Introduction to Organic Chemistry

1. Introduction to Organic Chemistry Chemical Bonding and Reactions

2. Scientific Method • A systematic approach to research • Hypothesis: a tentative explanation for a set of observations and experiments • Law: a description of a phenomenon that allows for general predictions • Theory: a well-established explanation for scientific data; not fully tested; can be disproven • Experiments: systematic observations and measurements performed under controlled conditions http://catalog.flatworldknowledge.com/bookhub/4309?e=averill_1.0-ch01_s02

3. Classification of Matter • Matter is any physically present substance that has a mass and occupies space • Matter is composed of atoms and molecules

4. Elements • An element is a singlesubstance in its simplest form that cannot be split into any more separate substances by chemical means • Everything around us is comprised of chemical elements • 112 elements, 90 of them naturally occurring • Only 25 of these are essential for the human body • Hydrogen (H), carbon (C), oxygen (O) and nitrogen (N) make up of ~97 % of body weight and 99 % of total atoms • Elements are made of atoms http://www.chem.wisc.edu/deptfiles/genchem/sstutorial/Text3/Tx33/tx33.html

6. Periodic Table • Periodic table is a chart in which elements with similar physical and chemical properties are grouped in a periodic way • The elements are arranged according to their atomic number • In a periodic table, horizontal rows are called periods and vertical groups are called groups • Elements within each group have similar chemical and physical properties • Groups 1-2 and 13-18 are called main group elements (also called 1A through 8A groups) • Groups 3-12 are called transition group elements (also called 3B through 12B group elements)

7. Periodic Table

8. Descriptive Names for Groups in the Periodic Table • 1A – alkali metals: lithium, sodium, potassium are most common, very reactive against air and water, hydrogen (H) is also in this group, but it is not a metal • 2A – alkaline earth metals: magnesium and calcium are the most abundant in nature among the group, found mainly as minerals • 7A – halogens: fluorine, chlorine, bromine, iodine are the most common – halogens react readily with metals to form salts (sodium chloride, calcium chloride) • 8A – noble gases: helium, neon, argon, krypton, xenon, radon – they are very unreactive gases – also called inert gases, they are present in monoatomic form • Transition metals (B group elements) – contain many of the common metals, such as iron, nickel, copper, cobalt, zinc, platinum, gold, silver

9. Essential Elements for the Body http://en.wikipedia.org/wiki/Composition_of_the_human_body#mediaviewer/File:201_Elements_of_the_Human_Body-01.jpg

10. Classification of Elements 17 nonmetals 8 semimetals

12. Atoms and Atomic Theory • The smallest unit (particle) of an element is atom • Atom is made up of subatomic particles; protons, neutrons and electrons – number of these determine the characteristic of an atom http://physics.taskermilward.org.uk/KS4/additional/html/atomic_structure.htm

13. Atoms • Atomic Number (Z):number of protons (or electrons in a neutral atom) in an atom • Mass Number (A): (number of protons) + (number of neutrons) http://physicsnet.co.uk/gcse-physics/atomic-structure/

14. http://commons.wikimedia.org/wiki/File:Atomic_number_depiction.jpghttp://commons.wikimedia.org/wiki/File:Atomic_number_depiction.jpg

15. Atoms and Ions • Ions:gain electron – anion, lose electron – cation(fluoride, F-; sodium cation, Na+) • Atoms form ions as part of their reaction with other atoms to form molecules. • The readiness with which an atom gains or loses electrons dictates its reactivity • F + 1e- F- 19 19 9 9 Neutral fluorine atom Fluorine anion 9 protons, 10 electrons 9 protons, 9 electrons

16. Isotopes of Atoms • Isotopes:atoms with the same number of protons and electrons, but different number of neutrons 16O, 17O, and 18O • Elements are present in nature as mixtures of their isotopes • Chemical behaviors of isotopes are identical, nuclear properties might be different; radioactivity • Atomic mass of an element is the weighted average mass of all the isotopes – not same as mass number • 35Cl (~75.8%) and 37Cl (~24.2%) – atomic mass is 35.45 http://chemistry.tutorcircle.com/inorganic-chemistry/isotopes.html

17. Isotopes are important in • biology and medicine • Radioactive isotopes are used • for monitoring biochemical activity http://chemistry.tutorcircle.com/inorganic-chemistry/isotopes.html

18. Representation of Atoms: Lewis Symbols • Representing atoms by showing only the valance electrons • Electrons (valance) are represented as dots around the chemical symbol of the atom • Dots can be placed on the 4 sides of the chemical symbol – place one electron each side, then start to add remaining electrons Each unpaired dot is available for bonding with other atoms https://classes.lt.unt.edu/Fall_2010/CECS_5030_026/mrp0113/Lewis%20Dot%20Project%20Page.htm

19. Atomic Orbitals and Energy Levels • Electrons of an atom are found in discrete shells around the nucleus – from closest to the nucleus to the farthest (valance shell) • These shells also correspond to energy levels; (n = 1, n = 2 etc.) • The energy level corresponds to the period number at the periodic table (hydrogen, n = 1, period 1) (Lithium, n = 2, period 2) Valance shell Calcium (Ca) is in the 4th period http://gcsechemistryhelp.tumblr.com/post/6753442513/periodic-table-electron-shells-part-1

20. Atomic Orbitals and Energy Levels • 1) Principal energy levels: Shown as n = 1, 2, 3 etc. – total electron capacity of a principal energy level is equal to 2(n)2 (for n=1, capacity 2 e-, for n=1, capacity 8 e-, for n = 3 capacity 18 e-) • 2) Sublevels:Within each principal energy level, there is a set of equal-energy orbitals – designated as s, p, d, f (Both principal energy level and type of sublevel is specified for describing the location of an electron) • 3) Orbital: Sublevels have atomic orbitals, which is a specific region of a sublevel where electron is located (probability of finding the electron is high); • 4)An orbital can have maximum 2 electrons

21. Octet Rule • Octet rule; atoms react in such a way that they have eight electrons in their valance (outermost) shell (more stable configuration) • This configuration of 8 electrons in the valance shell is also known as “noble gas configuration” • Noble gases (group 8A) are not reactive, since they have their valance shells already filled with 8 electrons (Helium is an exception and has 2 electrons in its only shell) • Other atoms lose/gain or share electrons to achieve the more stable noble gas configuration • By using octet rule, we can predict the • chemical changes between atoms http://www.masterorganicchemistry.com/2010/08/14/from-gen-chem-to-org-chem-pt-7-lewis-structures/

22. Shapes of Orbitals 1 kind of s, 3 kind of p, 5 kind of d orbitals http://butane.chem.uiuc.edu/pshapley/GenChem2/Intro/2.html

23. Electron configuration and Aufbau Principle • 1st principal energy level (n = 1) - 1s • 2ndprincipal energy level (n = 2) – 2s 2p • 3rdprincipal energy level (n = 3) – 3s 3p 3d • 4thprincipal energy level (n = 4) – 4s 4p 4d 4f • Aufbau principle:electrons fill the lowest-energy orbital that is available first

24. How to write the electronic configuration of an atom? Rules: • 1) Start filling the orbitals from the lowest energy; (1s orbital is the lowest energy orbital) • 2) Each principle energy level contain n sublevels and each sublevel contain certain number of orbitals • 3) No more than 2 electrons can be placed in an orbital For example, 1s < 2s < 2p < 3s < 3p is the order of energy for the first three principal levels Be: 1s2 2s2 O: 1s2 2s2 2p4 Ne: 1s2 2s2 2p6 Mg: 1s2 2s2 2p6 3s2 http://www.amasci.net/knowledge/oxidation-states.php?lang=eng

25. Molecular Interactions: How do molecules form? • Substances that are made of more than one element are called compounds, e.g. water (H2O) and carbon dioxide (CO2) • Valance electrons ;The valence shell holds the electrons located furthest from the nucleus • Valance electrons are important because; the rearrangement and redistribution of valence electrons between atoms enable atoms to ‘bond’ to one another • Full valance shell is the most stable form for an atom • The principal aim of chemical bond formation is to generate full valence shells Valance shell

26. Chemical Bond Formation • There are two types of chemical bonding: • In a “covalent bond” one or more pairs of electrons are shared equally between the atoms • In an “ionic bond” electrons are totally transferred from one atom to another • Two non-metal atoms will react to form a covalent compound • A non-metal will react with a metal to form an ionic compound

27. 1) Covalent Bond: Sharing of Electrons • In covalent bonding electrons are shared between atoms • The two orbitals with the valance electrons should overlap for covalent bond formation • This way the atoms sharing electrons gain full valance shell – more stable (octet rule) • Atoms which are linked by covalent bonds form discrete units called molecules; the smallest part of a single element (O2) or a compound (such as glucose, C6H12O6) • The molecular formula show the composition of one molecule of a covalent compound C3H8S (1-thiol), odour of onion C6H12O6 (glucose), sugar http://hyperphysics.phy-astr.gsu.edu/hbase/chemical/lewis.html

28. 2) Ionic Bond: Transfer of Electrons • Ionic bonds are formed when one or more electrons are fully transferred from one atom to another – one atom becomes positively charged (cation) another becomes negatively charged (anion) • The attraction between the oppositely charged cations and anions makes the the ‘ionic bond’ between the ions - electrostatic interaction • Ionic compounds exist as extended lattices–a network of cations and anions • Ionic compunds have an overall charge of zero due to equal number of positive and negative charges within the compound http://www.chemguide.co.uk/atoms/structures/ionicstruct.html

29. Covalent Bonds: Single and Multiple Bonds • Types of covalent bonds: Sigma (γ) and pi (π) bonds • Single or multiple bonds can form between two atoms • Single bonds are always sigma bonds • Single bond – one sigma bond • Double bond – one sigma bond + one pi bond • Triple bond – one sigma bond + 2 pi bonds http://hyperphysics.phy-astr.gsu.edu/hbase/chemical/lewis.html

30. Polar Covalent Bonding and Electronegativity • Although there is no electron transfer in covalent bonding, the atoms making the covalent bond might have partial charges • In a heteroatomic molecule, the electron distribution around the molecule is not even; electrons are not shared equally – this gives partial charges to atoms • Electronegativity is the measure of the ability of an atom to attract electrons in a chemical bond • Electronegativity determines which of the atoms in a molecule will be partially negative and which will be partially positive http://apbrwww5.apsu.edu/thompsonj/Anatomy%20&%20Physiology http://bio1151b.nicerweb.net/Locked/media/ch02/ http://www.f.u-tokyo.ac.jp/~fukuyama/interactive_trial

31. Chemical Bonding vs. Non-covalent (Intermolecular) Interactions • Non-covalent interactions are weak interactions between molecules • Non-covalent interactions determine physical properties such as boiling point, melting point, density etc. • These interactions are very important in biological systems (assembly of lipid bilayers, packing of genome etc.) • Although they are weak, multiple non-covalent interactions occur at the same time between two molecules to give a large overall effect

32. Type of Non-covalent Interactions 1) Electrostatic Interactions 2) Van der Waals Forces 3) Hydrogen bonding 4) Hydrophobic Interactions

33. 1) Electrostatic Interactions (Coulomb Interaction) • Opposite charges attract, like charges repel • Due to polar covalent bonds – one part of the molecule has partial negative and one part has partial positive charge – these molecules are said to have dipole • Ion-dipole and dipole-dipole interactions are types of electrostatic interactions • Not all molecules with polar bonds are indeed polar – such as CO2

34. 2) Van der Waals Interactions • 1) Dispersion forces: Interactions between all molecules due to induced dipole – the only form of non-covalent interaction between nonpolar molecules such as methane, • These interactions are due to temporary dipoles and short-lived • 2) Dipole-dipole İnteractions: Non-covalent interactions that occur between polar molecules due to attraction between opposite partial charges on the molecule • These interactions are due to permanent dipole of molecules and are long-lived

35. 2) Van der Waals Interactions • 3) Steric Repulsion: Repulsion between two molecules due to close proximity of their electrons --------------------------------------------------------------------- • Van der Waals interactions is the sum of the dispersion forces, dipole-dipole interactions and steric repulsions • Distance and medium are two important parameters that determine the magnitude of Van der Waals interactions

36. 3) Hydrogen Bonding • What is hydrogen bonding?:A hydrogen atom covalently bound to an oxygen (O), nitrogen (N) or fluorine (F) atom can interact with an unshared electron pair on another oxygen, nitrogen or fluorine atom to form a hydrogen bond 1) A hydrogen atom must be bonded to an atom of oxygen, nitrogenor fluorine 2) This hydrogen atom must interact with a lone pair on an atom of oxygen, nitrogen or fluorine • Hydrogen bonds are relatively weak compared to covalent bonds, but stronger than Van der Waals interactions • Hydrogen bonding is a special type of dipolar interaction Hydrogen bonding between water molecules http://commons.wikimedia.org/wiki/File:Hydrogen-bonding-in-water-2D.png http://www.cliffsnotes.com/sciences/biology/biochemistry-i/protein-structure/secondary-structure

37. Changing of The Three States of the Matter • The extent of physical (non-covalent) interactions between molecules determines the physical state of a substance; solid, liquid, gas • Solid > liquid > gas (the order of the strength of non-covalent interactions) • The physical state of a substance can be changed by altering the number of non-covalent interactions between its molecules; this is achieved by giving or taking energy from the substance – generally by heat energy http://scienceehs.blogspot.com.tr/2011/09/three-states-of-water.html

38. Three States of Matter • As we increase the energy of a substance, its molecules exhibit greater degree of movement and finally overcome the attractive forces holding the molecules together • Polar molecules have higher melting and boiling points, non-polar molecules have lower melting and boiling points (water b.p. =100 °C vs. methane b.p.= -161 °C) http://www.edplace.com/worksheet_preview.php?eId=2914&type=topic

39. Chemical Reactions • A chemical reaction involves breaking of bonds between atoms (reactants) and the formation of new bonds to form products • It is the movement of valence electrons that lies at the heart of many chemical reactions • In formation of molecules, valence electrons are shared between atoms in such a way that all atoms complete full valence shells (octet rule) • In a chemical reaction, reactants and products react in precise amounts (stoichiometry) • Stoichiometry is indicated by numbers in front of the chemical formula in the reaction scheme 6 CO2 + 6 H2O → C6H12O6 + 6 O2 (photosynthesis) 6 : 6 1 : 6 reactantsproducts

40. Nucleophiles and Electrophiles • A nucleophile (Nu– or Nuδ–), is an electron-rich species, which has a valence electron pair (which may be a non-bonding pair) that can be donated to form a covalent bond • An electrophile (E+ or Eδ+), is an electron-poor species, which can accept a complete electron pair and share it with the nucleophile to form a covalent bond http://science.uvu.edu/ochem/index.php/alphabetical/m-n/nucleophile/

41. Oxidation and Reduction Reactions • In oxidation and reduction reactions (also called redox reactions) oxidation of one molecule is couple to the reduction of the other molecule • A nucleophile can donate an electron(s) to an electrophile such that the nucleophile will lose electrons and the electrophile will gain electrons • The species that loses electron becomes oxidized and the species that gains electron becomes reduced http://www.meta-synthesis.com/webbook/15_redox/redox.php

42. In many cases; • loss of hydrogens is oxidation and gain of hydrogens is reduction; • loss of oxygen is reduction, gain of oxygen is oxidation • There are many examples of redox reactions in biology; for example many oxidation • reactions of organic compounds are couple to reduction of cofactors such as NAD+ or FAD http://www.meta-synthesis.com/webbook/15_redox/redox.php

43. Mechanism of a Reaction • The reaction mechanism tell us how electrons are redistributed during the change from reactants to products • A reaction goes through certain stages to form the product • These stages determine the mechanism of the reaction • Mechanism is the type of the changes of reactant into products (number of steps, nature of reaction etc.)

44. Mechanism of a Reaction • A reaction might be one step or multiple steps • Consider a one step mechanism: A + B  C • Reactants do not go into products suddenly; instead goes through a transition state • Transition state is the highest point of energy of a reaction • In transition state some bonds are partially broken and some bonds are partially formed http://chemistry.tutorvista.com/organic-chemistry/hammond-postulate.html

45. Transition States and Intermediates • Consider a multi-step reaction: • Reactants form an intermediate compound at each step and at the last step the product is formed • In a multi-step reaction, formation of each intermediate goes through a transition state • Intermediates are more stable than transition states and have a longer life-time

46. Types of Reaction Mechanisms 1) Substitution 2) Addition 3) Elimination 4) Condensation

47. 1) Substitution • In a substitution reaction, an atom on the reactant is replaced by a different atom • A + B - X ----> B + A - X (A is substituted with B) • A substitution reaction can be nucleophilic or electrophilic • Nucleophilic substitution reactions are more common

48. Nucleophilic Substitution • If a nucleophile attacks the parent molecule where substitution occurs, this reaction is called nucleophilic substitution reaction • A nucleophilic substitution reaction can occur in one or two steps http://chemwiki.ucdavis.edu/Organic_Chemistry/Organic_Chemistry_With_a_Biological_Emphasis/Chapter_08%3A_Nucleophilic_substitution_reactions_I

49. 2) Addition • In an addition reaction, two molecules combine to give one single product; the product contains all the atoms of both molecules • A + B ---> AB • The most common type of addition reactions is addition of small molecules to the carbon-carbon double bond of alkenes - double bond acts as a nucleophile and the adding molecule acts as an electrophile • Addition of a nucleophile to the carbon-oxygen double bond (carbonyl bond – a common functional group) is also a common addition reaction http://chemwiki.ucdavis.edu/Organic_Chemistry/Organic_Chemistry_With_a_Biological_Emphasis

50. 3) Elimination • In an elimination reaction, a molecule loses some of its part to form a compound with a double bond and the eliminated part becomes a new molecule: • An elimination reaction is the reverse of an addition reaction • Elimination reactions result in the formation of a double bond in a molecule • Elimination reactions can proceed through a one-step or two-step mechanism