Lecture 2 8/31/05

The Chemical Context of LifeAtoms, Bonding, Molecules

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Before we start…

http://www.uvm.edu/~dstratto/bcor011_handouts/

Questions from last time?

MatterMatterElementsElements CompoundsCompounds

Pure substancesPure substancesMade up of Made up of only Oneonly One

type of atomtype of atom

Bonded ElementsBonded ElementsMade up of two or moreMade up of two or more

Types of atoms bonded togetherTypes of atoms bonded togetherIn a fixed ratioIn a fixed ratio

NEW SUBSTANCE NEW SUBSTANCE Different PropertiesDifferent Properties

Sodium Chloride Sodium Chloride

+

Figure 2.2

ATOMS are the smallest unit of ATOMS are the smallest unit of matter that maintain the properties matter that maintain the properties

of an elementof an element

Why ATOMS bond together Why ATOMS bond together chemically chemically is because of their is because of their

subatomic structuresubatomic structure

Basis for Chemical BondingBasis for Chemical Bonding

Atomic StructureAtomic Structure

ProtonsProtons (+)(+)

Neutrons (o)Neutrons (o)

ElectronsElectrons(-)(-)

Atoms are electrically neutral !Atoms are electrically neutral !

nucleusnucleusAtomic number = protons Atomic number = protons

Atomic mass = Atomic mass = protons + neutronsprotons + neutrons

Electron numberElectron numberChemical Chemical propertiesproperties

Atoms differ by the Atoms differ by the numbernumber of protons and electronsof protons and electrons

Atomic“characteAtomic“character”r”

11 outer outer shell electronshell electron

44 outer outer shell electronsshell electrons

11 outer outer shell electronshell electron

7 7 outer outer shell electronsshell electrons

Electrons are arranged in SHELLS

Character determined by Character determined by Outer Shell ElectronsOuter Shell Electrons

• The periodic table of the elements– Shows the electron distribution for all the

elements

Secondshell

Helium

2He

Firstshell

Thirdshell

Hydrogen

1H

2He

4.00Atomic mass

Atomic number

Element symbol

Electron-shelldiagram

Lithium

3LiBeryllium

4BeBoron

3BCarbon

6CNitrogen

7NOxygen

8OFluorine

9FNeon

10Ne

Sodium

11NaMagnesium

12MgAluminum

13AlSilicon

14SiPhosphorus

15PSulfur

16SChlorine

17ClArgon

18Ar

Figure 2.8

BondingBonding: : achieve electronic stabilityachieve electronic stability

““full outer shells of electrons”full outer shells of electrons”

Ionic BondingIonic Bonding Covalent BondingCovalent Bonding

““TheftTheft””

““SharinSharing”g”

• Electronegativity– Is the attraction of a particular kind of

atom for the electrons in a covalent bond

• The more electronegative an atom– The more strongly it pulls shared

electrons toward itself

What determinesWhat determinesIonic or Covalent Bonding?Ionic or Covalent Bonding?

ElectronegativityElectronegativity

Ionic bondingIonic bonding

Atoms have very different Atoms have very different electronegativitieselectronegativities

Secondshell

Helium

2He

Firstshell

Thirdshell

Hydrogen

1H

2He

4.00Atomic mass

Atomic number

Element symbol

Electron-shelldiagram

Lithium

3LiBeryllium

4BeBoron

3BCarbon

6CNitrogen

7NOxygen

8OFluorine

9FNeon

10Ne

Sodium

11NaMagnesium

12MgAluminum

13AlSilicon

14SiPhosphorus

15PSulfur

16SChlorine

17ClArgon

18Ar

Figure 2.8

ElectronicallyElectronicallyStableStable

FullFullOuter Outer ShellsShellsNON-NON-

REACTIVEREACTIVE

StrongStrongElectro-Electro-

NegativeNegativeNearlyNearlyFull Full

Outer Outer shellsshells

WeakWeakElectro-Electro-

NegativityNegativityNearlyNearlyEmptyEmptyOuter Outer ShellsShells

Ionic Bonding:Ionic Bonding:““Theft & Abandonment”Theft & Abandonment”

Unfilled outer shellsUnfilled outer shells Electronically neutralElectronically neutral

Filled outer shellsFilled outer shells

CHARGED SPECIESCHARGED SPECIESNo longer atoms:No longer atoms:

IONSIONSAttraction between ionsAttraction between ions

is very strongis very strong

(Na(Na))

(Cl)(Cl) (Na(Na++)) (Cl(Cl--))

• An anion– Is negatively charged ions

• A cation– Is positively charged

Cl–

Chloride ion(an anion)

–

The lone valence electron of a sodiumatom is transferred to join the 7 valenceelectrons of a chlorine atom.

1 Each resulting ion has a completedvalence shell. An ionic bond can formbetween the oppositely charged ions.

2

Na NaCl Cl

+

NaSodium atom

(an unchargedatom)

ClChlorine atom(an uncharged

atom)

Na+

Sodium on(a cation)

Sodium chloride (NaCl)Figure 2.13

• An ionic bond– Is an attraction between anions and cations

Na+

Cl–

Figure 2.14

• Ionic compounds– Are often called salts, which may

form crystals

Secondshell

Helium

2He

Firstshell

Thirdshell

Hydrogen

1H

2He

4.00Atomic mass

Atomic number

Element symbol

Electron-shelldiagram

Lithium

3LiBeryllium

4BeBoron

3BCarbon

6CNitrogen

7NOxygen

8OFluorine

9FNeon

10Ne

Sodium

11NaMagnesium

12MgAluminum

13AlSilicon

14SiPhosphorus

15PSulfur

16SChlorine

17ClArgon

18Ar

Figure 2.8

IntermediateIntermediateElectro-Electro-

NegativityNegativity

Covalent Bonding: sharing betweenCovalent Bonding: sharing betweenatoms of similar electronegativity atoms of similar electronegativity

Covalent Bonding: Covalent Bonding: “Sharing”“Sharing”

• physical overlap physical overlap between atomsbetween atoms

• full outer shellsfull outer shells

• physically tied atphysically tied at the hipthe hip

• geometrical/spatialgeometrical/spatial orientation fixedorientation fixed

MOLECULESMOLECULES

HH HH

HH22

H-HH-H

Same electronegativitySame electronegativity

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

(c)

Methane (CH4). Four hydrogen atoms can satisfy the valence ofone carbonatom, formingmethane.

Water (H2O). Two hydrogenatoms and one oxygen atom arejoined by covalent bonds to produce a molecule of water.

(d)

HO

H

H H

H

H

C

Figure 2.11 C, D

Specific GeometrySpecific Geometry

• Each electron shell– Consists of a specific number of orbitals– Orbitals are defined areas of space that

electrons occupy within electron shells

Electron orbitals.Each orbital holds

up to two electrons.

1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals

(a) First shell (maximum 2 electrons)

(b) Second shell (maximum 8 electrons)

(c) Neon, with two filled shells (10 electrons)

Electron-shell diagrams.Each shell is shown withits maximum number of

electrons, grouped in pairs.

x

Z

Y

Figure 2.9

s orbital

ZThree p orbitals

X

Y

Four hybrid orbitals

(a) Hybridization of orbitals. The single s and three p orbitals of a valence shell involved in covalent bonding combine to form four teardrop-shaped hybrid orbitals. These orbitals extend to the four corners of an imaginary tetrahedron (outlined in pink).

Tetrahedron

Figure 2.16 (a)

• In a covalent bond– The s and p orbitals may hybridize, creating

specific molecular shapes

Space-fillingmodel

Hybrid-orbital model(with ball-and-stick

model superimposed)UnbondedElectron pair

104.5°

O

HWater (H2O)

Methane (CH4)

H

H H

H

C

O

H

H

H

C

Ball-and-stickmodel

H H

H

H

(b) Molecular shape models. Three models representing molecular shape are shown for two examples; water and methane. The positions of the hybrid orbital determine the shapes of the moleculesFigure 2.16 (b)

Products of Covalent bonding are called MOLECULES

COVALENT BONDING: Sharing

• A molecule– Consists of two or more atoms held together by

covalent bonds

• A single bond– Is the sharing of one pair of valence electrons

• A double bond– Is the sharing of two pairs of valence electrons

(a)

(b)

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

Hydrogen (H2). Two hydrogen atoms can form a single bond.

Oxygen (O2). Two oxygen atoms share two pairs of electrons to form a double bond.

H H

O O

Figure 2.11 A, B

• Single and double covalent bonds

Missing:Missing: 2 3 42 3 4 outer shell electronsouter shell electrons

alwaysalwaysmakes 2 makes 2 33 4 4 bondsbonds

waterwatercytosinecytosine

ValenceValenceElectronsElectrons

Molecular Shape and Function

• The precise shape of a molecule– Is usually very important to its

function in the living cell– Is determined by the positions of its

atoms’ valence orbitals

• Molecular shape– Determines how biological molecules

recognize and respond to one another with specificity

Morphine

Carbon

Hydrogen

Nitrogen

Sulfur

OxygenNaturalendorphin

(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds toreceptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.

(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.

Naturalendorphin

Endorphinreceptors

Morphine

Brain cell

Figure 2.17

• nonpolar covalent bond– The atoms have similar

electronegativities – Share the electron equally

Two Types of Covalent BondsTwo Types of Covalent Bonds

•polar covalent bond-The atoms have fairly different electronegativities- Share the electrons, but unequally

Figure 2.12

This results in a partial negative charge on theoxygen and apartial positivecharge onthe hydrogens.

H2O

–

O

H H+ +

Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.

• polar covalent bond– The atoms have differing electronegativities– Share the electrons unequally

Water

POLAR COVALENT BOND

the sharing of electrons in a bond is unequal

the molecule is LOPSIDED

NO NET CHARGEJUST ASYMMETRY

negative pole

positive pole

Asymmetry of Electrons within Waterhas some interesting Consequences

Individual Water Molecules have Considerable attraction for one another

Cohesion / Cohesive Properties

Water molecules act as little magnets

++

--

DipoleDipoleElectron withdrawingElectron withdrawing

Hydrogen BondsHydrogen Bonds

weak, dynamic,weak, dynamic,electrostatic interactionselectrostatic interactions* additive* additive

S NS NS N

+

+

+

+

+

+

+

+

• The polarity of water molecules– Allows them to form hydrogen bonds

with each other– Contributes to the various properties

water exhibits

Hydrogenbonds

+

+

H

H+

+

–

–

–

–

Figure 3.2

Properties of water due to PolarityProperties of water due to Polarity

1.1. Cohesion/surface tensionCohesion/surface tension2.2. Temperature moderationTemperature moderation

• High specific heatHigh specific heat• Evaporative coolingEvaporative cooling• Ice floatsIce floats

3.3. Solvent Ability Solvent Ability • Hydrophilicity and hydrophobicityHydrophilicity and hydrophobicity

4.4. Ionization ability (pH)Ionization ability (pH)

Summary Points of Lecture 2Summary Points of Lecture 2• Atomic StructureAtomic Structure• Atoms bond to achieve full outer electron Atoms bond to achieve full outer electron shellsshells• Ionic bonding “theft and abandonment”Ionic bonding “theft and abandonment”

- consequence: IONS, charged species- consequence: IONS, charged species- Consequence: strong attraction of ions- Consequence: strong attraction of ions

•Covalent Bonding “sharing”Covalent Bonding “sharing”- consequence: molecules- consequence: molecules- consequence: atoms physically tied at the hip - consequence: atoms physically tied at the hip

- consequence: precise 3-D spatial geometries- consequence: precise 3-D spatial geometries • POLAR Covalent MoleculesPOLAR Covalent Molecules

- Asymmetric charge distribution within - Asymmetric charge distribution within moleculemolecule

- “little magnets”- “little magnets”- water is most common example- water is most common example

Emergent properties of water contribute to Earth’s fitness for life

1. Cohesion 1. Cohesion - water molecules stick to one another- water molecules stick to one another

Water conducting cells

100 µmFigure 3.3

Figure 3.4

SurfaceSurfaceTensionTension

+

+

+

+

+

+

+

+

++

+

+

+

++

++

+

+

+

+

+

++

Gas = Steam

Liquid

Emergent properties of water contribute to Earth’s fitness for life

2. Temperature Moderation2. Temperature Moderation - water has a high specific heat - water has a high specific heat

(energy to raise 1g of substance 1(energy to raise 1g of substance 1ooC)C)- heat is absorbed when Hydrogen bonds breakheat is absorbed when Hydrogen bonds break- heat is released when Hydrogen bonds formheat is released when Hydrogen bonds form- keeps temperature of earth from fluctuating wildlykeeps temperature of earth from fluctuating wildly

- heat capacities in change of state (solid-liquid-gas)heat capacities in change of state (solid-liquid-gas)(heat of vaporization, heat of fusion)(heat of vaporization, heat of fusion)

+

+

+

+

+

+

+

+

++

+

+

+

++

++

+

+

+

+

+

++

Gas = Steam

Liquid

• Evaporative cooling– Is due to water’s high heat of

vaporization– Allows water to cool a surface

Some consequences Water hydrogen bondingSome consequences Water hydrogen bonding

• Solid Water – ICESolid Water – ICEIs less dense than Water – SO FLOATSIs less dense than Water – SO FLOATS- Insulates bodies of water- Insulates bodies of water

• The hydrogen bonds in ice– Are more “ordered” than in liquid

water, making ice less dense

Liquid water

Hydrogen bonds constantly break and re-form

Ice

Hydrogen bonds are stable

Hydrogen bond

Figure 3.5

The Solvent of Life

• Water is a versatile solvent due to its polarity

• It can form aqueous solutions

• The different regions of the polar water molecule can interact with ionic compounds called solutes and dissolve them

Negative

oxygen regions

of polar water molecules

are attracted to sodium

cations (Na+).

+

+

+

+Cl –

–

–

–

–

Na+Positive hydrogen regions

of water molecules cling to chloride anions

(Cl–).

++

+

+

–

–

–

–

–

–Na+

Cl–

Figure 3.6

• Water can also interact with polar molecules such as proteins

This oxygen is

attracted to a slight

positive charge on

the lysozyme

molecule.This oxygen is attracted to a slight

negative charge on the lysozyme

molecule.(a) Lysozyme molecule

in a nonaqueous

environment

(b) Lysozyme molecule (purple)

in an aqueous environment

such as tears or saliva

(c) Ionic and polar regions on the protein’s

Surface attract water molecules.

+

–

Figure 3.7