matter elements compounds - uvm
TRANSCRIPT
Lecture 2 8/31/05
The Chemical Context of LifeAtoms, Bonding, Molecules Website to get LECTURE NOTES
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 of matter that maintain the properties of
an elementan element
Why ATOMS bond together Why ATOMS bond together chemically chemically is because of their subatomic is because of their subatomic
structurestructure
Basis for Chemical BondingBasis for Chemical BondingAtomic 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 numbernumberof protons and electronsof protons and electrons
Atomic“character”Atomic“character”
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
Helium2He
Firstshell
Thirdshell
Hydrogen1H
2He
4.00Atomic mass
Atomic number
Element symbolElectron-shelldiagram
Lithium3Li
Beryllium4Be
Boron3B
Carbon6C
Nitrogen7N
Oxygen8O
Fluorine9F
Neon10Ne
Sodium11Na
Magnesium12Mg
Aluminum13Al
Silicon14Si
Phosphorus15P
Sulfur16S
Chlorine17Cl
Argon18Ar
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
““Theft”Theft” ““SharingSharing””
• 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
Helium2He
Firstshell
Thirdshell
Hydrogen1H
2He
4.00Atomic mass
Atomic number
Element symbolElectron-shelldiagram
Lithium3Li
Beryllium4Be
Boron3B
Carbon6C
Nitrogen7N
Oxygen8O
Fluorine9F
Neon10Ne
Sodium11Na
Magnesium12Mg
Aluminum13Al
Silicon14Si
Phosphorus15P
Sulfur16S
Chlorine17Cl
Argon18Ar
Figure 2.8
ElectronicallyElectronicallyStableStable
FullFullOuter Outer ShellsShellsNONNON--
REACTIVEREACTIVE
StrongStrongElectroElectro--NegativeNegativeNearlyNearlyFull Full
Outer Outer shellsshells
WeakWeakElectroElectro--
NegativityNegativityNearlyNearlyEmptyEmptyOuter Outer ShellsShells
Ionic Bonding:Ionic Bonding:““Theft & Abandonment”Theft & Abandonment”
Unfilled outer shellsUnfilled outer shellsElectronically neutralElectronically neutral
Filled outer shellsFilled outer shellsCHARGED SPECIESCHARGED SPECIES
No longer atoms:No longer atoms:IONSIONS
Attraction between ionsAttraction between ionsis very strongis very strong
(Na)(Na) ((ClCl)) (Na(Na++)) ((ClCl--))
• 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 uncharged
atom)
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
Helium2He
Firstshell
Thirdshell
Hydrogen1H
2He
4.00Atomic mass
Atomic number
Element symbolElectron-shelldiagram
Lithium3Li
Beryllium4Be
Boron3B
Carbon6C
Nitrogen7N
Oxygen8O
Fluorine9F
Neon10Ne
Sodium11Na
Magnesium12Mg
Aluminum13Al
Silicon14Si
Phosphorus15P
Sulfur16S
Chlorine17Cl
Argon18Ar
Figure 2.8
IntermediateIntermediateElectroElectro--
NegativityNegativity
Covalent Bonding: sharing betweenCovalent Bonding: sharing betweenatoms of similar atoms of similar electronegativityelectronegativity
Covalent Bonding: Covalent Bonding: “Sharing”“Sharing”
•• physical overlap physical overlap between atomsbetween atoms
•• full outer shellsfull outer shells
•• physically tied atphysically tied atthe hipthe hip
•• geometrical/spatialgeometrical/spatialorientation fixedorientation fixed
MOLECULESMOLECULES
HH HH
HH22
HH--HH
Same Same electronegativityelectronegativity
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(maximum2 electrons)
(b) Second shell(maximum8 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 orbitalsof a valence shell involved in covalent bonding combine to form four teardrop-shaped hybrid orbitals. These orbitalsextend 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 shapesSpace-filling
modelHybrid-orbital model
(with ball-and-stickmodel 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 calledMOLECULES
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 4outer 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
δ–
O
H Hδ+ δ+
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 Bondsweak, 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+
+
δ –
δ –
δ –δ –
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 •• HydrophilicityHydrophilicity and and hydrophobicityhydrophobicity
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 shellsAtoms bond to achieve full outer electron shells•• Ionic bonding “theft and abandonment”Ionic bonding “theft and abandonment”
-- consequence: IONS, charged speciesconsequence: IONS, charged species-- Consequence: strong attraction of ionsConsequence: strong attraction of ions
••Covalent Bonding “sharing”Covalent Bonding “sharing”-- consequence: moleculesconsequence: molecules-- consequence: atoms physically tied at the hip consequence: atoms physically tied at the hip -- consequence: precise 3consequence: precise 3--D spatial geometriesD spatial geometries
•• POLAR Covalent MoleculesPOLAR Covalent Molecules-- Asymmetric charge distribution within moleculeAsymmetric charge distribution within molecule-- “little magnets”“little magnets”-- water is most common examplewater is most common example
Emergent properties of watercontribute to Earth’s fitness for life
1. Cohesion 1. Cohesion -- water molecules stick to one anotherwater molecules stick to one another
Water conducting cells
100 µm3
Figure 3.4
SurfaceSurfaceTensionTension
+
+
+
+
+
+
+
+
++
+
+
+
+++
+
+
++
++
++
Gas = Steam
Liquid
Emergent properties of watercontribute 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 (solidheat capacities in change of state (solid--liquidliquid--gas)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 Solid Water –– ICEICEIs less dense than Water Is less dense than Water –– SO FLOATSSO FLOATS-- Insulates bodies of waterInsulates 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
IceHydrogen 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 lysozymemolecule.
This oxygen is attracted to a slight negative charge on the lysozyme molecule.
(a) Lysozyme molecule in a nonaqueousenvironment
(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.
δ+
δ–
Figure 3.7