and some phosphorus, and maybe the halogens (F, Cl, Br, and I). These are the main elements of organic chemistry. 

But organic chemistry has also benefitted from the exploration of (some would say takeover bid for) the rest of the periodic table. The organic chemistry of silicon, boron, lithium, tin, copper, zinc, and palladium has been particularly well studied and these elements are common constituents of organic reagents used in the laboratory. You will meet many of them throughout this book. Butyllithium, trimethylsilyl chloride, tributyltin hydride, diethylzinc, and lithium dimethylcuprate provide examples. 

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One powerful organizational device in chemistry is the periodic table. Its use in organizing and predicting the behavior of all of the known elements (and many of the compounds formed from these elements) is the subject of this chapter. 

Central to any discussion of chemistry is the Periodic Table, that masterpiece of organization formulated in the 19th century principally by Dmitri Mendeleev (1834-1907) and its basis understood in the 20th century once the structures of atoms had been explained. That the table is important is confirmed by its ubiquity it hangs on laboratory and lecture room walls and is printed in every introductory chemistry textbook. There is a version towards the end of this book. Its importance, though, should not be overstated. Working chemists do not gaze... 

In computational chemistry it can be very useful to have a generic model that you can apply to any situation. Even if less accurate, such a computational tool is very useful for comparing results between molecules and certainly lowers the level of pain in using a model from one that almost always fails. The MM+ force field is meant to apply to general organic chemistry more than the other force fields of HyperChem, which really focus on proteins and nucleic acids. HyperChem includes a default scheme such that when MM+ fails to find a force constant (more generally, force field parameter), HyperChem substitutes a default value. This occurs universally with the periodic table so all conceivable molecules will allow computations. Whether or not the results of such a calculation are realistic can only be determined by close examination of the default parameters and the particular molecular situation. ... 

Organic chemistry, then, is the study of carbon compounds. But why is carbon special Why, of the more than 30 million presently known chemical compounds, do more than 99% of them contain carbon The answers to these questions come from carbon s electronic structure and its consequent position in the periodic table (Figure 1.1). As a group 4A element, carbon can share four valence electrons and form four strong covalent bonds. Furthermore, carbon atoms can bond to one another, forming long chains and rings. Carbon, alone of all elements, is able to form an immense diversity of compounds, from the... 

This year marks the 100th anniversary of the death of one of the most famous scientists of all time, the Russian chemist Dmitri Ivanovich Mendeleev (1834-1907). The periodic table that he introduced in 1869 was a monumental achievement— a wonderful mnemonic and a tool that serves to organize the whole of chemistry. No longer were students of chemistry obliged to memorize the properties of all the known elements hereafter they could leam the properties of at least one element from each column and could, in principle, make sound predictions about the other elements in the column. 

The periodic table is one of the most notable achievements in chemistry because it helps to organize what would otherwise be a bewildering array of properties of the elements. However, the fact that its structure corresponds to the electronic structure of atoms was unknown to its discoverers. The periodic table was developed solely from a consideration of physical and chemical properties of the elements. 

In the Brpnsted picture, the acid is a proton donor, but in the Lewis picture the proton itself is the acid since it has a vacant orbital. A Brpnsted acid becomes, in the Lewis picture, the compound that gives up the actual acid. The advantage of Lewis theory is that it correlates the behavior of many more processes. For example, AICI3 and BF3 are Lewis acids because they have only 6 electrons in the outer shell and have room for 8. Both SnCU and SO3 have eight, but their central elements, not being in the first row of the periodic table, have room for 10 or 12. Other Lewis acids are simple cations, like Ag. The simple reaction A + B- A—B is not very common in organic chemistry, but the scope of the Lewis picture is much larger because reactions of the types... 

The four atoms attached to the stereocenter are C, C, O, and H. We rank them from 1 to 4 based on atomic number. To do this, we must either consult a periodic table every time or commit to memory a small part of the periodic table—just those atoms that are most commonly used in organic chemistry ... 

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