Topic outline

  • General

  • Topic 1

    Organic chemistry is the chemistry of carbon and/or other related elements like silicon. Our life is mostly based on carbon, an element that forms strong chemical bonds to other carbons as well as to many other atoms including hydrogen, oxygen, nitrogen, and the halogens.There are approximately more than five million known organic compounds in an area of scientificly based environments. However, still we have discovering and structural identifying many more organic chemistry-based molecules for their usages in biological systems (as drug candidates) and in industry-based facilities. Therefore, the organic chemistry is very important for all living creatures. 

  • Topic 2

    The atomic theory of electrons began in the early 1900s and gained acceptance around 1926 after Heisenberg and Schroedinger found mathematical solutions to the electronic energy levels found in atoms, the field is now called quantum mechanics.

  • Topic 3

    Molecules are built of permanent numbers of atoms joined together by covalent bonds, and can variety from the very small (even down to single atoms, as in the noble gases) to the very large (as in polymers, proteins or even DNA).

    The covalent bonds keeping the molecules together are very strong, but these are largely immaterial to the physical properties of the substance. Physical properties are ruled by the intermolecular forces - forces attracting one molecule to its neighbours - van der Waals attractions or hydrogen bonds.

  • Topic 4

    Molecular structure of biologically related molecules are also a branch of organic chemistry, molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules, especially proteins and nucleic acids, how they acquire the structures they have, and how alterations in their structures affect their function. These are all carbon based compounds and the interactions each other would be essential factors for the biological activity.

  • Topic 5

    Molecular structure properties also includes the facts that the discrepancy related different functional groups. Herein, we continue to explanations the molecular structure properties on;

    - Functional groups

    - Alkyl halides

    - Alcohols and ethers

    - Amines

    - Aldehydes, ketones, carboxylic acids, esthers, amides, and nitriles

  • Topic 6

    Organic reactions can be divided into several groups. In generally speaking, the below classification is fair enough to pharmacy students for the first term organic chemistry class. We are aware that there is no limit to the number of possible organic reactions and mechanisms. However, certain general patterns are observed that can be used to describe many common or useful reactions. Each reaction has a stepwise reaction mechanism that explains how it happens, although this detailed description of steps is not always clear from a list of reactants alone. 

    This is just for a introductory explanations for the beginning level of organic reactions. Next term a more detailed organic reaction will be given more attention to the students awareness.

  • Topic 7

    There is no limit to the number of possible organic reactions and mechanisms. However, certain general patterns are observed that can be used to describe many common or useful reactions. Each reaction has a stepwise reaction mechanism that explains how it happens, although this detailed description of steps is not always clear from a list of reactants alone. Organic reactions can be organized into several basic types. Some reactions fit into more than one category. For example, some substitution reactions follow an addition-elimination pathway. This overview isn't intended to include every single organic reaction. Rather, it is intended to cover the basic reactions. 

    In this section, we will deal on acid-base reactions and the acidity properties of carboxylic acids.

  • Topic 8

    The vast majority of organic reactions can be classified as acid/base reactions. Most reactions proceed by paired an area of extra electron density or negative charge – the base, with an atom that is electron deficient or positively charged – the acid. These notes serve to review acid/base concepts and how they may apply to organic chemistry. We will first review the more traditional Brønsted-Lowry acids and bases, and then discuss the broader definition of Lewis acids and bases.

  • Topic 9

    How to name organic compounds using the IUPAC rules?

    In order to name organic compounds you must first memorize a few basic names. These names are listed within the discussion of naming alkanes. In general, the base part of the name reflects the number of carbons in what you have assigned to be the parent chain. The suffix of the name reflects the type(s) of functional group(s) present on (or within) the parent chain. Other groups which are attached to the parent chain are called substituents.

  • Topic 10

    Stereochemistry, a subdiscipline of chemistry, involves the study of the relative spatial arrangement of atoms that form the structure of molecules and their manipulation. An important branch of stereochemistry is the study of chiral molecules. Stereochemistry is also known as 3D chemistry because the prefix "stereo-" means "three-dimensionality".

  • Topic 11

    Stereochemistry is the study of the static and dynamic aspects of the three-dimensional shapes of molecules. It has long provided a foundation for understanding structure and reactivity. At the same time, stereochemistry constitutes an intrinsically interesting research field in its own right.Many chemists find this area of study fascinating due simply to the aesthetic beauty associated with chemical structures, and the intriguing ability to combine the fields of geometry, topology, and chemistry in the study of three-dimensional shapes.

  • Topic 12

    A Fischer projection or Fischer projection formula is a convention used to depict a stereoformula in two dimension without destroying the stereochemical information, i.e., absolute configuration, at chiral centers. Fischer Projections are abbreviated structural forms that allow one to convey valuable stereochemical information to a chemist (or biochemist) without them having to draw a more detailed 3D structural representation of the molecule. These representations are only used for molecules that contain chirality centers, where the chirality centers are represented as simple crosses.

  • Topic 13

    There is a strong relationship among drug molecules (ligands) and biological system components related to the molecular stereoisomerism. The chirality and drug action are very close to determine the most important mode of activity of drugs. Therefore, the conformation of both ligant and protein would be one of the driving forces in the biological activity. We, then, would be available to study on how to find out the crucial factors for new drug discovery systems.

  • Topic 14

    Every organic compound needs an unambiguous name that clearly delineates all structural features of the molecule. The same is true for stereocenters. Because a stereocenter can exist in only two absolute configurations, IUPAC nomenclature is easily modified to name stereocenters. To name a stereocenter, we assign priority to the groups attached to the stereocenter, and then apply a label based upon the direction in which priorities decrease. Therefore, on the basis of the importance of stereoisomerism in drug action, student of Faculty of Pharmacy should have more practicing studies on overall comparation of molecules to find out what would be crucial for drug activity related to their molecular structure.