PharmaMatrixWorkshop2010 - University of Alberta

PharmaMatrix Workshop 2010 University of Alberta

July 12, 2010

Jonathan Y. Mane and Melissa Gajewski

Ma3er

Pure substance

Element Composed of atoms

Cannot be chemically decomposed

Compound Combina?on of >1 elements represented by chemical formula

Molecular/Covalent Electrons are shared between atoms (e.g. H2O)

Ionic Electrons not shared (e.g. NaCl)

Mixture

Homogeneous Uniform

throughout

Heterogeneous

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Elements, Compounds and the Periodic Table

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English name Symbol Non-‐English name English name Symbol Non-‐English name

An?mony Sb s?bium Potassium K kalium

Copper Cu cuprum Silver Ag argentum

Gold Au aurum Sodium Na natrium

Iron Fe ferrum Tin Sn stannum

Lead Pb plumbum Tungsten W wolfram

Mercury Hg hydragyrum

Element (Naming and interna?onal symbols)

First 1-‐2 dis?nguishing le3ers in the name

Not all names derived from English language

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The Periodic Table of Elements Alkali metals Alkaline earth metals

Halogens

Noble gases

d-‐transi?on metals

f-‐transi?on metals

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Elements and their common ions

caAons (lose e-‐) anions (gain e-‐)

hydride H-‐

fluoride F-‐

chloride Cl-‐

bromide Br-‐

oxide O2-‐

sulfide S2-‐

nitride N3-‐

Elemental anions

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Compound (= combina?on of >1 element represented by chemical formula)

Exercise •  Write the formula of the compound formed between

barium and bromine? •  Write the formula of the compound formed between

the ammonium ion and the carbonate ion? •  Break the formula Mg3(PO4)2 into its ions?

Chemical/molecular formula = specifies the number of atoms of each element in one unit/molecule of the substance

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ammonuim NH4+

nitrate NO3-‐

sulfate SO42-‐

carbonate CO32-‐

phosphate PO43-‐

cynanide CN-‐

hydroxide OH-‐

peroxide O22-‐

Common polyatomic ions

Molecular/covalent compound Electrons are shared between atoms (e.g. H2O)

Ionic compound Electrons are not shared but completely transferred (ca?on + anion : Na+ + Cl-‐ NaCl)

Covalent bonding

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Covalent bonding – sharing of electrons between atoms

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Core electrons = electrons other than the valence

= electrons in the outermost main energy level; involved in chemical reac?on

Covalent bonding – sharing of electrons between atoms

Lewis electron dot structure (G.N. Lewis, 1875-‐1946) – a symbolism that shows the number of valence electrons of atoms

Elements Metal ions (for ionic bonding)

Na+ Mg2+ Al3+

Anions

Bond and # of pairs of shared electrons Single bond = one ( 2 dots or single line)

Double bond = two ( 4 dots or 2 lines) Triple bond = three ( 6 dots or 3 lines)

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Examples

Covalent bonding – Lewis structure Rules for wriAng Lewis structures: 1.  Count the number of outermost electrons on each atom of the formula before bonding and obtain the

total number of electrons. 2.  Arrange the atoms by designa?ng a central atom and the rest surrounding it. (Hydrogen cannot be a

central atom; Oxygen never bond to another oxygen except in O2(g), ozone (O3), and peroxide (O22-‐).

3.  Distribute the electrons by placing 8 electrons (dots) around all atoms, one pair on each side (making only single bonds for now), except for any hydrogen (max. 2 dots).

4.  Step 1 #e-‐ = Step 3 #e-‐, celebrate your structure is CORRECT!. 5.  Step 1 #e-‐ ≠ Step 3 #e-‐, create double or triple bonds between the central atom and other atoms. 6.  If the central atom is phosphorus, or atoms of elements to the right and/or below phosphorus in PT, the

central atom may accommodate more than 8 electrons, if necessary, to make the counts in Steps 1 and 4 match.

O

H H C

Cl

Cl

ClCl

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Examples

water carbon tetrachloride nitrate

resonance structures

Covalent bonding – formal charge

The following must be saAsfied to get zero formal charge for these atoms

C = 4 bonds | N = 3 bonds | O = 2 bonds | Halogens = 1 bond

FC = group number – # e-‐ in lone pairs – 0.5( # e-‐ in bonding pairs)

O

H HC

Cl

Cl

ClCl

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How to calculate formal charge (FC):

Geometry of molecules

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Valence shell electron-‐pair repulsion theory A theory that helps in predic?ng geometric shapes of molecules based on the concept that the electron pairs, be it bonding or non-‐bonding pairs, will repel each other.

Prerequisite: Knowledge of drawing Lewis electron-‐dot structure

A = central atom X = number of sigma bonds between the

central atom and the other atom (mul?ple bond counts as one X)

E = number of lone electron pairs surrounding the central atom

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Exercise – Geometric shapes of molecules Draw the Lewis electron dot diagram and predict the shape of the following molecules using VSEPR theory:

Carbon dioxide CO2

Nitrite NO2-‐

Carbonate CO32-‐

Ammonia NH3

Phosphate PO43-‐

Sulfur tetrafluoride SF4

Xenon tetrafluoride XeF4

Iodine heptafluoride IF7

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Geometric shapes of molecules

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Atomic Orbitals

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Structure and QM model of the atom Essence of the QM model: •  Energies are quan?zed •  Electrons exist in principal energy levels, n (aka shells), in energy sublevels (aka subshells) within these principal levels, and in regions of space called orbitals within the sublevels •  Each orbital can hold a maximum of 2 e-‐

•  Electrons have a par?cular spin direc?on

Shell, n = 1, 2, 3, … Max number of e-‐ possible in level n = 2n2

n Max # of e-‐ # orbitals Orbital types

1 2 1 1s

2 8 4 1s, 3p

3 18 9 1s, 3p, 5d

4 32 16 1s, 3p, 5d, 7f

Number of orbitals in level n = n2 Subshell = s, p, d, f, g, etc.

Subshell Max # of e-‐

s 2

p 6

d 10

f 14

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Atomic orbitals and shapes

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Rela?onship between atomic orbitals and the periodic table

•  Period = main energy level •  Subshells s, p, d, f = block or group of elements

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Filling up orbitals and electronic configura?on Hund’s rule: All orbitals within a given sublevel must get one electron before any get two.

Electronic configuraFon

1s 2s 2px 2py 2pz

H 1s1

He 1s2

Li 1s22s1

Be 1s22s2

B 1s22s22p1

C 1s22s22p2

N 1s22s22p3

O 1s22s22p4

F 1s22s22p5

Ne 1s22s22p6

Na [Ne] 3s1

Paired e-‐

Unpaired e-‐

Core e-‐

Valence e-‐

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Filling up orbitals and electronic configura?on

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Molecular Orbital

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Molecular Orbitals

•  Regions of space in which shared electrons reside in covalent bonding •  Overlap of atomic orbitals (end-‐to-‐end and side-‐to-‐side) •  The number of molecular orbitals is EQUAL to the number of atomic orbitals

End-‐to-‐end overlap Side-‐to-‐side

σ-‐bond •  always present in any covalent bond •  one of the bonds in double or triple bond (formed from two p orbitals)

π-‐bond •  overlap between two p orbitals; •  always accompanied by a σ-‐bond •  only occur in double or triple bonds •  a double bond = 1 π-‐bond •  a triple bond = 2 π-‐bond

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Orbital hybridizaFon (the concept of mixing atomic orbitals to form new hybrid orbitals suitable for the qualita?ve descrip?on of atomic bonding proper?es)

sp3 hybridizaFon -‐  combinaAon of four orbitals (one s and three p-‐orbitals) forming a tetrahedral geometry

sp2 hybridizaFon -‐ one s and two p-‐orbitals from each C are used to construct a σ-‐bond network forming a trigonal geometry -‐  the remaining one p-‐orbital from each C are orthogonal to the σ-‐bond network

used to construct the π-‐bond network

Con?nuous π-‐cloud above and below the σ-‐bond plane

sp hybridizaFon -‐ one s and one p-‐orbital from each C are used to construct a σ-‐bond network forming linear geometry

Con?nuous π-‐cloud sur-‐rounding the σ-‐bond plane

H

H

H

H

H H

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Wri?ng chemical structure

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Examples using acyclic hydrocarbons

# of C Alkyl name Alkane

1 methyl methane

2 ethyl ethane

3 propyl propane

4 butyl butane

5 pentyl pentane

6 hexyl hexane

7 heptyl heptane

8 octyl octane

9 nonyl nonane

CH2H3C

CH3

Explicit C and H

Explicit C and H terminals H3C

CH3

Implicit C and H terminals

Alkenes (replace alkane suffix –ane with –ene)

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CH3CH2CH3

cis-‐2-‐butene trans-‐2-‐butene

propane

Examples using cyclic hydrocarbons

# of C Cycloalkane

3 cyclopropane

4 cyclobutane

5 cyclopentane

6 cyclohexane

… …

n n-‐cycloalkane

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Isomerism and Chirality

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Conforma?onal Isomerism

ConformaAonal isomers = molecules with the same structural formula and connec?vity but differs in their 3D structures due to rota?ons about one or more σ bonds. •  gauche, an?, and eclipse conformers of butane •  boat and chair conformers of cyclohexane

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Configura?onal Isomerism

cis-‐2-‐butene trans-‐2-‐butene

Cis-‐trans isomers = a form of stereoisomerism describing the orienta?on of groups (func?onal groups) within a molecule.

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E = entgegen means opposite(=trans) Z = means together zusammen (=cis)

3D Structures on paper and chirality

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C

Cl

BrH

F

C

Cl

BrH

F

Lines and wedges EnanAomers or opAcal isomers = mirror images of a molecule that cannot be superposed onto each other

R/S Configura?on •  An important nomenclature system for deno?ng enan?omers •  Labels a chiral center according to a system by which its subs?tuents are each assigned a priority based on atomic number •  R = priority decreases in clockwise direc?on •  S = priority decreases in counterclockwise (S)-‐alanine (R)-‐alanine

Chiral center = an atom that is bonded to four different atoms or groups of atoms in such a manner that it has a non-‐superimposable mirror image

Func?onal Groups

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Common Func?onal Groups (R, R’, R” = hydrocarbon radicals or H)

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R X

Alkyl halide

CH3CH2Br

bromoethane

R OH

CH3CH2OH

Alcohol

ethanol

R O R'

Ether

O CH3H3C

dimethyl ether Phenol

OH

Phenol

R C

O

H

Aldehyde

butanal

CH3CH2CH2 C H

O

C

O

R

R'

Ketone

H3C C CH3

O

propanone

R C

O

OH

Carboxylic acid

H3C C OH

O

propanoic acid

Ester

R C

O

O R'

H3C C O

O

CH3

methyl acetate


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1o Amine

R NH2

CH3NH2

methylamine

2o Amine

R N H

R'

3o Amine

R N R"

R'

Nitrile

acetonitrile

R C N

CH3C N

Nitro

R N

O

O

nitromethane

CH3NO2

1o Amide 2o Amide 3o Amide

R C

O

NH2

R C

O

NH

R'

R C

O

N

R'

R"

C

O

NH2

acetamide


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Sulfide

dimethyl sulfide

Sulfoxide Sulfone Thiol

methanethiol

R S R'

H3C S CH3

H3C S CH3

O

R S R'

O

dimethyl sulfoxide

R R'

O

O

S2+

H3C CH3

O

O

S2+

dimethyl sulfone

R S H

H3C S H

Introduc?on to chemical reac?on

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Reactant/s Product/s

Law of ConservaAon of Mass “in a chemical reac?on, mass can be neither created nor destroyed”

Balanced chemical equaAon

Δ 2H2(g) + O2(g) 2H2O(l)

elect 2H2O(l) 2H2() + O2()

Stoichiometric number, states, special symbols

3N2(g) + 5H2O(g) + 7CO(g) +7C(s) 2

Chemical Reac?on – Amino acids and pep?des

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PharmaMatrixWorkshop2010 - University of Alberta