initially scientists believed there was a special

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! 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.”! 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! 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! Understanding Organic Chemistry is Learning about Bonding and the location of Electrons ! O H H H H H H Consider a molecule called acetone! Shorthand drawing! All atoms indicated! 3-dimensional drawing! O O H H H H H H Electron density plot! wedge and dash! lines have meaning! By understanding, and predicting, the properties and orientation of bonds! Organic reactions can be predicted without memorization! Compare these compounds:! Why does carbon form such a variety of bonds?! Realize position in the periodic table! 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’! 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! 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)! [...]... (every acid becomes a conjugate base after the reaction) base H Cl acid H 2O conjugate acid H3O Cl conjugate base 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... indication of how much the electrons are ‘attracted’ to a certain atom As the number becomes larger, the electrons are attracted more by that atom 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:... 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 Conjugate Acid and Base An important concept with the Brønsted-Lowry acid/base definition is the resultant conjugate acid and base... designate e-pair shifts (not atomic motion) Start arrow at e-pair location in starting material End arrow at e-pair location in product Acid-Base Reactions HO- NH3: HO- NH3: H+ HO-H Arrhenius H+ +   NH3-H Brønsted/Lowry BH3 -­‐   HO-BH3 Lewis BH3 +              -­‐   NH3-BH3 Lewis All of these acid-base reactions follow a similar arrow pushing mechanism Acid Strength Organic acids are defined... new bond Lewis base: a species that donates a lone pair of electrons to form a new bond H2O base H Cl H3O Cl 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 -... (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... with F2 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 CH4 molecular formula) 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... ammonium: Formal Charge = 5 – 0 – 1/2 (8) = +1 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 dissoicates in water to give hydronium ion (H3O+) Bases – something that dissociates in water to give hydroxide... electrons can allow both atoms to fill the outer shell Consider F2 (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 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... 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 (2nd) shell 4 atomic orbitals (1s and 3p) with 2 electrons per orbital Electronic Configuration for Carbon through Fluorine When filling degenerate orbitals electrons will go into different orbitals before pairing . 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. 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. lipids, fats, carbohydrates, nucleic acids, etc.)! And the metabolic and other interactions in the body involve organic reactions! Understanding Organic Chemistry is Learning about Bonding and the