Chemistry 102 Deming

1. Chemistry 102Deming 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 • Biochemistry • Ch 18 amino acids, proteins • Ch 19 enzymes • Ch 22 carbohydrates • Ch 24 lipids (fats, oils, hormones) • Ch 26 DNA, RNA 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

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. group or family

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)

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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 Single Double 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. What is the difference between Organic and Inorganic Chemistry? Organic chemistry is the study of carbon containing compounds except elemental carbon (diamond, graphite, coal), CO2, CO, carbonates (CO32- group) and cyanides (CN- group) Inorganic chemistry studies all the rest of the elements.

17. What holds things together? • Plus (+) , Minus (-) Charge Attractions • 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 (–) attractionthe 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)

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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 polarIf 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) Strongest - Full “+” and “-” charges (on different atoms or 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) Lone pair of electrons Small “+” and small “-” on same molecule Weakest - really tiny “+” and tiny “-” on same molecule (or formed temporarily)

24. Intermolecular Forces(between molecules) Energy of Attraction Energy of Disruption • 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 High velocity Low MassHigh vibration High TEMPat same at same Force TEMPERATURE Low Temp Low VibrationLow Velocity High Mass

25. Intermolecular Forces (between molecules) Same force higher MW  higher mp, higher bp, lower vapor pressure Same approx. mass higher force  higher mp, higher bp, lower vapor pressure = Energy of Attraction (additive) Energy of Disruption Effect of Mass • London Dispersion Forces (LDF)Non polar molecule (all molecules) aromatic > -ynes > -enes > -anes (only C,H) • Dipolar net polar moleculeester > 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-bondingH-bonding + polar + partially ionizescarboxylic acid COOH • Ionicmust be an ionic compound (made of charges)starts with metal or ammonium Effect of Temp. High TEMP(higher velocity) Low Mass (MW) High Vibration High Velocity Given:Same temp. Same forceHigh Mass (MW) Low Vibration Low Velocity gas bp Increase Net Energy of Attraction liquid Increase Energy of Disruption mp solid Low TEMP(lower velocity)

27. Functional Groups • Just C’s and H’s • single bondsdouble bondstriple bondsaromatics • Six common functional groups (with O and N)

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

29. NO O or N’s Ch 12, 13 1 connections to O or N Ch 14, 15 Chapter Twelve

30. 2 connections to O Ch 16 3 connections to O (or N) Ch 18 Chapter Twelve