Lesson 1 Organic Chemistry


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Lesson 1 Organic Chemistry

  1. 1. BIO-ORGANICCHEMISTRYLesson 1 OBJECTIVES: INTRODUCTION 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
  2. 2. BIO-ORGANICCHEMISTRY BEGINNINGS OF ORGANIC CHEMISTRYLesson 1 The name organic chemistry came from the word organism. INTRODUCTION 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 Aristotles 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. ust-nursing
  3. 3. BIO-ORGANICCHEMISTRY ORGANIC CHEMISTRY is the study of theLesson 1 compounds of carbon. INTRODUCTION 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 ust-nursing
  4. 4. BIO-ORGANICCHEMISTRYLesson 1 Why is carbon special? “The uniqueness of INTRODUCTION carbon among elements is that its atoms can bond to each other http://www.webelements.com/webelements/elements/text/C/key.html successively many times”. Polyethylene molecule, a plastic polymer DNA molecule- blue print of life ust-nursing
  5. 5. BIO-ORGANICCHEMISTRYLesson 1 Why is carbon special? As a group 4A element, INTRODUCTION carbon atoms can share four valence electrons and form four strong covalent bonds. http://www.webelements.com/webelements/elements/text/C/key.html Molecular model of Aspirin (ASA), a Structure of tetrahedral bonded pain reliever amorphous carbon. ust-nursing
  6. 6. BIO-ORGANICCHEMISTRYLesson 1 INTRODUCTION Why is carbon special? Carbon atoms can form very stable bonds to many other elements such as H, F, Cl, I, O, N, S and P. http://www.webelements.com/webelements/elements/text/C/key.html 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. ust-nursing
  7. 7. BIO-ORGANICCHEMISTRYLesson 1 Why is carbon special? Complex organic INTRODUCTION compounds produce biologically functional molecules such as proteins, DNA, RNA, carbohydrates, enzymes, http://www.webelements.com/webelements/elements/text/C/key.html lipids and ATP. This image depicts the HIV Viral capsid entering a T Cell and the HIV virus These complex releasing its viral capsid into the host T- cells cytoplasm. compounds are present in foods, medicine, fuels and industrial products. ust-nursing
  8. 8. BIO-ORGANICCHEMISTRYLesson 1 INTRODUCTION Organic vs Inorganic Compounds Can you classify the following as organic or inorganic? a. NaOH b. CH3OH c. C6H6 d. Mg(NO3)2 ust-nursing
  10. 10. BIO-ORGANICCHEMISTRY Atomic StructureLesson 1 A schematic view of an atom. The dense POSITIVELY charged nucleus contains most of the atom’s mass and is INTRODUCTION surrounded by NEGATIVELY charged electrons. Nucleus (Protons + Neutrons) Volume around nucleus occupied by orbiting 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. ust-nursing
  11. 11. BIO-ORGANICCHEMISTRYLesson 1 Atomic Structure All the atoms of a given element INTRODUCTION 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.. Atomic Number (Z) gives the number of protons or electrons in an atom. Mass Number (A) gives the number of protons plus neutrons in an atom. ust-nursing
  12. 12. BIO-ORGANICCHEMISTRYLesson 1 Electronic Configuration The lowest-energy arrangement or ground-state electron INTRODUCTION configuration 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) ust-nursing
  13. 13. BIO-ORGANICCHEMISTRY Electronic ConfigurationLesson 1 INTRODUCTION http://images.encarta.msn.com/xrefmedia/aencmed/targets/illus/ilt/1e67a7af.gif RULE 2 Only two electrons can occupy an orbital, and they must be of opposite spin. 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. ust-nursing http://www.physchem.co.za/Atomic/Electron%20Configuration.htm
  14. 14. BIO-ORGANICCHEMISTRY Atomic OrbitalsLesson 1 WHAT ARE ATOMIC ORBITALS AND WHAT ARE MOLECULAR ORBITALS? INTRODUCTION 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? 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
  15. 15. BIO-ORGANICCHEMISTRY Atomic OrbitalsLesson 1 WHAT IS A P-ORBITAL? INTRODUCTION 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. ust-nursing Illustration of p-orbitals.
  16. 16. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 A carbon atom does not form ions easily, since it has four INTRODUCTION 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) ust-nursing
  17. 17. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 Hybridization: sp3 Orbitals INTRODUCTION •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. ust-nursing
  18. 18. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 •All four sp3 orbitals are at the same energy level, with INTRODUCTION one electron in each hybrid orbital. ust-nursing
  19. 19. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 •To minimize electron-electron repulsion, the sp3 orbitals INTRODUCTION are arranged in the shape of a tetrahedron around a central carbon atom with bond angles of 109.5o. ust-nursing
  21. 21. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 Hybridization: sp2 Orbitals INTRODUCTION 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). ust-nursing
  22. 22. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 Hybridization: sp2 Orbitals INTRODUCTION The sp2 orbitals are arranged in a trigonal planar shape around the central carbon atom, with bond angles of 120o. The unhybridized p orbital is perpendicular to this plane. ust-nursing
  23. 23. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 Hybridization: Structure of Ethylene INTRODUCTION 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 σ -bond (sigma bond) -Side-to-side overlap of the unhybridized p orbitals to make a π -bond (pi bond). ust-nursing
  24. 24. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 Hybridization: Structure of Ethylene INTRODUCTION Free rotation is not possible along a pi-bond. ust-nursing
  25. 25. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 Hybridization: Structure of Ethylene INTRODUCTION 120o Bonding in ethylene – It assumes a planar configuration with a bond angle of 120O. ust-nursing
  26. 26. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 Hybridization: Structure of Ethylene INTRODUCTION The planar structure of ethylene ust-nursing
  27. 27. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 Hybridization: sp Orbitals INTRODUCTION 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. ust-nursing
  28. 28. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 Hybridization: sp Orbitals INTRODUCTION The two sp orbitals are linear, or 180o apart on the x-axis and the remaining two p orbitals are perpendicular on the y-axis and the z-axis. ust-nursing
  29. 29. BIO-ORGANICCHEMISTRY Hybridization: sp OrbitalsLesson 1 INTRODUCTION Representation of the formation of an sp-hybrid carbon atom. ust-nursing
  30. 30. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 Hybridization: Structure of Acetylene INTRODUCTION When two sp-hybridized carbon atoms approach each other, sp hybrid orbitals from each overlap head-on to form a strong sp-sp σ−bond. The remaining two unhybridized p-orbitals overlap similarly thus forming two π- bonds. ust-nursing
  31. 31. BIO-ORGANICCHEMISTRY BONDING IN ORGANIC COMPOUNDSLesson 1 Hybridization: Structure of Acetylene INTRODUCTION The remaining two sp-hybrid orbitals forms a σ-bond with hydrogens to complete the structure of acetylene – a linear molecule. ust-nursing
  32. 32. BIO-ORGANICCHEMISTRY COVALENT BONDINGLesson 1 DEFINE A COVALENT BOND INTRODUCTION 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) ust-nursing
  33. 33. BIO-ORGANICCHEMISTRY COVALENT BONDINGLesson 1 WHAT IS VALENCE? INTRODUCTION 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. 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 http://www.olysun.com/Chem_139/Bond.html ust-nursing
  34. 34. BIO-ORGANICCHEMISTRY DIPOLE-DIPOLE INTERACTIONSLesson 1 WHAT IS VAN DER WAAL’S ATTRACTION? When there are no polarizing atoms in the molecules, the INTRODUCTION 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. ust-nursing http://stezlab1.unl.edu/reu1999/dputn226/ChemHelp/RET_Web_Pages/im_forces/Intmole_Forces.htm
  35. 35. BIO-ORGANICCHEMISTRY HYDROGEN BONDSLesson 1 WHY IS THE ATTRACTION BETWEEN TWO GROUPS BEARING AN O-H GROUP STRONGER THAN BETWEEN INTRODUCTION TWO GROUPS BEARING A C=O GROUP? When hydrogen forms a polar covalent bond with heteroatoms, the hydrogen takes the δ+ 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. www.sp.uconn.edu/~terry/images/mols/atomfig5.html Figure showing the formation of H-Bonds in water molecules. ust-nursing