Lecture 2 8/31/05 The Chemical Context of Life Atoms, Bonding, Molecules Before we start Website to get LECTURE NOTES http://www.uvm.edu/~dstratto/bcor011_handouts/ Questions from last time? Elements Pure substances Made up of only One type of atom Matter Compounds Bonded Elements Made up of two or more Types of atoms bonded together In a fixed ratio NEW SUBSTANCE Different Properties ATOMS are the smallest unit of matter that maintain the properties of an element Why ATOMS bond together chemically is because of their subatomic structure Figure 2.2
Basis for Chemical Bonding Atomic Structure Atomic number = protons nucleus Protons () Neutrons (o) Atomic mass = protons neutrons nucleus Electrons (-) Electron number Chemical properties Atoms differ by the number of protons and electrons Atomic character Atoms are electrically neutral! Electrons are arranged in SELLS 1 outer electron 4 outer electrons Character determined by Outer Shell Electrons 1 outer electron 7 outer electrons
The periodic table of the elements Shows the electron distribution for all the elements Bonding: achieve electronic stability full outer s of electrons First ydrogen 2 1 e Atomic mass 4.00 Atomic number Element symbol Electron- diagram elium 2 e Ionic Bonding Covalent Bonding Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon 3 Li 4 Be 3 B 6 C 7 N 8 O 9 F 10 Ne Second igure 2.8 Third Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon 11 Na 12 Mg 13 Al 14 Si 15 P 16 S 17 Cl 18 Ar Theft Sharing What determines Ionic or Covalent Bonding? Electronegativity 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 Figure 2.8 Ionic bonding Atoms have very different electronegativities First Second Third ydrogen 2 1 e Atomic mass 4.00 Atomic number Element symbol Electron- diagram elium 2 e Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon 3 Li 4 Be 3 B 6 C 7 N 8 O 9 F 10 Ne Electronica Stable Full Strong Outer Electro- Shells Negative NON- Nearly REACTIV Full Outer Weak Electro- Negativity Nearly Empty Outer Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon 11 Na 12 Mg 13 14 Si 15 P 16 S Cl 17 Ar 18
Ionic Bonding: Theft Theft & Abandonment (Na) (Cl) (Na ) (Cl - ) An anion Is negatively charged ions A cation Is positively charged Unfilled outer s Filled outer s Electronically neutral CARGED SPECIES No longer atoms: IONS Attraction between ions is very strong An ionic bond Is an attraction between anions and cations 1 The lone valence electron of a sodium atom is transferred to join the 7 valence electrons of a chlorine atom. 2 Each resulting ion has a completed valence. An ionic bond can form between the oppositely charged ions. Ionic compounds Are often called salts, which may form crystals Na Cl Na Cl Na Sodium atom (an uncharged atom) Cl Chlorine atom (an uncharged atom) Na Sodium on (a cation) Sodium chloride (NaCl) Cl Chloride ion (an anion) Figure 2.14 Na Cl
igure 2.8 Covalent Bonding: sharing between atoms of similar electronegativity First Second Third ydrogen 2 1 e Atomic mass 4.00 Intermediate Atomic number Element symbol Electron- diagram elium 2 e Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon 3 Li 4 Be 3 B 6 C Electro- 7 N 8 O 9 F 10 Ne Negativity Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon 11 Na 12 Mg 13 Al 14 Si 15 P 16 S 17 Cl 18 Ar Covalent Bonding: Sharing Same electronegativity - 2 physical overlap between atoms full outer s physically tied at the hip geometrical/spatia orientation fixed MOLECULES Name (molecular formula) Electron diagram Structural formula Spacefilling model Each electron Consists of a specific number of orbitals Orbitals are defined areas of space that electrons occupy within electron s (c) Water ( 2 O). Two hydrogen atoms and one oxygen atom are joined by covalent bonds to produce a molecule of water. (d) Methane (C 4 ). Four hydrogen atoms can satisfy the valence of one carbon atom, forming methane. Figure 2.11 C, D O C Electron orbitals. Each orbital holds up to two electrons. Electron- diagrams. Each is shown with its maximum number of electrons, grouped in pairs. Figure 2.9 Z 1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals (a) First (maximum 2 electrons) x (b) Second (maximum 8 electrons) Y (c) Neon, with two filled s (10 electrons)
In a covalent bond The s and p orbitals may hybridize, creating specific molecular shapes Space-filling model Ball-and-stick model Unbonded Electron pair ybrid-orbital model (with ball-and-stick model superimposed) O O Z Three p orbitals Four hybrid orbitals Water ( 2 O) 104.5 s orbital X Y Tetrahedron (a) ybridization of orbitals. The single s and three p orbitals of a valence involved in covalent bonding combine to form four teardrop-shaped hybrid orbitals. These orbitals extend to the four corners of an imaginary tetrahedron igure 2.16 (a) (outlined in pink). Methane (C 4 ) (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 Figure 2.16 (b) shapes of the molecules C C 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 Products of Covalent bonding are called MOLECULES
Single and double covalent bonds Name (molecular formula) Electron diagram Structural formula Spacefilling model Missing: 2 3 4 Valence Electrons outer electrons (a) ydrogen ( 2 ). Two hydrogen atoms can form a single bond. (b) Oxygen (O 2 ). Two oxygen atoms share two pairs of electrons to form a double bond. O O always makes 2 3 4 bonds igure 2.11 A, B water cytosine 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 Figure 2.17 Natural endorphin Carbon ydrogen Morphine Nitrogen Sulfur Oxygen (a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match. Natural endorphin Morphine Brain cell Endorphin receptors (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.
Two Types of Covalent Bonds nonpolar covalent bond The atoms have similar electronegativities Share the electron equally polar covalent bond The atoms have differing electronegativities Share the electrons unequally Water Because oxygen (O) is more electronegative than hydrogen (), shared electrons are pulled more toward oxygen. δ polar covalent bond -The atoms have fairly different electronegativities - Share the electrons, but unequally Figure 2.12 O δ 2 O δ This results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens. POLAR COVALENT BOND the sharing of electrons in a bond is unequal negative pole Asymmetry of Electrons within Water has some interesting Consequences Individual Water Molecules have Considerable attraction for one another the molecule is LOPSIDED NO NET CARGE JUST ASYMMETRY Cohesion / Cohesive Properties Water molecules act as little magnets positive pole
- S N S N S N Electron withdrawing ydrogen Bonds weak, dynamic, electrostatic interactions * additive Dipole The polarity of water molecules Allows them to form hydrogen bonds with each other Contributes to the various properties water exhibits δ δ δ δ ydrogen bonds Properties of water due to Polarity 1. Cohesion/surface tension 2. Temperature moderation igh specific heat Evaporative cooling Ice floats 3. Solvent Ability ydrophilicity and hydrophobicity 4. Ionization ability (p) Figure 3.2
Summary Points of Lecture 2 Atomic Structure Atoms bond to achieve full outer electron s Ionic bonding theft and abandonment - consequence: IONS, charged species - Consequence: strong attraction of ions Covalent Bonding sharing - consequence: molecules - consequence: atoms physically tied at the hip - consequence: precise 3-D 3 D spatial geometries POLAR Covalent Molecules - Asymmetric charge distribution within molecule - little magnets - water is most common example 3 Emergent properties of water contribute to Earth s fitness for life 1. Cohesion - water molecules stick to one another Water conducting cells Figure 3.4 100 µm Surface Tension Liquid Gas = Steam Emergent properties of water contribute to Earth s fitness for life 2. Temperature Moderation - water has a high specific heat (energy to raise 1g of substance 1 o C) - heat is absorbed when ydrogen bonds break - heat is released when ydrogen bonds form - keeps temperature of earth from fluctuating wildly - heat capacities in change of state (solid-liquid liquid-gas) (heat of vaporization, heat of fusion)
Gas = Steam Some consequences Water hydrogen bonding Liquid Evaporative cooling Is due to water s high heat of vaporization Allows water to cool a surface Solid Water ICE Is less dense than Water SO FLOATS - Insulates bodies of water The hydrogen bonds in ice Are more ordered than in liquid water, making ice less dense The Solvent of Life Water is a versatile solvent due to its polarity It can form aqueous solutions Figure 3.5 ydrogen bond Ice ydrogen bonds are stable Liquid water ydrogen bonds constantly break and re-form
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 ). Positive hydrogen regions of water molecules cling to chloride anions (Cl ). Cl Na Na Cl Water can also interact with polar molecules such as proteins (a) Lysozyme molecule in a nonaqueous Figure 3.7 environment (b) Lysozyme molecule (purple) in an aqueous environment such as tears or saliva This oxygen is attracted to a slight δ positive charge on the lysozyme δ molecule. This oxygen is attracted to a slight negative charge on the lysozyme molecule. (c) Ionic and polar regions on the protein s Surface attract water molecules. Figure 3.6