Chapter 1 Structure and Bonding

1.1 Atomic Structure: The Nucleus a specific atom is described by its atomic number [Z] and its mass number [A] atoms with the same Z but different A are isotopes an elements atomic mass is the average mass in amu of an elements naturally occurring isotopes 1.2 Atomic Structure: Orbitals wave equation has a wave function or orbital as its solution; denoted by the letter psi, o plotting the square (2) in 3D space gives the volume of the space that an e will most likely occupy s and p orbitals are the most common orbitals in organic and biological chemistry o s orbitals are spherical w/ nucleus at center o p orbitals are dumbbell-shaped orbitals are organized into layers (electron shells) o level 1 contains only 1 1s orbital (2 electrons) o level 2 contains 1 2s orbital and 3 2p orbitals (8 electrons) o level 3 contains a 3s, 3 3p and 5 3d (18 electrons) the three p orbitals are oriented along mutually perpendicularly directions px, py and pz the two lobes (+ and in the wave function) of each p orbital are separated by a node (zero electron density) 1.3 Atomic Structure: Electron Configurations the ground state electron configuration is the lowest-E arrangement of an atom listing of the orbitals occupied 1. lowest-E orbitals fill up first (1s2s2p3s3p4s3d) = aufbau principle (note 4s comes before 3d) 2. electrons act like theyre spinning around an axis, and must be paired spin up and spin down ( pauli exclusion) 3. if 2+ orbitals of equal E are available, one e occupies each w/ spins parallel until all are half-full (Hunds rule) 1.4 Development of Chemical Bonding Theory carbon is tetravalent it always forms 4 bonds when it joins other elements in stable compounds it has a tetrahedral shape in this formation E (usually as heat) is always released and flows out of the chemical system when a chemical bond forms o E must be put into the system to break a chemical bond The # of covalent conds an atom forms depends on how many additional valence it needs for an octet o H has one and needs one more to achieve the He 1s 2 formation (exception to octet) Valence es not used for bonding are called lone-pair electrons or nonbonding electrons 1.5 The Nature of Chemical Bonds: Valence Bond Theory According to VBT, a covalent bond forms when 2 atoms approach each other closely and singly occupied orbital on one atom overlaps a singly occupied orbital on the other parallel electrons and mutual attraction to nuclei If a plane were passed between the H atoms in H2, the midsection would be a circle cylindrically symmetrical Bonds formed by head-on overlap of 2 orbitals along a line drawn between nuclei are sigma bonds () bond strength is the E necessary to break a bond o or to form it in the first place 2HH2 releases 436 kJ/mol; because the product has 436 kJ/mol less than the reactants, its bond strength is 436 kJ/mol bond length is the distance between the nuclei in a covalent bond every covalent bond has a characteristic bond strength and length 1.6 sp3 Hybrid Orbitals and the Structure of Methane (CH4) carbon has four valence (2s2 2p2) and, in this instance, forms four bonds carbon uses two kinds of orbitals to bond: 2s and 2p all four CH bonds are identical (not 2 kinds as you might expect) and are spatially oriented towards the corners of a regular tetrahedron o the s and 3 p orbitals hybridize to form 4 equivalent orbitals w/ tetrahedral orientation sp3 hybrids the 3 is the # of each orbital type forming the hybrid, not how many electrons occupy it sp3 orbitals are unsymmetrical one lobe is much bigger and can overlap more effectively w/ another orbital o so sp3 hybrids form stronger bonds than unhybridized s or p orbitals o the asymmetry arises due to the + and lobes of a p orbital

when a p orbital hybridizes w/ an s, the positive p lobe adds to the s orbital but the negative one subtracts from the s orbital asymmetrical and strongly oriented in one direction tetrahedral angle = 109.5

1.7 sp3 Hybrid Orbitals and the Structure of Ethane (C2H6) the same hybridization accounting for methanes structure accounts for the bonding of carbon in chains and rings ethane is the simplest molecule w/ a CC bond the C atoms bond by overlap of an sp3 from each and the other 3 sp3s overlap w/ 1s orbitals of 3 H atoms 1.8 sp2 Hybrid Orbitals and the Structure of Ethylene (C2H4) ethylene has a II-bond between carbons and is planar (flat) w/ bond angles of 120 the 2s orbital combines w/ only 2 of the 3 2p orbitals, resulting in 3 sp2 hybrids and a normal 2p the sp2 hybrids lie in a plane at 120 angles w/ the remaining p perpendicular the 2 sp2 carbons -bond by sp2 overlap unhybridized p orbitals have sideways overlap (-bond) combo of an sp2sp2 -bond and a 2p-2p -bond sharing of 4 electrons and formation of C C II-bond -bond electrons occupy region between nuclei and -bond electrons occupy regions above and below a line drawn between the nuclei 4 H atoms -bond w/ remaining 4 sp2s the C=C bond is both shorter and stronger than a CC bond b/c it involves 4 electrons rather than 2 (but isnt twice as strong b/c the sideways overlap in the -bond isnt as good as the head-on -bond) 1.9 sp Hybrid Orbitals and the Structure of Acetylene (C2H2) carbon can form a triple bond by sharing 6 electrons the carbon 2s orbital hybridizes with a single 2p orbital, resulting in 2 sp hybrids and two normal p orbitals the 2 sp hybrids are 180 apart on the x-axis while the 2 p orbitals are perpendicular on the y and z sp hybrid orbitals on each carbon overlap head-on in a strong spsp -bond the pZ orbitals from each carbon form a pZ-pZ bond by sideways overlap (as do the pY orbitals) this creates a triple bond w/ 6 shared electrons and the 2 remaining sp hybrids each -bond to H C2H2 is linear w/ HCC bond angles of 180 the III-bond is the shortest/strongest CC bond 1.10 Hybridization of Nitrogen, Oxygen, Phosphorus and Sulfur the valence-bond concept of hybridization goes for more than just carbon for example, NH3 in methylamine the bond angle is 107.1 in HNH and 109.5 CNH, both of which are close to the 109.5 tetrahedral angle assume that the N hybridizes to form four sp3 orbitals o one orbital is occupied by a lone pair phosphorus is most commonly found in organophosphates sulfur is most commonly found in thiols and sulfides 1.11 The Nature of Chemical Bonds: Molecular Orbital Theory MO theory describes covalent bond formation as coming from mathematical combinations of atomic orbitals (wave functions) on different atoms to form molecular orbitals these belong to the entire molecule o Describes a region of space around the entire molecule where an electron may be found In H2, 2 singly occupied 1s atomic orbitals combine to form 2 molecular orbitals in an additive or subtractive way o Additive MO that is lower in E and roughly egg-shaped A single egg-shaped MO not the same as 2 overlapping 1s atomic orbitals in valence theory o Subtractive MO that is higher in E and has a node between nuclei Single molecular orbital w/ shape of an elongated dumbbell Additive is lower in E than the 2 H 1s atomic orbitals and is called a bonding MO b/c its electrons spend part of their time between the nuclei (bonding the atoms together)

Subtractive is higher in E than the 2 H 1s orbitals and is called an antibonding MO b/c its electrons cant occupy that central region (where theres a node) so they cant contribute to bonding nuclei repel each other In ethylene, combo of 2 p atomic orbitals bonding and antibonding MOs Lower-E bonding MO has no node from combo of p lobes w/ the same sign Higher-E antibonding MO has a node between nuclei from combo of lobes w/ opposite signs Only the bonding MO is occupied MO theory is useful for describing -bonds in compounds w/ 2+ II-bonds

Chapter 2 Polar Covalent Bonds; Acids and Bases

2.1 Polar Covalent Bonds: Electronegativity Most bonds are somewhere between ionic and covalent polar covalent bonds: bonding electrons are more attracted to one atom than the other asymmetrical electron distribution Bond polarity is due to electronegativity (EN), an atoms intrinsic ability to attract shared electrons Uses an arbitrary scale; F is highest (4.0) and Cs is lowest (0.7) Metals on the left side of the periodic table have low EN; O, N and halogens on the right have higher EN Nonpolar covalent: ENs differ by <0.5; polar covalent: 0.5 2; largely ionic: >2.0 o CH bonds are relatively nonpolar as their difference is only 0.4 o CO is polarized electrons drawn away from C (2.5) toward O (3.5) C has partial positive charge (+) and O has partial negative () crossed arrows indicate polarity direction; es are displaced in arrow direction (epoor + looks like a +) color indicates electron-rich (red, ) and electron-poor (+) areas on electrostatic potential maps inductive effect: shifting of electrons in a -bond in response to EN of nearby atoms (used to refer to an atoms bond -polarizing ability) o metals such as Li and Mg inductively donate electrons o non-reactive metals like O and N inductively withdraw them 2.2 Polar Covalent Bonds: Dipole Moments molecular polarity results from the vector summation of all individual bond polarities and lone-pair contributions net molecular polarity is measured by the dipole moment assume theres a center of mass of all +charges (nuclei) in a molecule and a center of mass of all charges (electrons) if these dont coincide net polarity dipole moment () = Q x r (Q = magnitude of charge at either end of the dipole; r = distance between charges) o expressed in debyes (D) where 1 D = 3.336E-30 (C x m) NaCl has a big moment b/c its ionic Even small molecules like water, methanol and ammonia have substantial b/c they contain atoms w/ high EN and lone-pairs (which stick out into space away from +nuclei, creating considerable charge separation) Carbon dioxide, methane, ethane and benzene have 0 b/c of their symmetrical structures (all charge s cancel out) 2.3 Formal Charges Particularly useful for atoms w/ apparently abnormal # of bonds Example in dimethyl sulfoxide, S atom has 3 bonds rather than 2 formal + charge; O has 1 rather than 2 formal negative charge Dont imply actual ionic charges bookkeeping devices how many electrons an atom owns Formal charge = # valence # bonding # nonbonding

2.4 Resonance 2 different individual line-bond structures for the same molecule are resonance forms, the only difference being the placement of the and/or nonbonding valence electrons o the atoms themselves occupy exactly the same place, and the connections and shape are the same a resonance hybrid is the single unchanging structure of the 2 individual forms (has characteristics of both) difficulty is representation on paper, not the molecule itself useful concept for things like benzene has 6 seemingly alternating I and II CC bonds, but its true structure is a hybrid w/ 6 equivalent CC bonds and symmetrical electron distribution (as shown on colored map) 2.5 Rules for Resonance Forms 1. individual resonance forms are imaginary (real structure is a composite/hybrid of the forms) 2. resonance forms differ only in the placement of or nonbonding electrons neither position nor hybridization of an atom moves an atoms -electrons of its II-bond lone pair on that atom (and vice versa) 3. they dont have to be equivalent ex: compounds containing a C=O, like acetyl CoA, can become anions by reacting w/ a base resulting anion has 2 resonance forms, one w/ C=O (charge on C) and one w/ C=C (chg on O) even though these arent equivalent, they both contribute to the overall hybrid o hybrid is closer to the more stable form (the one w/ charge on O in this case) 4. they obey normal rules of valency: octet rule for 2nd row atoms still applies (C has 4 bonds, 8 valence) 5. resonance hybrids are more stable than any resonance form the more resonance forms, the more stable a substance is b/c electrons are spread out over a larger part of the molecule and are closer to more nuclei 2.6 Drawing Resonance Forms in general, any 2-atom grouping w/ a p orbital on each has 2 resonance forms. X, Y and Z might be C, N, O, P or S and the * might mean that the p orbital on Z is vacant, that it contains a single electron or that it contains a lone pair the forms differ simply by exchange in position of II-bond and the * from one end of the grouping to another 2.7 Acids and Bases: The Brnsted-Lowry Definition a BL acid donates a proton and a BL base accepts a proton o proton = H+ ion, b/c loss of the valence e from a neutral H leaves only the H nucleus (a proton) when HCL dissolves in H2O, HCL acts as an acid (donates H+) while a water acts as a base (accepts it) H3O+ H3O+ is the conjugate acid of H2O and Cl is the conjugate base of HCl Water can act either as an acid or base, depending on the circumstance (rxn w/ NH 3, yields NH4+ and OH) 2.8 Acid and Base Strength acids differ in their ability to donate H+ stronger acids react almost completely w/ H 2O and weaker ones react only slightly the acidity constant (Ka) for acid-dissociation equilibrium describes exact strength of an acid, HA, in H 2O solution o remember that [] is C in mol/L and [solvent] is ignored in the equilibrium expression stronger acids have their equilibria toward the right and thus have larger Ka; weaker toward left w/ smaller Ka enormous range: from about 1015 for strong to 1060 for weak strength is normally expressed in pKa (logKa) o stronger acids have smaller pKa and weaker have larger there is an inverse relationship between acid strength and the strength of its conjugate base

strong acids have weak CBs and vice versa (strong acids lose H+ easily so its CB holds on weakly)

2.9 Predicting Acid-Base Reactions from pKa Values H+ will always go from the stronger acid to the stronger base o That is, an acid donates a proton to the CB of a weaker acid and that weaker acids CB will remove the proton from a stronger acid o Since water (pKa=15.74) is weaker than acetic acid (pka=4.76), an OH ion holds a proton tighter than an acetate ion OH ion will therefore react w/ acetic acid to yield acetate and H 2O The product CA in an acid-base rxn must be weaker/less reactive than the starting acid (same goes for CB/base) 2.10 Organic Acids and Organic Bases Organic acids are characterized by presence of positively polarized H atom 2 kinds o Those w/ H bonded to O like methanol and acetic acid Acidic b/c the CB is stabilized by having its neg. charge on a strongly EN oxygen CB of acetic acid is stabilized by resonance o Those w/ H bonded to a C next to a C=O like acetone and acetyl-CoA (O=CCH) Acidic b/c the CB is stabilized by resonance One of the resonance forms stabilizes the neg. charge by placing it on EN oxygen

Carboxylic acids, containing CO2H, are abundant in all organisms and are involved in metabolism

o At typical cell pH (7.3), theyre usually dissociated and existing as carboxylate anions, CO2 Organic bases are characterized by presence of an atom w/ a lone pair that can bond to H + N-containing compounds like methylamine are the most common (involved in metabolism) o O-containing compounds can also act as bases in rxn w/ sufficiently strong acid (some act as both acids and bases depending on the circumstance like water, methanol and acetone) Amino acids (contain NH2 and CO2H) make up proteins o Zwitterions: doubly charged form arising b/c AAs have both acidic/basic sites internal acid-base rxns

2.11 Acids and Bases: The Lewis Definition Broader and more encompassing b/c its not limited to substances that donate/accept protons Lewis acids accept electron pairs and Lewis bases donate them o The donated pair is shared between the acid and the base in a covalent bond Lewis acids, since they accept electron pairs, must have either a vacant low-E orbital or a polar bond to H so it can donate H+ (which has an empty 1s orbital) o Metals like Mg2+ can be LAs b/c they accept a pair when bonding to a base o Compounds of group 3A elements like BF3 are LAs b/c they have unfilled valence orbitals Curved arrows always mean movement of a pair of electrons Lewis bases are more similar to BL bases o H2O, w/ its 2 lone pairs on O, acts as an LB by donating one to H+ forming H3O+ Most N and O-containing organic compounds can be LBs b/c they have lone pairs Compounds w/ multiple atoms w/ a lone pair can react at multiple sites (usually tends towards one) 2.12 Noncovalent Interactions between Molecules Collectively called inter-molecular forces, van der Waals forces or noncovalent interactions Dipole-dipole forces occur between polar molecules b/c of electrostatic interactions among dipoles o Can be attractive or repulsive (like or opposite charges) Dispersion forces occur between all neighboring molecules b/c electron distribution is constantly changing

o Distribution is likely to be non-uniform at any given instant temporary dipoles tiny attractions o Collectively this can be strong enough to increase density and change a substances phase H-bonds are the most important attraction between H bonded to O or N and a lone pair on another O or N o Very strong dipole-dipole involving polarized OH or ON bonds o Cause water to be liquid rather than gas at extraordinary temps; hold enzymes in necessary shapes; cause pairing and coiling of DNA stands Hydrophilic=water-loving; hydrophobic=water-fearing o Hydrophilic substances usually have ionic charges or polar OH groups so they can form H-bonds o Hydrophobic substances dont have groups that can form H-bonds limited to weak dispersion

Chapter 3 Organic Compounds: Alkanes and their Stereochemistry

3.2 Alkanes and Alkane Isomers Long chains of singly bonded carbons ( overlap of an sp3 from each) Saturated hydrocarbons b/c they contain only C and H and have the maximum # of H due to single C bonds General formula CnH2n+2 Sometimes referred to as aliphatic compounds Straight-chain alkanes have C all in a row and branched-chain alkanes are branched Constitutional isomers have differently connected atoms Straight-chain are named according to the # of C they contain o Meth-(1), eth-(2), prop-(3), but-(4), pent-(5), hex-(6), hept-(7), oct-(8), non-(9), dec-(10), undec-(11), dodec-(12), tridec-(13), icos-(20), triacont-(30) 3.3 Alkyl Groups Alkyl groups are what youd have if you removed a hydrogen from an alkane they are not stable along; they are simply parts of larger molecules Straight-chain alkyl groups are generated by removing a H from an end carbon and branched alkyl groups are generated by removing a H from an internal carbon Primary carbons are attached to 3 H and 1 R; secondary have 2 R groups; tertiary have 3 and quaternary have 4 o citric acid is a tertiary alcohol b/c its alcohol group (OH) is on a C that is bonded to 3 other carbons o these prefixes refer to the number of other carbon atoms attached to the branching carbon o can also speak about H atoms in this way secondary H are attached to secondary C (no quaternary) 3.4 Naming Alkanes chemical names in the IUPAC system have 4 parts: prefix, parent, locant and suffix o prefix specifies location/identity of various substituent groups o parent selects a main part of the molecule and tells how many carbons there are in it o locant give location of primary functional group o suffix IDs the primary functional group all but the most complex branched-chain alkanes can be named by these steps (sometimes 5) 1. find the parent hydrocarbon a. longest continuous chain b. if 2 chains of equal length, choose the one w/ more branch points 2. number the atoms in the longest chain a. start at the end nearer the 1st branch point and number each carbon in the parent chain b. if there is branching equal distance from both ends, start at the end nearer the 2nd branch point 3. ID and number all substituents a. Assign a # (locant) to each substituent to find its point of attachment C3, C4 etc. b. If there are 2 on the same carbon they have the same number 4. Write the name on as a single word using a. Use hyphens to separate the different prefixes and commas to separate numbers b. If 2+ substituents are present, cite them in alphabetical order

If 2+ identical substituents are present on the parent chain, use a multiplier (di-, tri-, tetra- etc) but dont use them for alphabetizing 5. Name a branched substituent as if it were a compound a. Start numbering at point of attachment and ID it normally b. It is alphabetized according to the first letter of its complete name, including any numerical prefix c. Set off in parentheses when naming entire molecule Some of the simpler branched-chain alkyl groups have nonsystematic common names o The nonhyphenated prefix iso- is considered part of the name for alphabetizing, but the hyphenated and italicized sec- and tert- are non (isopropyl is under i and sec-butyl is under b)

c.

Chapter 4 Organic Compounds: Cycloalkanes and their Stereochemistry

4.1 Naming Cycloalkanes Saturated cyclic hydrocarbons are called cycloalkanes or alicyclic (aliphatic cyclic) compounds They have the general formula CnH2n and can be represented as polygons in skeletal drawings (triangle for propane, square for butane etc.) For most compounds there are only 2 steps: 1. Find the parent count the # of C atoms in ring and number the longest chain a. If the # of C in the ring is equal to or greater than the substituent it is named as an alkyl-

substituted cycloalkane b. If the # of C in the largest substituent is greater than the number in the ring, its named as a cycloalkyl-substituted alkane 2. Number the substituents and write the name a. For an alkyl-substituted cycloalkane, choose a point of attachment as carbon 1 and number the substituents so that the 2nd has as low a number as possible (if ambiguity go for fourth, fifth etc.)

b. When 2+ different alkyl groups could receive the same numbers, number them alphabetically ignoring numerical prefixes such as di- and tri-

c.

Treat halogens just like alkyl groups

# ( 4 3 2 3 2

Number of e- pairs bonding # non-bonding bonds) (unshared) 0 1 2 0 0

total 4 4 4 3 2

hybridization sp3 sp3 sp3 sp2 sp

shape tetrahedral trigonal pyramidal angular (bent) trigonal planar linear

bond angle 109.4 <109 <109 120 180

example CH4 NH3 H2O BF3 BeH2