1. Chemistry 102 Deming Week 1 Monday 8-6-12

2. Chemistry 102 Organic and Biochemistry for the Allied Health Fields Dr Mark Deming

3. Introduction We are about try and cover an introduction to organic chemistry and biochemistry This is very ambitious. Both Organic and Biochemistry themselves are a year long course. Biochemistry is very complex and we are still discovering new aspects to it every day.

4. Chem 102 Overall Objectives Organic Chemistry I Ch 12 straight chains, rings Ch 13 double, triple bonds, aromatics Organic Chemistry II Ch 14 alcohols Ch 15 amines Ch 16 aldehydes, ketones Ch 17 acids, esters Biochemistry Ch 18 amino acids, proteins Ch 19 enzymes Ch 22 carbohydrates Ch 24 lipids (fats, oils, hormones) Ch 26 DNA, RNA

5. What is an Atom? An atom is made from –Protons- positively charged particles –Neutrons- neutral particles –Electrons- negatively charged particles The nucleus is in the center of the atom with the protons and neutrons and the electrons fly on the outside

6. What is an Element? An Element is an atom that has a specific number of protons For Example the element Carbon, C, has six protons in its nucleus. Any atom in the universe that has six protons in its nucleus is called carbon. The number of protons defines the element

7. Elements (cont.) There are about 112 known elements, many not natural on this world (because when formed they only last a short time, but they are formed in exploding stars momentarily) Biologically we are concerned with only a few of these elements and in the class we will even have a shorter list. We will skip the math stuff concerning elements and chemical relationships (we skip ch 1-9) and to understand organic chemistry at a basic level we can skip those sections.

8. 123456789101112131415161718 IAIIAIIIAIVAVAVIAVIIAVIIIA 1IIIBIVBVBVIBVIIBVIIIIBIIB 2 1H He 1.008 4.003 345678910 2 LiBeBCNOFNe 6.9419.01210.8112.0114.0116.0019.0020.18 1112 131415161718 3 NaMg AlSiPSClAr 22.9924.31 26.9828.0930.9732.0735.4539.95 192021222324252627282930313233343536 4KCaScTiVCrMnFeCoNiCuZnGaGeAsSeBrKr 39.1040.0844.9647.8850.9452.0054.9455.8558.9358.6963.5565.3969.7272.6174.9278.9679.9083.80 373839404142434445464748495051525354 5RbSrYZrNbMoTcRuRhPdAgCdInSnSbTeIXe 85.4787.6288.9191.2292.9195.94(99)101.1102.9106.4107.9112.4114.8118.7121.8127.6126.9131.3 555657†727374757677787980818283848586 6CsBaLaHfTaWReOsIrPtAuHgTlPbBiPoAtRn 132.9137.3138.9178.5180.9183.9186.2190.2192.2195.1197.0200.6204.4207.2209.0(209)(210)(222) 878889‡104105106107108109110111112113114115116117118 7FrRaAcRfDbSgBhHsMt Ds UuuUubUuqUuh Uuo (223)(226)(227)(261)(262)(263)(264)(265)(268)(269)(272)(277) (285) (289)? ?? 5859606162636465666768697071 † Lanthanide 6CePrNdPmSmEuGdTbDyHoErTmYbLu Series140.1140.9144.2(145)150.4152.0157.3158.9162.5164.9167.3168.9173.0175.0 90919293949596979899100101102103 ‡ Actinide7ThPaUNpPuAmCmBkCfEsFmMdNoLr Series232.0231.0238.0(237)(244)(243)(247) (251)(252)(257)(258)(259)(262)

9. Elements Element Symbols start with a capital letter and the second letter, if present, is always in lower case Example O is oxygen Br is Bromine

10. Which Elements do we need to know? There are about 114 Elements that we know about but we will be concerned with only a few C, H, O, N P, S F, Cl, Br, I (halogens, they are in the column called the halogen group) Na, K, Ca, Fe (metals, they are charged)

11. 123456789101112131415161718 IAIIAIIIAIVAVAVIAVIIAVIIIA 1IIIBIVBVBVIBVIIBVIIIIBIIB 2 1H He 1.008 4.003 345678910 2 LiBeBCNOFNe 6.9419.01210.8112.0114.0116.0019.0020.18 1112 131415161718 3 NaMg AlSiPSClAr 22.9924.31 26.9828.0930.9732.0735.4539.95 192021222324252627282930313233343536 4KCaScTiVCrMnFeCoNiCuZnGaGeAsSeBrKr 39.1040.0844.9647.8850.9452.0054.9455.8558.9358.6963.5565.3969.7272.6174.9278.9679.9083.80 373839404142434445464748495051525354 5RbSrYZrNbMoTcRuRhPdAgCdInSnSbTeIXe 85.4787.6288.9191.2292.9195.94(99)101.1102.9106.4107.9112.4114.8118.7121.8127.6126.9131.3 555657†727374757677787980818283848586 6CsBaLaHfTaWReOsIrPtAuHgTlPbBiPoAtRn 132.9137.3138.9178.5180.9183.9186.2190.2192.2195.1197.0200.6204.4207.2209.0(209)(210)(222) 878889‡104105106107108109110111112113114115116117118 7FrRaAcRfDbSgBhHsMt Ds UuuUubUuqUuh Uuo (223)(226)(227)(261)(262)(263)(264)(265)(268)(269)(272)(277) (285) (289)? ?? 5859606162636465666768697071 † Lanthanide 6CePrNdPmSmEuGdTbDyHoErTmYbLu Series140.1140.9144.2(145)150.4152.0157.3158.9162.5164.9167.3168.9173.0175.0 90919293949596979899100101102103 ‡ Actinide7ThPaUNpPuAmCmBkCfEsFmMdNoLr Series232.0231.0238.0(237)(244)(243)(247) (251)(252)(257)(258)(259)(262)

12. Carbon is Unique Organic Chemistry is the chemistry of the compounds (things made by combining more than one type of element) made from carbon Carbon can combine in so many ways that there over 6 million organic compounds It can make long strings of connections and branches We don’t have time to go through all the uniqueness of carbon

13. Quick Facts about bonding We are only concerned about outer electrons, which either bond or don’t bond A bond is a shared pair of electrons between elements A lone pair is a pair of electrons that do not bond With few exceptions all electrons will be paired with the non transistion metal elements Unpaired electrons on an C, N, O are called free radicals and are never good for us ( they want to be paired so they may steal an electron from somewhere else)

14. Quick Facts about bonding Carbon has four bonds (connections shown as lines) Oxygen has two bonds Nitrogen has three bonds if neutral and four bonds if charged plus (+) Hydrogen has one bond Halogens (F, Cl, Br, I) have one bond SingleDouble Triple

15. Organic (Ch 12-17) For each chapter: How to Name (the molecules of that functional group) What are the Properties (solubility, melting and boiling point) What are the Reactions Some Special Features or Applications

16. –Organic chemistry is the study of carbon containing compounds except elemental carbon (diamond, graphite, coal), CO 2, CO, carbonates (CO 3 2- group) and cyanides (CN - group) –Inorganic chemistry studies all the rest of the elements. What is the difference between Organic and Inorganic Chemistry?

17. What holds things together? 1.Plus (+), Minus (  ) Charge Attractions 2.Sharing of electrons (as pairs) called bonds Molecules are held together internally only by bonds (sharing of electrons)

18. What Holds Molecules Together Internally? (Inside molecules) Atoms in a molecule are only held by bonds (shared electrons, we will show these as lines) Each bond will contain 2 electrons (shared pair) There can be single, double, triple bonds between atoms Atoms can also have pairs of electrons attached that do not bond (lone pairs). For this class any element besides carbon probably will have lone pairs

19. What Holds Molecules Together? Attractive Forces called: InterMolecular Forces (IMF) (between molecules) Molecules are held externally together by one of two things: charges and bonds Charges – plus (+) to minus (–) attraction the larger the charges the greater the attraction Bonds – shared electrons

20. What is Polar (part 1)? Atoms share only the outer layer (shell) of electrons (called valence electrons) Even though atoms share they do not necessarily share equally Electronegativity (EN) is a measure of the attraction for electrons in a bond Low (C, H), I, Br, Cl, N, O High ( F?) A difference in EN results in a slight charge separation between the two atoms The bigger the difference in EN results in a larger charge separation between the two atoms (but the charge separation is never full charges only part)

21. 123456789101112131415161718 IAIIAIIIAIVAVAVIAVIIAVIIIA 1IIIBIVBVBVIBVIIBVIIIIBIIB 2 1H H He 1.008 4.003 345678910 2 LiBeBCNOFNe 6.9419.01210.8112.0114.0116.0019.0020.18 1112 131415161718 3 NaMg AlSiPSClAr 22.9924.31 26.9828.0930.9732.0735.4539.95 192021222324252627282930313233343536 4KCaScTiVCrMnFeCoNiCuZnGaGeAsSeBrKr 39.1040.0844.9647.8850.9452.0054.9455.8558.9358.6963.5565.3969.7272.6174.9278.9679.9083.80 373839404142434445464748495051525354 5RbSrYZrNbMoTcRuRhPdAgCdInSnSbTeIXe 85.4787.6288.9191.2292.9195.94(99)101.1102.9106.4107.9112.4114.8118.7121.8127.6126.9131.3 555657†727374757677787980818283848586 6CsBaLaHfTaWReOsIrPtAuHgTlPbBiPoAtRn 132.9137.3138.9178.5180.9183.9186.2190.2192.2195.1197.0200.6204.4207.2209.0(209)(210)(222) 878889‡104105106107108109110111112113114115116117118 7FrRaAcRfDbSgBhHsMt Ds UuuUubUuqUuh Uuo (223)(226)(227)(261)(262)(263)(264)(265)(268)(269)(272)(277) (285) (289)? ?? 5859606162636465666768697071 † Lanthanide 6CePrNdPmSmEuGdTbDyHoErTmYbLu Series140.1140.9144.2(145)150.4152.0157.3158.9162.5164.9167.3168.9173.0175.0 90919293949596979899100101102103 ‡ Actinide7ThPaUNpPuAmCmBkCfEsFmMdNoLr Series232.0231.0238.0(237)(244)(243)(247) (251)(252)(257)(258)(259)(262)

22. What is Polar (part 2)? A polar bond is a bond that has a permanent charge separation due to electronegativity differences Molecules can be made of many atoms connected together by bonds A polar molecule is a molecule that has a part of it that polar bonds (it is a little more complex that this and polar bonds can cancel but we will not see these in our class) General rule: C,H is non polar C-N is polar C-O is very polar If you see a N or O the molecule is polar We will talk about molecules having non-polar parts (C,H only) (hydrophobic) and polar parts (N and O) (hydrophilic)

23. InterMolecular Forces (IMF) (between molecules) Ionic H-bonding N-H, O-H, to lone pair on N, O Dipolar (net polar molecule- contains O or N) Dispersion (London Dispersion Forces, LDF) Non polar molecule (only C’s and H’s) Small “+” and small “  ” on same molecule Strongest - Full “+” and “  ” charges (on different atoms or molecules) Weakest - really tiny “+” and tiny “  ” on same molecule (or formed temporarily) Lone pair of electrons

24. Intermolecular Forces (between molecules) Ionic (made of charges) H-bonding from a N-H, O-H to a lone pair on N or O Dipolar (net polar molecule) Dispersion (London Dispersion Forces, LDF) Non polar molecule Energy of AttractionEnergy of Disruption High velocity Low Mass High vibration High TEMP at same at same Force TEMPERATURE Low Temp Low Vibration Low Velocity High Mass

25. Intermolecular Forces (between molecules) London Dispersion Forces (LDF) Non polar molecule (all molecules) aromatic > -ynes > -enes > -anes (only C,H) Dipolar net polar molecule ester > amide (no H) > aldehyde > ketone > ether H-bonding from a O-H > N-H to a lone pair on O: > N: Amide (with H) > alcohol (OH) > amine (NH) Super H-bonding H-bonding + polar + partially ionizes carboxylic acid COOH Ionic must be an ionic compound (made of charges) starts with metal or ammonium = Energy of Attraction (additive) Energy of Disruption Low Mass (MW) High Vibration High Velocity Given: Same temp. Same force High Mass (MW) Low Vibration Low Velocity High TEMP (higher velocity) Low TEMP (lower velocity) Same force  higher MW  higher mp, higher bp, lower vapor pressure Same approx. mass  higher force  higher mp, higher bp, lower vapor pressure mp bp solid liquid gas Effect of Temp. Effect of Mass

27. Functional Groups Just C’s and H’s single bonds double bonds triple bonds aromatics Six common functional groups (with O and N)

28. Ch 15 Functional Groups alkane ketone also AROMATIC ! alkyne alcohol ether amine carboxylic acid ester amide aldehyde Ch 12 Ch 13 Ch 14 Ch 16 Ch 18 alkene straight, branched, ring Nomenclature (memorize) Reactions (memorize) Physical Properties VP, BP, MP  IMF, MW Ch 18

29. Copyright © 2010 Pearson Education, Inc. Chapter Twelve29 1 connections to O or N NO O or N’s Ch 12, 13 Ch 14, 15

30. Copyright © 2010 Pearson Education, Inc. Chapter Twelve30 2 connections to O 3 connections to O (or N) Ch 16 Ch 18