ORGANIC CHEMISTRY. Meaning of Organic?

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1 ORGANIC CHEMISTRY Meaning of Organic? Initially scientists believed there was a special force in living organisms -this was assumed the unique component of organic material In 1828 Wöhler synthesized urea (a known component of organic material) from inorganic ammonium cyanate

2 Later Justus von Liebig, a noted 19 th century chemist, declared the synthesis of urea the very first beginning of the actual scientific organic chemistry In a subsequent paper Wöhler and Liebig wrote: sugar, salicin, and morphium will be produced artificially. Of course, we do not know the way yet by which the end result may be reached since the prerequisite links are unknown to us from which these materials will be develop - however, we will get to know them.

3 Organic chemistry is now considered the chemistry of carbon **Not only carbon! There are few forms of only pure carbon (no other elements present) Some examples of compounds with only carbon present: graphite diamond C 60 spherical ball carbon nanotube

4 Carbon can form strong bonds with not only carbon but with other elements (e.g. hydrogen, nitrogen, oxygen, halogens) Depending upon the order of the bond connections (both constitution and configuration) millions of compounds, all with potentially different properties, can be prepared Why is this so important? Almost every component of living organisms involve organic chemistry (proteins, enzymes, lipids, fats, carbohydrates, nucleic acids, etc.) And the metabolic and other interactions in the body involve organic reactions

5 Understanding Organic Chemistry is Learning about Bonding and the location of Electrons Consider a molecule called acetone O H O H H O H H H H H H H H H Shorthand drawing All atoms indicated 3-dimensional drawing wedge and dash lines have meaning Electron density plot

6 By understanding, and predicting, the properties and orientation of bonds Organic reactions can be predicted without memorization Compare these compounds:

7 Why does carbon form such a variety of bonds? Realize position in the periodic table

8 Organic Chemistry focuses on the second row of the periodic table Carbon is in the exact middle of the second row This position allows carbon to form various bonds **more specifically it allows carbon to share electrons easily to form bonds Organic chemistry is fundamentally about what electrons do, and how they behave

9 In Organic Chemistry we study how compounds react During a reaction old bonds are broken and new bonds form Bonds form two atoms share electrons Bonds break two atoms no longer share electrons Therefore, if we know more about the electrons we can understand organic chemistry What do we want to know? Where are the electrons? How tightly are the electrons held in a bond? We already know many of these basic concepts from general chemsitry

10 Background of an atom An atom consists of three types of particles: Proton (positively charged) Neutron (neutral) Electron (negatively charged) The number of protons determines the element (also is the atomic number) Carbon therefore has 6 protons located in the nucleus Usually the nucleus also contains an identical number of neutrons as protons If the number is different it is called an isotope These two particles have similar mass (~1830 times greater than an electron)

11 Consider a Carbon Atom Nucleus means kernel of a nut Nucleus size is ~2 fm (1 fm = m), atom size is ~1 Å (1 Å = m) For an uncharged 12 C atom, there are 6 protons, 6 neutrons and 6 electrons Therefore the nucleus, which is responsible for ~3600/1 parts of the mass, only encompasses ~1 x part of the volume (remember V = 4/3 πr 3 )

12 Electrons Unlike the protons and neutrons which are in the nucleus (a relatively fixed point) we cannot say with certainty where an electron is located at a certain time (Heisenberg uncertainty principle) What we can say is that on time average the electrons are located in orbitals (regions of space) *much bigger region than the nucleus As the number of electrons increase they reside in concentric shells where each shell contains subshells known as atomic orbitals of different properties and shapes shell atomic orbital 1 s 2 s,p 3 s,p,d 4 s,p,d,f

13 The different types of atomic orbitals have a characteristic number of orbitals s 1 p 3 d 5 f 7 Organic chemistry is primarily concerned with only the first two shells (therefore only the s and p atomic orbitals) Also due to only two spin states for an electron Only two electrons can be placed in each orbital (Pauli exclusion principle) Orbitals are filled by electrons starting in the lowest energy orbital Carbon can therefore only have a maximum of 8 electrons in its outer (2 nd ) shell 4 atomic orbitals (1s and 3p) with 2 electrons per orbital

14 Electronic Configuration for Carbon through Fluorine When filling degenerate orbitals electrons will go into different orbitals before pairing in the same orbital (Hund s rule)

15 Bonding Octet rule atom is most stable if its outer shell of electrons is filled Called octet rule since second row atoms (which comprise organic compounds) have 8 electrons in their outer shell Therefore an atom will give up, accept, or share electrons in order to achieve a filled outer shell Often the inner shell of electrons is ignored (not counted for the octet rule) Outer shell of electrons is also referred to as valence electrons

16 Type of Bonds If atoms give up or accept electrons an ion is formed Consider lithium (3 total electrons) There is only one valence electron

17 Lithium will therefore easily lose an electron to create a lithium ion (which has a filled outer shell) The energy required to remove an electron is referred to as the ionization energy Since lithium readily loses an electron to leave an atom with a complete outer shell it is called electropositive

18 Halogens, on the other hand, readily gain an electron to complete the outer shell Consider fluorine (9 electrons, 7 valence electrons) The outer shell needs one electron to be filled

19 In a covalent bond, however, electrons are shared between two atoms (not lose or accept as in the formation of ions) The sharing of electrons can allow both atoms to fill the outer shell Consider F 2 (fluorine gas) Each fluorine atom needs one electron to fill the outer shell One atom cannot donate an electron and have both atoms with a filled outer shell

20 An alternative is to share two electrons (one from each atom) between both atoms Represent each electron with a dot (called Lewis dot structures) (only show valence electrons for a Lewis dot structure) Both atoms now have 8 electrons in the outer shell (therefore octet rule is obeyed)

fluorine Each outer shell is filled, but no electron density

21 Differences between Ionic and Covalent Bonding Lithium Fluoride Forms ionic bond by lithium donating an electron to fluorine Each outer shell is filled, but no electron density between two atoms Fluorine gas Forms covalent bond by sharing electrons

22 Representation of Organic Structures Lewis Structures As already shown with F 2 each valence electron is represented by a dot Two dots between two atoms represents a single bond (two shared electrons) Consider methane (a molecule with CH 4 molecular formula)

23 Different Ways to Draw Organic Compounds Organic chemistry has a shorthand for drawing compounds (need a way to indicate what atoms are connected by these covalent bonds) Lewis Structures Other representations All structures shown represent the same compound (propane)

24 Polar Bonds All covalent bonds shown so far have been between identical atoms What happens if a covalent bond is formed between two different elements? *Both atoms do not need to share the electrons equally Even though the electrons are shared, the electrons can be closer, on time average, to one nucleus than the other How to predict where the electrons are located?

25 Electronegativity Tables Linus Pauling established values to associate with each element Elements toward the upper righthand of the periodic table are more electronegative Also can predict the relative electronegativity of two atoms by their relative placement in the periodic table H (2.2) Li (1.0) Be (1.6) B (1.8) C (2.5) N (3.0) O (3.4) F (4.0) The numbers are a relative indication of how much the electrons are attracted to a certain atom Cl (3.2) Br (3.0) I (2.7) As the number becomes larger, the electrons are attracted more by that atom

26 Formal Charges A formal charge represents a full charge on the atom (assuming no polarity of the covalent bond) To calculate: Formal charge = (group number) (nonbonded electrons) ½(shared electrons) Use group numbers, not atomic numbers! Consider ammonium: Formal Charge = 5 0 1/2 (8) = +1

27 Acid/Base Reactions Important considerations for Organic chemistry: What makes a compound acidic? How do we determine acid strengths? Need to first consider what definition of acid/base reactions we are using Arrhenius definition: Acids something that dissociates in water to give hydronium ion (H 3 O+) Bases something that dissociates in water to give hydroxide ion (HO-)

28 The Arrhenius definition is used to determine the strength of an acid The strength is determined by how easily the molecule dissociates in water to give a hydronium ion K w = [H 3 O+][HO-] = 1 x In neutral solution the concentration of [H 3 O+] and [HO-] are equal Therefore [H 3 O+] = [HO-] = 1 x 10-7 M Acidic solutions have an excess of [H 3 O+] Therefore [H 3 O+] > 1 x 10-7 and [HO-] < 1 x 10-7

29 Due to the magnitude, the acid strength is expressed in a logarithmic scale ph = -log10 [H 3 O+] Therefore in neutral solutions ph = 7 Acidic solutions ph < 7 Basic solutions ph > 7 The Arrhenius definition is poor for organic compounds Since very few will dissociate into hydroxide ions

30 Brønsted-Lowry definition is better for organic compounds Acid any species that can donate a proton Base any species that can accept a proton As can be seen from the reaction above, every Arrhenius acid and base are still considered acids and bases with the Brønsted-Lowry definition Other compounds, however, would not be considered bases under Arrhenius which do qualify with Brønsted-Lowry

31 Conjugate Acid and Base An important concept with the Brønsted-Lowry acid/base definition is the resultant conjugate acid and base (every acid becomes a conjugate base after the reaction) base conjugate acid H Cl H 2 O H 3 O Cl acid conjugate base

32 Lewis Definition of Acids and Bases G.N. Lewis postulated that an acid/base reaction need not involve a transfer of a proton An acid/base reaction can refer to any reaction that involves the formation of new bonds Lewis acid: a species that accepts a lone pair of electrons to form a new bond Lewis base: a species that donates a lone pair of electrons to form a new bond H 2 O H Cl H 3 O Cl base acid This definition is far more general, but any acid or base in Brønsted/Lowry definition remains the same in the Lewis definition Introduces new terms that are used in many organic reactions A Lewis base is called a nucleophile - lover of nuclei A Lewis acid is called an electrophile - lover of electrons

33 Evolution of Acid-Base Theories Theory Acid Base Lavoisier (1789) oxidized substance substance to be oxidized increasing generality Arrhenius (1887) Brønsted/Lowry (1923) H+ source HO- source H+ donor H+ acceptor Lewis (1923) e-pair acceptor electrophile e-pair donor nucleophile HOMO-LUMO (1960 s) unusually low LUMO unusually high HOMO

34 Acid-Base Reactions HO- H+ HO-H Curved arrows designate e-pair shifts (not atomic motion) Start arrow at e-pair location in starting material End arrow at e-pair location in product

35 Acid-Base Reactions HO- H+ HO-H Arrhenius + NH 3 : H+ NH 3 -H Brønsted/Lowry HO- BH 3 HO-BH 3 - Lewis + - NH 3 : BH 3 NH 3 -BH 3 Lewis All of these acid-base reactions follow a similar arrow pushing mechanism

36 Acid Strength Organic acids are defined by the acid dissociation constant (K a ) Similar to ph measurements, this quantity is expressed in the logarithmic form pk a = -log K a The stronger the acid, the smaller the pk a Don t confuse pk a with ph pk a is a constant for a given acid referring to the ph where half of the acid is ionized ph refers to the concentration of hydronium ions in solution

37 How to Predict the Relative Strength of Acids - Common point is the ability to stabilize a negative charge (molecules that can handle more excess electron density after deprotonation are stronger acids) 1. Amongst atoms of similar size, the atom with a greater electronegativity will be a stronger acid

38 2. Bigger atoms will be stronger acids Consider size of atom where charge is located This trend usually is relevant when comparing atoms in the same column (as the atom becomes larger going down a column, the excess negative charge is more stabilized)

39 3. Polar bonds near anion source can stabilize negative charge (inductive effect) Consider acetic acid derivatives: Electron withdrawing groups can pull electron density away from another region of molecule (this through bond effect is called inductive)

40 Look at a nitro group 4. Resonance can lower electron density on a given atom What is resonance? (also called delocalization ) The negative charge on the oxygen could be placed on either oxygen using Lewis structures Which structure is correct? It turns out neither structure is correct, but the charge is delocalized onto both oxygens - This process of being able to delocalize the charge onto more than one atom is called resonance

41 Rules of Resonance 1. All resonance structures must be valid Lewis structures (e.g. cannot have 10 electrons on one carbon in one structure) 2. Only electrons move (cannot move nuclei, only electrons usually double bonds or lone pairs connected through an extended p orbital system) 3. Number of unpaired electrons must be constant

42 How does resonance explain acidity? Consider pk a of organic molecules Both structures place a negative charge on oxygen after loss of proton, but the pk a difference is greater than 11

43 A carbonyl group is a common resonance source The negative charge can therefore be delocalized over both oxygen atoms

44 Resonance of Acetate Anion

45 Rotation of Acetate Group

46 Comparison of Electron Density for Ethoxide versus Acetate anion The excess negative charge is more stable on the acetate anion that can resonate, thus the conjugate acid is more acidic

47 Important to Remember: Not all resonance structures need to contribute equally If two resonance structures are not of equal energy, then they will not contribute equally to the actual structure This leads to major and minor contributors

48 Actual hybrid structure

49 Remember also that number of paired electrons must be constant

50 Factors to affect stability of resonance structures: - Placement of charge When the only difference is the location of formal charge, structure is more stable when anion is placed on more electronegative atom

51 - Amount of Charge Also related to number of bonds in a structure While structure with four formal charges shown is a valid resonance form, if structure is dramatically higher in energy then it is practically an irrelevant resonance form

52 - Octet rule is important Having all atoms with a filled octet rule is more stable than a resonance form that only has 6 electrons in one outer shell Even if this requires a positive formal charge to be placed on a more electronegative atom Second row atoms are always more stable with a filled outer shell

53 Curved arrows represent movement of electrons As already observed in acid/base reactions, a curved arrow indicates movement of electrons Arrows always show where electrons are moving Formal charges on atoms are a result of electrons moving

Drawing resonance structures properly is an aid to predict location of electrons Remember actual structure is a hybrid of all relevant resonance forms These resonance

54 Drawing resonance structures properly is an aid to predict location of electrons Remember actual structure is a hybrid of all relevant resonance forms These resonance forms allow a chemist to predict where excess electron density is located in a molecule Excess negative charge is located on three carbon atoms, not on all five equally

55 Empirical Evidence for Resonance Chemical properties of molecule are not like one resonance form Have already observed this with acidity difference between ethanol and acetic acid

56 Observe also with dipole values for compounds with resonance H 3 C H N O 3 C H 3 C N N O N N O 4.47 D 1.30 D Interatomic distances do not correspond to single, double, or triple bonds H 3 C CH 3 H 2 C CH Å 1.54 Å 1.32 Å

Acids and Bases. Acids and Bases

Acids and Bases. Acids and Bases BrØnsted-Lowry A BrØnsted-Lowry acid is a proton donor. A BrØnsted-Lowry base is a proton acceptor. H + = proton BrØnsted-Lowry Some molecules contain both hydrogen atoms and lone pairs and thus, can act