lesson 1 organic chemistry

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Lesson 1 BIO- ORGANIC CHEMISTRY INTRODUCTION OBJECTIVES: At the end of the lesson students are expected to: 1. Recognize the works of scientists in the development of organic chemistry as a science. 2. Understand the general importance of organic chemical compounds. 3. Explain some general differences between inorganic and organic compounds. 4. Determine the type of bonds present in organic compounds. 5. Identify the different functional groups present in organic compounds. 6. Differentiate isomers of organic compounds. ust-nursing

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Page 1: Lesson 1 Organic Chemistry

Lesson 1

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OBJECTIVES:At the end of the lesson students are expected to:

1. Recognize the works of scientists in the development of organic chemistry as a science.

2. Understand the general importance of organic chemical compounds.

3. Explain some general differences between inorganic and organic compounds.

4. Determine the type of bonds present in organic compounds.

5. Identify the different functional groups present in organic compounds.

6. Differentiate isomers of organic compounds.

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Page 2: Lesson 1 Organic Chemistry

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BEGINNINGS OF ORGANIC CHEMISTRY

The name organic chemistry came from the word organism.

Vitalism in the foundations of chemistry

In the history of chemistry, vitalism played a pivotal role, giving rise to the basic distinction between organic and inorganic

substances, following Aristotle's distinction between the mineral kingdom and the animal and vegetative kingdoms.

The basic premise of these vitalist notions was that organic materials differed from inorganic materials in possessing a

"vital force", accordingly, vitalist theory predicted that organic materials could not be synthesized from inorganic

components.

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ORGANIC CHEMISTRY is the study of the compounds of carbon.

The only distinguishing characteristic of organic compound is that all contain the element CARBON.

http://www.angelo.edu/faculty/kboudrea/index_2353/Notes_Chapter_01.pdf

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Why is carbon special?

http://www.webelements.com/webelements/elements/text/C/key.html

“The uniqueness of carbon among elements is that its atoms can bond to each other successively many times”.

DNA molecule- blue print of life

Polyethylene molecule, a plastic polymer

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Why is carbon special?

http://www.webelements.com/webelements/elements/text/C/key.html

As a group 4A element, carbon atoms can share four valence electrons and form four strong covalent bonds.

Molecular model of Aspirin (ASA), a pain reliever

Structure of tetrahedral bonded amorphous carbon.

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Why is carbon special?

http://www.webelements.com/webelements/elements/text/C/key.html

Carbon atoms can form very stable bonds to many other elements such as H, F, Cl, I, O, N, S and P.

With numerous ways of bonding and complexity, carbon atoms can form a multitude of different compounds. More than 16,000,000 are known compared to inorganic compounds

which are about 600,000.

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Why is carbon special?

http://www.webelements.com/webelements/elements/text/C/key.html

Complex organic compounds produce biologically functional molecules such as proteins, DNA, RNA, carbohydrates, enzymes, lipids and ATP.

These complex compounds are present in foods, medicine, fuels and industrial products.

This image depicts the HIV Viral capsid entering a T Cell and the HIV virus releasing its viral capsid into the host T-cells cytoplasm.

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Page 8: Lesson 1 Organic Chemistry

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Organic vs Inorganic Compounds

Can you classify the following as organic or inorganic?

a. NaOH b. CH3OH c. C6H6 d. Mg(NO3)2

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Page 10: Lesson 1 Organic Chemistry

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Atomic Structure

Nucleus (Protons + Neutrons)

Volume around nucleus occupied by orbiting electrons

A schematic view of an atom. The dense POSITIVELY charged nucleus contains most of the atom’s mass and is surrounded by NEGATIVELY charged electrons.

• Nucleus consists of protons (positively charged) and neutrons (electrically neutral).

•The nucleus contains essentially all the mass of the atom ~ 10-14 to 10-15.

•Electrons have negligible mass and orbit the nucleus at a distance ~ 10-10 m.

•The diameter of a typical atom is about 2 x 10-10 m or 200 picometer.

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Atomic Structure

Atomic Number Atomic Number (Z)(Z) gives the number of protons or electrons in an atom.

Mass Number Mass Number (A)(A) gives the number of protons plus neutrons in an atom.

All the atoms of a given element have the same atomic number--- 1 for H, 6 for C, 17 for Cl. The average mass in atomic mass units (amu) of many atoms of an element is called the element’s atomic weight --- 1.008 amu for H, 12.011 amu for C and so on..

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Electronic ConfigurationThe lowest-energy arrangement or ground-state electron ground-state electron configurationconfiguration of an atom is a description of the orbitals that the atom’s electrons occupy.

One can predict the arrangement of electrons in an atom by the following ways…

RULE 1

The orbitals of lowest energy are filled first, according to the order 1s 2s 2p 3s 3p 4s 3d… (as shown at the left figure)

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Electronic Configuration

RULE 2

Only two electrons can occupy an orbital, and they must be of opposite spin.

http://images.encarta.msn.com/xrefmedia/aencmed/targets/illus/ilt/1e67a7af.gif

http://www.physchem.co.za/Atomic/Electron%20Configuration.htm

RULE 3

If two or more empty orbitals of equal energy are available, one electron occupies each with the spins parallel until all orbitals are half-full.

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Atomic OrbitalsWHAT ARE ATOMIC ORBITALS AND WHAT ARE MOLECULAR ORBITALS?WHAT ARE ATOMIC ORBITALS AND WHAT ARE MOLECULAR ORBITALS?

The space occupied by electrons is described by the term orbital. If the electrons are associated with the atom of a free element, they are said to be atomic orbitals. Once bonds have been formed, the atomic elements become part of molecules, and the electronic positions are described by molecular orbitals.

WHAT IS AN S-ORBITAL?WHAT IS AN S-ORBITAL?

It is a spherically symmetrical orbital at a discreet distance from the nucleus. This corresponds to the first quantum level.

Illustration of an s-orbital.ust-nursing

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Atomic OrbitalsWHAT IS A P-ORBITAL?WHAT IS A P-ORBITAL?

Beginning in the second row, there is a second energy level fro elements. First, there is a 2s orbital, but there is also a 2p level composed of three identical p-orbital. A p-orbital is “dumbbell” shaped with electron density on the other side of the nucleus.

Illustration of p-orbitals.ust-nursing

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BONDING IN ORGANIC COMPOUNDS

A carbon atom does not form ions easily, since it has four valence electrons (1s2 2s2 2p2). It satisfies the octet rule in compounds by sharing electrons.

These are the orbitals that exist on atomic carbon (not connected to anything)

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BONDING IN ORGANIC COMPOUNDS

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•When carbon atoms form bonds with each other, the resulting bonds are described by hybrid orbitals, which are formed my mixing (hybridizing) the carbon’s atomic orbitals. (Linus Pauling, 1931)

•When carbon atoms bond to 4 other atoms, the 2s and all three 2p orbitals in the valence shell combine to produce four sp3 orbitals.

Hybridization: sp3 Orbitals

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BONDING IN ORGANIC COMPOUNDS

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•All four sp3 orbitals are at the same energy level, with one electron in each hybrid orbital.

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BONDING IN ORGANIC COMPOUNDS

•To minimize electron-electron repulsion, the spsp33 orbitals

are arranged in the shape of a tetrahedrontetrahedron around a

central carbon atom with bond angles of 109.5109.5oo.

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Hybridization: The Structure of METHANE

BONDING IN ORGANIC COMPOUNDS

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BONDING IN ORGANIC COMPOUNDS

Hybridization: sp2 Orbitals

When 2s orbital combines with two of the three available 2p orbitals, this results to the formation of an sp2 hybrid with one unhybridized orbital (leftover p orbital).

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BONDING IN ORGANIC COMPOUNDS

Hybridization: sp2 Orbitals

The spsp22 orbitals are arranged in a trigonal planartrigonal planar shape

around the central carbon atom, with bond angles of 120120oo.

The unhybridized p orbital is perpendicular to this plane.

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BONDING IN ORGANIC COMPOUNDS

Hybridization: Structure of Ethylene

When two sp2 hybridized carbons are next to each other, two kinds of overlap are formed:

-End-on-end overlap of the sp2 orbitals to make a-bond-bond (sigma bond)

-Side-to-side overlap of the unhybridized p orbitals to make a -bond-bond (pi bond).

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BONDING IN ORGANIC COMPOUNDS

Hybridization: Structure of EthyleneFree rotation is not possible along a pi-bond.

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BONDING IN ORGANIC COMPOUNDS

Hybridization: Structure of Ethylene

Bonding in ethylene – It assumes a planar configuration with a bond angle of 120O.

120o

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BONDING IN ORGANIC COMPOUNDS

Hybridization: Structure of Ethylene

The planar structure of ethylene

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BONDING IN ORGANIC COMPOUNDS

Hybridization: sp Orbitals

Instead of combining two or three 2p orbitals, the carbon 2s orbital hybridizes with only a single 2p orbital. Two sp hybrid orbitals result, and two p orbitals remain unchanged.

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BONDING IN ORGANIC COMPOUNDS

Hybridization: sp Orbitals

The two sp orbitals are linearlinear, or 180180oo apart on the x-axis and the remaining two p orbitals are perpendicular on the y-axis and the z-axis.

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Hybridization: sp Orbitals

Representation of the formation of an sp-hybrid carbon atom.

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BONDING IN ORGANIC COMPOUNDS

Hybridization: Structure of Acetylene

When two sp-hybridized carbon atoms approach each other, sp hybrid orbitals from each overlap head-on to form a strong sp-sp bond. The remaining two unhybridized p-orbitals overlap similarly thus forming two - bonds.

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The remaining two sp-hybrid orbitals forms a -bond with hydrogens to complete the structure of acetylene – a linear molecule.

BONDING IN ORGANIC COMPOUNDS

Hybridization: Structure of Acetylene

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COVALENT BONDINGDEFINE A COVALENT BOND

A covalent bond is usually composed of two electrons that are shared between two atoms.

This type of bond occurs when the atom cannot easily gain or lose electrons (there is very little electronegativity difference)

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COVALENT BONDINGWHAT IS VALENCE?

Valence is usually defined as the number of bonds an atom can form to satisfy the octet rule and remain electrically neutral. This is not to be confused with valence electrons, which are the number or electrons in the outermost shell.

WHAT IS POLARIZED COVALENT BOND?

When a bond is formed between two atoms that are not identical, the

electrons do not have to be equally shared. If one atom is more

electronegative, it will pull a greater share of electrons from the bond.

http://www.olysun.com/Chem_139/Bond.html

Which of the following are polar covalent bonds? For the polarized bond, identify the negative and the positive poles? ANSWERS

a) C-O b) C-C c) O-H d) C-N e) C-Li f) O-O

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DIPOLE-DIPOLE INTERACTIONSWHAT IS VAN DER WAAL’S ATTRACTION?

When there are no polarizing atoms in the molecules, the only attraction between molecules results from the electrons of one molecule being attracted to the positive nuclei of atoms in another molecule.

WHAT IS DIPOLE-DIPOLE INTERACTION?

This is an intermolecular electrostatic interaction.

http://stezlab1.unl.edu/reu1999/dputn226/ChemHelp/RET_Web_Pages/im_forces/Intmole_Forces.htm

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HYDROGEN BONDSWHY IS THE ATTRACTION BETWEEN TWO GROUPS BEARING AN O-H GROUP STRONGER THAN BETWEEN TWO GROUPS BEARING A C=O GROUP?

When hydrogen forms a polar covalent bond with heteroatoms, the hydrogen takes the + charge of the dipole. Since the classical Bronsted acid is H+, a polarized hydrogen in O-H can be considered somewhat acidic since it has positive character. The increased acidity and bond polarity leads to stronger interaction with a negative heteroatom when brought into close proximity to a positive polarized hydrogen. Resulting to a significantly stronger than normal dipole-dipole interaction known as HYDROGEN BOND.

Figure showing the formation of H-Bonds in water molecules.

www.sp.uconn.edu/~terry/images/mols/atomfig5.html