Chemistry 102 Deming Week 1 Monday 8-6-12. Chemistry 102 Organic and Biochemistry for the Allied Health Fields Dr Mark Deming

Chemistry 102Deming

• Week 1

• Monday 8-6-12

Chemistry 102

• Organic and Biochemistry for the Allied Health Fields

• Dr Mark Deming

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.

Chem 102 Overall ObjectivesOrganic 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

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

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

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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18IA IIA IIIA IVA VA VIA VIIA VIIIA

1 IIIB IVB VB VIB VIIB VIII IB IIB 21 H He 1.008 4.003

3 4 5 6 7 8 9 102 Li Be B C N O F Ne 6.941 9.012 10.81 12.01 14.01 16.00 19.00 20.18

11 12 13 14 15 16 17 18 3 Na Mg Al Si P S Cl Ar

22.99 24.31 26.98 28.09 30.97 32.07 35.45 39.95 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 364 K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr 39.10 40.08 44.96 47.88 50.94 52.00 54.94 55.85 58.93 58.69 63.55 65.39 69.72 72.61 74.92 78.96 79.90 83.80 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 545 Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe 85.47 87.62 88.91 91.22 92.91 95.94 (99) 101.1 102.9 106.4 107.9 112.4 114.8 118.7 121.8 127.6 126.9 131.3 55 56 57† 72 73 74 75 76 77 78 79 80 81 82 83 84 85 866 Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn 132.9 137.3 138.9 178.5 180.9 183.9 186.2 190.2 192.2 195.1 197.0 200.6 204.4 207.2 209.0 (209) (210) (222) 87 88 89‡ 104 105 106 107 108 109 110 111 112 113 114 115 116 117 1187 Fr Ra Ac Rf Db Sg Bh Hs Mt Ds Uuu Uub Uuq Uuh Uuo (223) (226) (227) (261) (262) (263) (264) (265) (268) (269) (272) (277) (285) (289)? ??

58 59 60 61 62 63 64 65 66 67 68 69 70 71† Lanthanide 6 Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu

Series 140.1 140.9 144.2 (145) 150.4 152.0 157.3 158.9 162.5 164.9 167.3 168.9 173.0 175.0

90 91 92 93 94 95 96 97 98 99 100 101 102 103

‡ Actinide 7 Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No LrSeries 232.0 231.0 238.0 (237) (244) (243) (247) (247) (251) (252) (257) (258) (259) (262)

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

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)


1 IIIB IVB VB VIB VIIB VIII IB IIB 21 H He 1.008 4.003

3 4 5 6 7 8 9 102 Li Be B C N O F Ne 6.941 9.012 10.81 12.01 14.01 16.00 19.00 20.18

11 12 13 14 15 16 17 18 3 Na Mg Al Si P S Cl Ar



Series 140.1 140.9 144.2 (145) 150.4 152.0 157.3 158.9 162.5 164.9 167.3 168.9 173.0 175.0

90 91 92 93 94 95 96 97 98 99 100 101 102 103


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

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)

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

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

– Organic chemistry is the study of carbon containing compounds

•except elemental carbon (diamond, graphite, coal), CO2, CO, carbonates (CO3

2- group) and cyanides (CN- group)

– Inorganic chemistry studies all the rest of the elements.

What is the difference between Organic and Inorganic Chemistry?

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)

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

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

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)


1 IIIB IVB VB VIB VIIB VIII IB IIB 21 H H He 1.008 4.003

3 4 5 6 7 8 9 102 Li Be B C N O F Ne 6.941 9.012 10.81 12.01 14.01 16.00 19.00 20.18

11 12 13 14 15 16 17 18 3 Na Mg Al Si P S Cl Ar



Series 140.1 140.9 144.2 (145) 150.4 152.0 157.3 158.9 162.5 164.9 167.3 168.9 173.0 175.0

90 91 92 93 94 95 96 97 98 99 100 101 102 103


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)

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

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 Attraction Energy of Disruption

High velocity Low MassHigh vibration

High TEMP

at same at same Force TEMPERATURE

Low Temp Low VibrationLow Velocity High Mass

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-bondingH-bonding + polar + partially ionizescarboxylic acid COOH

• Ionicmust 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

Functional Groups• Just C’s and H’s single bonds double bonds triple bonds aromatics

• Six common functional groups (with O and N)

-OH

-NH2

-C-H

-C-

CH3CH2OH

CH3CH2NH2

CH3CHO

CH3CCH3

O

CH3COHO

-C-OH

Example

Alcohol

Amine

Aldehyde

Ketone

Carboxylic acid

Ethanol

Ethanamine

Ethanal

Acetone

Acetic acid

NameFamilyFunctionalgroup

CH3COCH2CH3

O-C-ORCarboxylic ester Ethyl acetate

O

O

O

O

Ch 15

Functional Groups

C C

O

H

alkane

ketoneC C

O

C

C C

O

O H

C C

O

O C

C C

C CC C

C O H

C O C

C C

O

N

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

C N

Copyright © 2010 Pearson Education, Inc.

Chapter Twelve 29

1 connections to O or N

NO O or N’s

Ch 12, 13

Ch 14, 15

Copyright © 2010 Pearson Education, Inc.

Chapter Twelve 30

2 connections to O

3 connections to O (or N)

Ch 16

Ch 18

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Chemistry 102 Deming Week 1 Monday 8-6-12. Chemistry 102 Organic and Biochemistry for the Allied Health Fields Dr Mark Deming