O CHEM 2 CONCEPT PACKET Complete

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1 O CHEM 2 CONCEPT PACKET Complete Written by Jeremy Robinson, Head Instructor Find Out More +Private Instruction +Review Sessions

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3 Valence Bond Theory Octet Rule is that most atoms seek a minimum energy state of completely filled and orbitals for a total 8 electrons: Group 1A Alkali Metal Atom will lose its one valence electron in forming an aqueous solution or an ionic bond. Group 2A Alkaline Metal Atom will lose its two valence electrons in forming an aqueous solution or an ionic bond. Upper Right Nonmetals will gain other atom electrons in forming an ionic bond, polar covalent bond, or covalent bond. Duet Rule is that Hydrogen and Helium have a orbital only that is filled with just 2 electrons. Lithium (Group 1A) will lose its one valence electron and Beryllium (Group 2A) will lose its two valence electrons to a filled orbital. Hextet Rule is that Group 3A Aluminum, Boron, Indium have 6 electrons in three covalent bonds and an empty orbital. Decatet and Dodecatet Rule is that Phosphorous, Sulfur, Chlorine, Bromine, Iodine use orbital for 10 or 12 electrons. Each atom in a molecule has a Formal Charge assigned to it, a measurement of its tendency to be in the Lewis Structure Lone Pair Electrons is the Number of Electrons involved in a lone pair around the atom, 2 for each lone pair Bond Complex Electrons is the Number of Electrons in each bond, 2 for single bond, 4 for double bond, 6 for triple bond Higher electronegative atoms have a negative Formal Charge while lower electronegative have a positive Formal Charge. Atom Form 1 Form 2 Form 3 Form 4 Form 5 Notes Hydrogen Hydrogen only forms one bond Alkali 1A Li,Na,K,Rb,Cs The Alkali Group 1A always lose one electron in forming ionic bonds for Formal Charge 1+ Alkaline 2A Be,Mg,Ca,Sr,Ba Group 3A B,Al,Ga,In Carbon C Nitrogen N Phosphorous P Oxygen O Sulfur S Halogen 7A F,Cl,Br,I The Alkaline Group 2A always lose two electrons in forming ionic bonds for Formal Charge 2+ The Group 3A is the Hextet Rule with an empty p orbital, but can follow the Octet Rule Carbon follows the Octet Rule with four bonds and readily forms multiple bond complexes Nitrogen follows the Octet Rule and prefers three bonds with one lone pair but may have four bonds Phosphorous is the Octet Rule at three bonds with one lone pair or the Decatet Rule at five bonds Oxygen follows the Octet Rule at two bonds with two lone pairs or one bond with three lone pairs Sulfur follows the Octet Rule at two bonds with two lone pairs, four bonds, or six bonds Fluorine is a terminal atom only with Form 1. Others may exceed the Octet Rule as central atoms 3

4 and Atomic Orbitals The orbital has a spherical shape and has a distribution closer to the nucleus of the atom. The orbital has a dumbbell shape and has a distribution further away from the nucleus of the atom. Hybrid Atomic Orbitals The Hybrid Orbitals are created when the single valence electron orbital and number of valence electron orbitals interact and combine together forming number of Hybrid Orbitals. These Hybrid Orbitals will form number of Bond Complexes or Lone Pairs around the atom. The remaining number of valence electron orbitals are available to form number of extra bonds in the Bond Complexes, creating multiple bonds. The value of is called the index of the Hybrid Orbital. The index determines the size of the orbital and the angle associated with the orbital: an orbital has a larger angle ( ) and a smaller radius and a orbital has a smaller angle ( ) and a larger radius. The larger the index of a Hybrid Orbital, the larger the character and the larger the radius associated with the orbital, but the smaller the character and the smaller the angle associated with the orbital. Hybrid Atomic Orbitals The Hybrid Orbitals are created when the single valence electron orbital, number of valence electron orbitals and number of valence orbitals interact and combine together forming number of Hybrid Orbitals. These Hybrid Orbitals will form number of Bond Complexes or Lone Pairs around the atom. The atom will then exceed the Octet Rule, instead reaching the Decatet Rule (10 electrons) or Dodecatet Rule (12 electrons). Atomic Bond Complexes, Lone Pairs, and Radicals Two atoms will combine their valence electron wavefunctions and form bonds in one of two different ways: Valence Electrons of each and every bonded atom will be involved either in a Bond Complex or in a Lone Pair. A Bond Complex is formed by the shared valence electrons between two atoms as their wavefunctions combine A Bond Complex exists between every pair of bonded atoms in a molecule, and the energy holds the molecule together A Lone Pair is formed by two valence electrons that are not shared in bonding as their wavefunctions combine A Lone Pair exists around some atoms in a molecule, but always away from any Bond Complexes of that atom A Radical is formed by one unpaired valence electron that is not shared in bonding as their wavefunctions combine A Radical exists around some atoms in a molecule, but always away from any Bond Complexes of that atom Atom Hybridization Type The Atom Hybidization Type is a value attributed to each atom in a molecule and determines the number of Electron Domains around the particular atom. Each Electron Domain holds either a Bond Complex or a Lone Pair. Hybridized Atoms one Electron Domain at : one single bond. Only Hydrogen exists as this Hybridization Type. Hybridized Atoms two Electron Domains at : two double bonds or triple bond plus one single bond or lone pair Hybridized Atoms three Electron Domains at : one double bond plus two total single bonds or lone pairs Hybridized Atoms four Electron Domains at : four total single bonds or lone pairs Hybridized Atoms five Electron Domains three at and two at : five total single bonds or lone pairs Hybridized Atoms six Electron Domains at : six total single bonds or lone pairs 4

5 Electron Domain Geometry and Molecular Geometry Electron Domain Geometry describes the configuration of the Electron Domains around a particular atom. Molecular Geometry describes the configuration of just the Bond Complex Domains around a particular atom and ignores the Lone Pair Domains which always remain closer to the atom and are not noticeable in the overall atomic shape. To determine: 1. Draw the entire Lewis Structure of the molecule including the Lone Pairs on any atoms. 2. Count the number of Electron Domains, which include both Bond Complex Domains and Lone Pair Domains. 3. Determine the number of both Bond Complex Domains and Lone Pair Domains. 4. Use the table to determine the Electron Domain Geometry, Molecular Geometry, Hybridization, and Bond Angle Number of Electron Domains Electron Domain Geometry Hybridization and Bond Angle Bond Complex or Bonding Domains Lone Pair or Nonbonding Domains Molecular Geometry 2 Linear 2 0 Linear 3 Trigonal Planar 3 0 Trigonal Planar 3 Trigonal Planar 2 1 Bent 4 Tetrahedral 4 0 Tetrahedral 4 Tetrahedral 3 1 Trigonal Pyramidal 4 Tetrahedral 2 2 Bent 5 Trigonal Bipyramidal 5 0 Trigonal Bipyramidal 5 Trigonal Bipyramidal 4 1 Seesaw 5 Trigonal Bipyramidal 3 2 T Shaped 5 Trigonal Bipyramidal 2 3 Linear 6 Octahedral 6 0 Octahedral 6 Octahedral 5 1 Square Pyramidal 6 Octahedral 4 2 Square Planar Electronegative Difference, Dipole Moment, and Polar Molecules The difference in the Electronegativity between two atoms will determine the type of bond that they will form Any bond made between two identical atoms will have no electronegative difference as electrons are equally shared. Any bond made between two different atoms will have an electronegative difference as electrons are unequally shared. A bond with an electronegative difference will have a dipole moment arrow pointed from the less electronegative atom towards the more electronegative atom and with a magnitude equal to the electronegative difference within the bond. If all dipole arrows contained within a molecule cancel in magnitude and direction, the molecule will not be a Polar Molecule and will have a net magnetic dipole moment of zero even if some of the bonds within the molecule are polar. If one or more dipole arrows contained within a molecule do not cancel in magnitude and direction, the molecule will be a Polar Molecule and have a net magnetic dipole moment in the direction summation of all bond dipole moments. Some Molecular Geometries will not be a Polar Molecule if all atoms bonded to the central atom are exactly the same: Some Molecular Geometries will always be a Polar Molecule regardless of the atoms bonded to the central atom: Intermolecular Forces Intermolecular Forces hold molecules together in liquid and solid states. The stronger the intermolecular forces, the higher the boiling point and the lower the vapor pressure of the liquid. The types of intermolecular forces are: London Dispersion Forces(All Molecules especially larger ones) induced dipole moments by electron cloud deformities. Dipole Interactions(Ion-Dipole, Dipole-Dipole) attraction between two polar molecules or polar with cations and anions. Ion Interactions (Ion-Ion, Ion Dipole) attraction between two ionic molecules or an ionic molecule with a polar molecule. Hydrogen Bonding (Molecules with bonded directly to,, or ) large electronegative difference with a polar bond. 5

6 Organic Structures, Nomenclature, and Substituents Structure Molecular Formula Condensed Structures Suffix Notes Alkane Has only single carbon-carbon bonds but not in a ring Alkene Alkyne Cycloalkane Conjugated Cycloalkene Has all single except exactly one double carbon-carbon bond Has all single except exactly one triple carbon-carbon bond Has at least three or more ringed single carbon-carbon bonds Has alternating single and double conjugated carbon-carbon bonds Prefix of an organic molecule is determined by the number of carbons contained in the longest chain of the molecule: Suffix of an organic molecule is determined by whichever structures or functional groups the molecule contains: Structure of the molecule is determined by the carbon-carbon bond complexes and the ring shapes of the molecule: Functional Group Group Formula Condensed Structures Suffix Notes Alcohol Weak Acid by donating from the group Amine Ketone Aldehyde Carboxylic Acid Ester Ether Epoxide Moderate Base by bonding the nitrogen N lone pair Weak Base by bonding the carbonyl double bonded oxygen O lone pair Weak Base by bonding the carbonyl double bonded oxygen O lone pair Moderate Acid by donating from the carboxyl group Moderate Base by bonding the carbonyl double bonded oxygen O lone pair Weak Base by bonding the oxygen O lone pair Weak Base by bonding the oxygen O lone pair 6

7 Lewis Acids and Lewis Bases A Lewis Acid is any molecule that accepts electrons into an empty orbital: nonspectator cations, boron, or aluminum. A Lewis Base is any molecule that donates electrons from a filled orbital: nonspectator anions, lone pairs, bonds. HOMO stands for the Highest Occupied Molecular Orbital, the highest energy orbital containing one or more electrons. LUMO stands for the Lowest Unoccupied Molecular Orbital, the lowest energy orbital containing zero electrons. Lewis Acid Electrophile Lewis Acids are atoms or molecules that are electron acceptors, which includes molecules with metal, boron, aluminum, or that are nonspectator cations. Electron acceptor Lewis Acids have a Low LUMO energy, or low energy vacant electron orbitals in the LUMO that are attracted to the High HOMO energy electrons of a Lewis Base and may bond with such a molecule. The atom has the lowest possible LUMO energy, the orbital and is therefore a very strong Lewis Acid. Lewis Base Nucleophile Lewis Bases are atoms or molecules that are electron donors, which includes molecules with Lone Pairs, Bonds, or that are nonspectator anions. Electron donor Lewis Bases have a High HOMO energy, or high energy valence electron filled orbitals in the HOMO that are attracted to the Low LUMO energy orbitals of a Lewis Acid and may bond with such a molecule. Nonbonding lone pair electrons have a high HOMO energy and are therefore a moderate Lewis Base. Lewis Acid and Lewis Base Interactions and Reactions During an Acid Base Reaction, a Lewis Acid empty Critical LUMO overlaps with a Lewis Base filled Critical HOMO to form two molecular orbitals, one that is a lower energy bonding orbital and one that is a higher energy antibonding orbital. The electrons originally contained in the filled Critical HOMO are then transferred into the lower energy bonding orbital. 7

8 Activation Energy, Reaction Profile, Rate Law, and Molecule Strain Energies The activation energy is the minimum energy needed for a mole of molecules to be raised to the energy of the first transition state, the next occurring peak on an energy versus reaction coordinate graph. All peaks are transition states, and any valleys between them are the intermediates. The reactants are the left side of the graph and the products are the right side of the graph for a forward reaction and the reactants are the right side of the graph and the products are the left side of the graph for a backward reaction. The distance between the level of the reactants and the next occurring peak, or an intermediate and the next occurring peak, is the activation energy. A reaction can have multiple activation energies, one for the reactants and one for each of the intermediates. This energy is needed to bring the reactant molecules together against their repelling electron clouds and break the necessary bonds to reach the transition state. The transition state will last very briefly due to instability, but while it does exist it will take a form that most resembles whichever reactants, products, or transition states are nearest to it in energy. The transition state molecules will then form the necessary bonds to reach a more stable state, either an intermediate or the final product. Rate Law The Rate Law is the Reaction Rate as a function of the concentrations for each Reactant raised to a certain exponent on each reactant from the Slow Step known as the Order of the particular Reactant. The overall Rate Law will take the form Where is the Rate Constant, whose value depends on the particular reaction, the Reactant A Order is the stoichiometric coefficient of reactant A as determined by the Slow Step, the Reactant B Order is the stoichiometric coefficient of reactant B as determined by the Slow Step, and the sum of is the Total Order of the reaction. Catalysts are used up as a reactant in one or more elementary steps of a reaction and then created again as a product in one or more later elementary steps, so they do not affect equilibrium, but they do increase the Rate Law constant. A catalyst lowers the activation energies and increases the rates for both the forward reaction and the reverse reaction. Homogeneous Catalyst has the same state solid (s), liquid (l), gas (g), or aqueous (aq) as all of the reactants Heterogeneous Catalyst has a different state solid (s), liquid (l), gas (g), or aqueous (aq) than all of the reactants Reaction Profile before Catalyst is added has significant activation energy Reaction Profile after a Catalyst is added has lowered activation energies Molecule Strain Energies Angle Strain Energy is created by unnatural angles in a molecule, prevalent in small rings cyclopropane and cyclobutane. Eclipsing Torsional Strain Energy is created by adjacent atoms additional bonds that are in line with each other. Steric Strain Energy is created by larger substituents being forced close to each other due to the molecular geometry. 8

9 Stereochemistry Stereochemistry involves the three dimensional structure of molecules. It focuses in particular on Chiral molecules, or molecules that have a different three dimensional structure when two bonds on any one atom are interchanged. Each different structure is known as a Stereoisomer relative to the original and will almost always react chemically different. Stereochemistry Symbols and Meanings Stereochemistry is indicated by different symbols as wedges, bars, or squiggles that have the following meanings: Wedges are used to indicate absolute stereochemistry for any substituent that has a definite single orientation. A solid wedge indicates the substituent is out of the plane of the paper and a dash wedge indicates the substituent is into the plane of the paper. This allows the three dimensional geometry of tetrahedral central atoms, rings, allene molecules, and rings with bonds comprised of adjacent double bonds to be shown on two dimensional surfaces such as paper. Even Carbon Allene has Odd Carbon Allene has Tetrahedral Plane Ring has two terminal substituent terminal substituent shape has two ring bonds in plane bonds relative in plane bonds out of plane so Plane Ring substituents are bonds in plane, and for non bond so either all four are in two are in plane on one out of plane relative to the one bond at, atoms, one bond at plane or one at and one end and one at and one bond substituents which one bond away. and one bond away. away on each end. away on the other end. are in plane with the ring. Bars are used to indicate relative stereochemistry for any two substituents that have a definite relative orientation but individually have both absolute stereochemistry directions out of the plane of the paper and into the plane of the paper. Squiggles are used to indicate relative stereochemistry for any substituents to an already existing absolute wedge. 9

10 Chiral and Stereoisomer Relations Molecules that become different through the interchange of two bonds on any one atom are Stereo. The interchanged bond molecules are Stereoisomers relative to each other, but depending on their structure they may also be related as: Enantiomer is the relationship between an original molecule and any molecule that is itself an exact mirror image but is nonsuperimposable onto the original molecule in that it has a different molecular geometry than the original molecule due to interchanged bonds. The two molecules are then considered as enantiomers relative to each other. Diastereomer is the relationship between an original molecule and any other molecule that is identical except with a different molecular geometry than the original molecule due to two or more interchanged bonds but it is not the exact mirror image of the original molecule. The two molecules are then considered as diastereomers relative to each other. Atom Bond Priorities Atom Bond Priorities classify a stereoisomer and are assigned to each immediately bonded atom by atomic number as: The immediate bonded atom determines each bond priority relative to the other three bonds but with any identical immediate bonded atoms compared to each other by their own three bonded atoms including all bonds or bonds until either a difference exists or the bonds are relatively nonprioritizable. It is not possible to go backwards over a bond, but it is always necessary to go backwards over any bonds to account for the successive three bonded atoms. 10

11 Stereocenter or Chiral Center A Stereocenter or Chiral Center is any molecule atom, usually carbon C or four bond nitrogen N, with four single bonds either bonded directly to four different atoms or bonded directly to four eventually different molecule structures. R Configuration or S Configuration can be assigned to each molecule stereocenter individually by rotating the molecule so that the stereocenter lowest priority bond is directed either away from the observer or toward the observer and then tracing the remaining three bonds in order from first to second to third as either clockwise or counterclockwise. rotate rotate Clockwise Clockwise Lowest In Plane Counterclockwise Lowest In Plane Clockwise Lowest Away Lowest Toward Rotate around Lowest Away Rotate around Lowest Away Retain as Reverse to toward wedge Retain toward wedge Retain Meso Molecule has two or more stereocenters but is not chiral due to internal plane of symmetry (dash line in picture). Rotate one end Geometric Isomer A Geometric Isomer is any even carbon allene (double bonds between two or more adjacent chain carbons or any ring replacing any double bond) with two different substituents on one end and again two different substituents on the other end. A Geometric Isomer will have its substituent pairs on each end exist in plane parallel with each other. E or Trans Configuration and Z or Cis Configuration can be assigned to each even carbon allene or ring in the molecule individually by comparing whether the highest priority bond from each end is on the same side or on the opposite side. Highest on Same Side Highest on Opposite Side Highest on Same Side Highest on Opposite Sides Chiral Shape A Chiral Shape is any odd carbon allene (double bonds between three or more adjacent chain carbons or any ring replacing any double bond) with two different substituents on one end and again two different substituents on the other end. A Chiral Shape will have its substituent pairs on each end exist out of plane perpendicular with each other. Induced Stereocenter An Induced Stereocenter occurs for a Meso Molecule whose symmetry plane passes through an atom that has four different substituents due to R on one side and S on one side resulting in multiple Meso Molecules when the other two subsituents switch, or for a symmetric nonprioritizable molecule with a central atom that has four different substituents due to E on one side and Z on one side resulting in different molecules when the other two subsituents switch. 11

12 NMR and IR Spectroscopy The location of each signal range is due to the partial positive charge carried by the proton H due to the deshielding or the displacement away of its own electron, with more upfield corresponding to a less partial positive charge H and more downfield corresponding to a more partial positive charge H. The partial positive charge of a proton H is strongly affected by the partial charge of its parent C atom, the atom to which it is directly bonded. The partial charge of the parent C atom is changed either by having one or more different electronegative atoms bonded directly to the parent C atom or by having the parent C atom involved in bonding with an adjacent atom. In the situation where the parent C atom is bonded to one or more different electronegative atoms, the partial positive charge is increased for each additional bond to a higher electronegative atom, whether it be bonds to a single higher electronegative atom or bonds to multiple higher electronegative atoms, and the partial positive charge is decreased for each bond to a lower electronegative atom such as another hydrogen atom. In the situation where the parent C atom is involved in bonding with an adjacent atom, the double bond is more downfield, since the triple bond proton H resides in a high s character hybrid, near the parent C atom, and is more shielded by the parent C atom electrons. For the aromatic H, the aromatic resonance draws electron density away from the proton H causing it to be more deshielded and end up more downfield. For the vinyl H, alkyne H, or the substituted benzene aromatic H, asymmetric bond partial charges on the parent C atom due to resonance or inductive effects can cause the proton H signal to shift outside of its normal range, upfield of its normal range for a partial negative charge and downfield of its normal range for a partial positive charge on the parent C atom. The shift is most pronounced for the vinyl proton H that resides in a trans position relative to the substituent causing resonance or inductive effects Broadband-Decoupled DEPT-90 DEPT 135 Subtract DEPT-135 from DEPT-90 only Negative Broadband-Decoupled DEPT-135 only Subtract DEPT-90 from Positive DEPT

13 A Bronsted Acid with a lower is a stronger acid. The Bronsted Acid disassociation equilibrium constant is for the following Bronsted Acid disassociation reaction and the acid base reaction equilibrium constant is for the following Bronsted Acid and Lewis Base reaction Each Bronsted Acid has a conjugate Bronsted Base that is strong enough to deprotonate any acid with a lower than the conjugate acid or equivalently if the reaction equilibrium constant is such that. The carbon connected to the amine functional group has priority number 1 Arylamines including aniline are less basic than their alkylamine counterpart due to the stabilization of the nitrogen lone pair in phenylic resonanc. Base strength can be increased with the proper substitution. Arylamines including aniline have a nitrogen lone pair that becomes more basic with an electron donating group especially in the para (or ortho) position and will become less basic with an electron withdrawing group. The bottom right nitrogen in each heterocycle has priority number 1 and each successive perimeter vertex atom in a counterclockwise direction around the perimeter has the next highest priority in order until completing the cycle. 13

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21 Sin Addition or Cis Product has two added subtituents bond on the relative same side of the reactant molecule. Anti Addition or Trans Product has two added subtituents bond on the relative opposite side of the reactant molecule. Markovnikov Product has any reactant nucleophile bond on the more substituted carbon of the final product. Antimarkovnikov Product has any reactant nucleophile bond on the less substituted carbon of the final product. Zaitsev Product has any resultant bonds form between the more substituted carbons of the final product. Tautomer is a less stable high energy intermediate that can internally rearrange its bonds to become a stable product. Angle Strain Energy is created by unnatural angles in a molecule, prevalent in small rings cyclopropane and cyclobutane. Eclipsing Torsional Strain Energy is created by adjacent atoms additional bonds that are in line with each other. Steric Strain Energy is created by larger substituents being forced close to each other due to the molecular geometry. Electron Flow Arrows One or more electrons always change roles during a chemical reaction, whether becoming a different bond between atoms, interchanging between a bonding pair and a nonbonding lone pair, or interchanging between a radical and a bonding pair or nonbonding pair. Electron flow arrows indicate the exchange of electrons in the reaction mechanism, a double arrow head indicating the exchange of a pair of electrons and a single arrow head indicating the exchange of a single radical electron. Some of the more common mechanism electron flow arrows are the following: 21

22 Amino Acids 22