Altius Ochem 1

Alcohol and Hydroxyl (Alkoxy)

-OH or hydroxyl group attached to organic compound OH on own or as radical is just Hydroxyl group but when bonded to C it is less reactive and acts as alcohol Alkoxy: when alkyl (CH based) group is bonded to an O atom

How to Draw Resonance Structures?

1. Atoms NEVER move 2. single bonds NEVER move (only electrons in pi bonds move) 3. all structures must OBEY OCTET RULE (except for first 4 elements, B, Al, and elements in 3rd period or higher which have d orbitals) 4. all structures must have same number of valence electrons: electrons don't disappear/appear later, resonance is that electrons are delocalized but still in structure 5. arrows denote electron flow, only lone pair, double bond, or triple bond electrons will flow in resonance check the formal charges valence in ground state - valence in bonded state it is helpful to draw Hydrogens in for easy visualization of formal charge KHAN MCAT https://www.khanacademy.org/science/organic-chemistry/organic-structures/formal-charge-resonance/v/resonance-intro-jay Patterns to understand resonance https://www.khanacademy.org/science/organic-chemistry/organic-structures/formal-charge-resonance/v/resonance-pattern-jay

Converting Line Diagrams into Fischer Projections

1. Number Carbons 2. Identify Stereocenters (R) (S) write these down on page Fischer projections are for molecules with steroecenters, otherwise not really worth making a fischer projection 3. draw Carbon skeleton vertical line (go into page) # the Cs draw cross for each stereocenter C just place atoms on steroecenter (don't worry about getting it all right just get on the page) 4. figure out stereocenter either go 1-2-3-4 and flip (Horizontal out of page towards, Vertical into page) or mentally flip structure 90 to right or left (towards #1 or #1 is coming out at you eclipsing C, vertical lines into page now pop up to left or right and H or #4 is in back) https://www.youtube.com/watch?v=VGRARhqr3tI

2 types of Coordinate covalent bonds seen

1. nucleophile with lone pair abstracts proton NH3 + HCl -> NH4 + Cl- NH3 binds a fourth H, but the electron belonging to Hydrogen stays with Cl. (so NH3 donates both electrons that now form covalent bond between N and 4th H) 2. metal coordinated with one or more molecules that have lone pairs [Fe(NH3)4]2+ or [Co(NH3)6]3+ look like ionic compounds however amine doesn't have a charge (so can't be ionic) well then how are the amines attached to metals? via coordinate covalent bonds covalent bonds are not ionic bonds they are formal charges that have lone pairs becoming bonds (changes formal charge without changing the number of electrons) AMAZING VIDEO SHOWING DOT STRUCTURES AND FORMAL CHARGE EASILY https://www.youtube.com/watch?v=_wIoUjZfIlI

the 3 Exceptions to Octet rule

1. too few electrons/electron deficient the first 4 elements up to Boron never obtain octet H (1) when bond max of 2 He (2) has noble gas Li (1) can lose to obtain He config Be (2) when bond max of 4 B (3) when bond max of 6 2. too many electrons/expanded octets thanks to 3d orbital, elements in period 4 and beyond can expand their valence shell and accommodate more than 8 electrons SF2 Sulfur fulfills octet with 2 partners (S has ve of 6e-) but thanks to 3d orbital SF4 with S having 10 ve- SF6 with S having 12 ve- P has ve- of 5 (only needs 3 partners to have 8ve PO4 3- (3 oxygens have single bond, 1 O has double bond) 10ve 3. Lonely electrons/Free radicals stable molecules have pair of electrons class of compounds with odd number in valence shell: Free radicals at least 1 unpaired electron in valence shell therefore all odd number of electrons tend to be free radicals Nitrogen (IV) Oxide or NO2 Molecular Oxygen O=O (each O has 2 l.ps.) and can become a radical by attracting 1 e- each (superoxide and peroxide) https://www.thoughtco.com/octet-rule-explanation-in-chemistry-606457

sp shape and angle

2 partners LINEAR 180

sp2 shapes and angles

3 partners TRIGONAL PLANAR 120 1 l.p. 2 partners BENT v shaped

Excellent system to tell if two molecules are enantiomers or same.

3 steps. 1. Check connectivity of each (are they bonded to same 4 partners) (constituitional isomers have different connectivity, stereoisomers and enantiomers have same connectivity) 2. Check R/S for each stereocenter (enantiomers have all chiral centers opposite, diastereomers have 1 or more chiral centers the same) 3. Double check for Symmetry (only possible when 2 or more stereocenters) if opposite stereocenters and symmetry then its a Meso compound (C2 is R and C4 is S and symmetrical around middle carbon) symmetry can exist between bonds. SEE IT TO BELIEVE IT https://www.youtube.com/watch?v=dpgq-cvZiAo I WANT TO BELIEVE https://www.youtube.com/watch?v=6ew_t24Pd_w DON't MESS WITH MESO https://www.youtube.com/watch?v=cljiNbg7CKE

sp3 shapes and angles

4 partners TETRAHEDRAL 109.5 1 l.p. 3 partners TRIGONAL PYRAMIDAL (center forms top tip and 3 partners form 3D base) <109.5 2 l.p. 2 partners BENT <<109.5

sp3d shapes and angles

5 partners TRIGONAL BIPYRAMIDAL 90/120 imagine trigonal planar (3 partners) with linear (2 partners) through center linear parts serve as tip while trigonal planar serves as base resulting in 2 pyramids trigonal part has 120 angle linear is interrupted by trigonal so instead of angle 180 it is 90 all 3 l.p are taken from trigonal planar 1 l.p 4 partners SEESAW linear with 2 of trigonal planar 2 l.p 3 partners T-SHAPED linear with 1 of trigonal planar 3 l.p 2 partners LINEAR (all of trigonal planar is replaced by l.p)

sp3d2 shapes and angle

6 partners OCTAHEDRAL 90 think of a cross (4 points) and linear (2 points) through the center l.p are taken away from linear, cross left alone (though since all have 90 degrees, any side can be visualized as linear, just remember that 2nd l.p is taken from 180 point away for max distance) 1 l.p 5 partners SQAURE PYRAMIDAL remaining linear serves as tip while cross serves as base 2 l.p 4 partners SQAURE PLANAR all of linear is taken away, just left with cross and looks like square when traced partner to partner

How do we predict the max number of optically active stereo-isomers for any compound?

A stereoisomer that is chiral rotates plane polarized light in one specific direction. Either rotate light left or right. (this is not R or S which deal with atomic weight) (light rotation is designated D or L (+ or -) an enantiomer will be either R or S, D or L, but not every R gives D some Rs are S NOTICE THERE ARE 2 OPTIONS (either R or S, either D or L) 2*2*2 for each chiral center/stereocenter 2^n where n is number of chiral centers in a fisher projection each cross is a stereocenter/chiral center (4 different partners) in a 6 C sugar there are 4 stereocenters each can be R or S (2 options) 2*2*2*2 possible number of optically active stereoisomers

What are Anomers?

ANOMERS are diastereomers they only differ in spatial orientation at anomeric carbon of RING STRUCTURE if anomeric OH/OR group and the CH2OH group are on SAME side of ring = BETA if anomeric OH/OR group and CH2OH on OPPOSITE side of ring = ALPHA cyclization creates a new stereocenter which can have two possible diastereomers at the anomeric Carbon DEPENDING ON DIRECTION OF ATTACK. the two possible stereoisomers that can result are anomers for a linear sugar (as in fisher projection) to form a ring, have to turn aldehyde or ketone into a hemiacetal or hemiketal (OR-C-OH) HOW as in from what direction the OH on last chiral C attacks the Carbonyl carbon or first C (making the ring) determines which diastereomer the anomeric carbon has WHY THE LAST CHIRAL C? because it creates the most stable product, usually a 6 or 5 carbon ring Steps: 1. OH on last chiral C loses H and bond moves as lone pair onto O 2. nucleophile O- attacks carbonyl carbon (partial positive) 3. electrons in double bond move up to carbonyl O and attracts a H+ becoming an OH THE CARBONYL O now OH is the anomer that can be in an up or down (R or S)configuration depending on how last chiral C's O attacked the carbonyl this is reversible, and once it returns to linear form it can rotate and reform to make the other diastereomer (technically another molecule) Therefore because both configurations are possible for the same stereocenter we call it anomeric WHAT ARE THE DESIGNATIONS? like geometric isomers we compare whether two partners are on the same or opposing sides. C5 with OH (now as OR to C1) and CH2OH on upside C1 with O (now as OH) in either Up or Down if former O from carbonyl is on same side as CH2OH = BETA if former O from carbonyl is on opposite side as CH2OH = ALPHA if C1 has same stereochemistry as last chiral C = BETA if C1 has opposite stereochemistry as last chiral C = ALPHA https://www.youtube.com/watch?v=UPgpYH9ZtMA

Bonding Sigma bonds vs Pi bonds which is stronger? Why?

All bonds are result of unpaired electrons: one orbital has 1 e- and bonds to another orbital with 1 e- together they share 2 e- filling both orbitals (stability) sigma bonds are stronger than pi FIRST BOND FORMED BETWEEN TWO ELEMENTS IS ALWAYS A SIGMA BOND sigma bonds are direct head to head overlap of two atomic orbitals pi bonds are side-to-side overlap SECOND AND THIRD BONDS ARE PI BONDS FORMED ABOVE AND BELOW THE PLANE OF ATOMS (aka side-by-side bonding that prevents relative rotation) pi bonds require atoms to be close together, as radius of either atom increases, p orbitals are spread further apart resulting in less overlap = weaker bond = easier to break= higher energy WHICH HAS A STRONGER BOND: C=N or C=O? C=O, O has shortest radius which means smallest distance between atoms the key to bonds is electron sharing relative to + charge nucleus. closer electron is to nucleus, the stronger the attraction and the more energy required to take electron away sigma bonds have high density of electrons as close to nucleus as possible, pi bonds have electron density above or below, it is easier to push or pull electrons away = less stability = less strength = more energy (to do something which is break) Triple bonds > Double bonds > Single bonds pi bond is weaker than sigma, but sigma+pi bond is stronger and sigma+pi+pi is strongest. strength or stability denotes distance (closer atoms are, the more energy it takes to push them apart) so each additional bonds brings atoms closer together the pi bonds will be the first to break having the highest potential. further distance (outside of plane of atoms) = weaker bond strength = lower stability = higher reactivity sigma bonds have highest density at closest distance, strong bonds = high stability = low reactivity STRENGTH IS DETERMINED BY DEGREE OF OVERLAP OF ORBITALS more overlap = closer distance sigma bonds between nuclei form first and that locks atoms together, then orbitals that form pi can partially overlap (weaker bond)

Acetal/Ketal and Hemiacetal/Hemiketal

C=O to HO-C-OR (hemi) to H2O+-C-OR to C=OR+ to OR-C-OR (full) this is under equilibrium, so acetal/ketal can easily go back to carbonyl form. This is the basis of sugars forming cyclic compounds vs straight chains acetal is related to aldehyde so C is bonded to 1R 1H ketal is related to ketone so C is bonded to 2R hemi is the transition period where OH and OR

isopropyl

CH3 - C - CH3 propyl = 3 carbons iso = when all but 1 C form a continuous chain

sec-butyl

CH3CH2-C-CH3 or 2C - C - 1C butyl = 4 carbons secondary = attached to 2 Cs . methyl and ethyl on either side

Carbonyl, Acyl, Aldehyde, and Ketone and Acetyl

Carbonyl: C double bond to O Acyl: C double bond to O, C is also bonded to 1 R group, it is a general term and is in aldehydes and ketones Aldehydes: Carbonyl/Acyl at end of chain, R-CHO, key part is Hydrogen single bonded to Carbonyl carbon Ketones: Carbonyl/Acyl in interior of chain, R-CO-R Acetyl: R-Carbonyl-CH3

Types of ISOMERS

Conformational Structural Stereoisomers Enantiomers Diastereomers Meso

What is a Dipole Moment? How is it made?

Dipole moment is when charge is unevenly distributed in a bond this creates a net positive (electron starved) and net negative (electron rich) region Caused by atoms of 2 different electronegativities one will pull more and have higher electron density than the other HOW DO WE CALCULATE DIPOLE MOMENT? dipole moment = charge * distance greater distance means more separation of charge, that makes one atom more electron rich and other more electron starved, hence greater dipole moment the charge is amount (either positive or negative) one electron and one proton have equal magnitude charge 1.6*10^-19 WHAT DO THE ARROWS REPRESENT? they point to where electrons are attracted to (the more electronegative elements) WHAT IS A NET DIPOLE? describes the whole molecule's polarity Need to know molecule's GEOMETRY when there are 2 bonds, and 2 dipole moments they form a vector that adds together either to cancel or increase just like force vectors in pic, CO2 shows when dipole moments oppose each other and cancel out so that the overall molecule has no dipole then H2O shows when dipole moments add together. the horizontal left and right components cancel out, but the vertical components add up together but be careful because different elements will have different magnitudes of dipole moments KHAN MCAT https://www.khanacademy.org/science/organic-chemistry/gen-chem-review/electronegativity-polarity/v/dipole-moment

Draw the Six conformers of butane and rank them according to their relative stability

Draw a newman projection look along C2-C3 bond C1 and C4 positions Conformations stability depends on keeping electron groups as far apart as possible. the closer the bulkier groups are, the more repelling = less stability the farther away bulkier groups are, the less repelling = more stability

What are Epimers?

EPIMERS are diastereomers diastereomers that differ at ONLY 1 chiral stereocenter nice to have specific term when only difference is 1 stereocenter, to be an enantiomer ALL stereoisomers have to be opposite to be a diastereoisomer at least 1 many pairs of carbohydrates are epimers (glucose and galactose in fisher projection only differ on C4 (see One Note: Diastereomers)

Bond Polarity

Electronegativity Dipole Moment

Describe forces responsible for the strength of a bond. What is the relationship between potential energy and bond length?

Electrostatic forces Coulombs law: F= kq1q2/r^2 attraction of electrons to positive nucleus repulsion of like charges electrons to other electrons Potential Energy is energy stored in distance higher distance or further apart = more potential energy closer distance = less potential energy short bond lengths have less Potential Energy (stable) (not reactive) long bond lengths have high PE (not stable) (reactive) the bond represents lowest possible potential energy sweet spot increasing or decreasing bond length would raise the energy of the bond and therefore weaken it WHY INCREASE OR DECREASE FROM SWEET SPOT? because 2 electrostatic force interactions nucleus- electron (attraction) electron- electron (repulsion) both need to be properly balanced hence sweet spot

Why do we measure light rotation to differentiate enantiomers?

Enantiomers are isomers with the same # of elements and same type of connectivity. They only differ in 3D spatial arrangement. this means they have identical physical properties: density, boiling points, melting points, and refractive indeces (same degree of rotation) THE ONE PHYSICAL PROPERTY IN WHICH ENANTIOMERS DIFFER: THEIR ABILITY TO ROTATE PLANE-POLARIZED LIGHT plane polarized: normally light is in every, any, and all directions, but if use filter that lets in only one plane of light in a single plane (up-down only or right-left only) any chiral compound will rotate light that passes through them Enantiomers will differ in the DIRECTION Dextrorotary (D) or + rotates light clockwise or to the right Levorotary (L) or - rotates light counterclockwise or to the left chiral compounds will have specific rotation that is equal in magnitude but opposite in direction (D) and (L) do NOT CORRELATE with R/S configurations R and S is in terms of atomic weight D and L is in terms of light rotation optical activity is not related to atomic weight a compound with D optical activity may be in R or S configuration

Rotation of Plane Polarized Light

Enantiomers rotate plane-polarized light. R and S enantiomers rotate this light to the same degree but in opposite directions. R and S can rotate light clockwise (D or +) R and S can rotate light counterclockwise (L or -) why does this matter? because enantiomers have nearly identical physical chemistry (not the same and differences have meant death in certain drugs ): same atoms, same connectivity, only difference is arrangment in 3D space. enantiomers have the same melting point, boiling point, density the only way to distinguish enantiomers is by which direction they rotate plane polarized light. the magnitude of rotation is identical, only the direction is opposite

Carboxylic acid derivatives: Ester, Amide, Anhydride (and Acyl)

Ester: carbonyl - OR just as ether is R-O-R, focus on OR; the ester is a carbonyl with carbon bonded to OR Anhydride: carbonyl - O - carbonyl Amide: carbonyl - NHR amine is N to 3 partners (H or R), amide is N to 3 partners where 1 is a carbonyl Acyl: if carbonyl-R or X (amides esters, ketones, aldehydes are all acyl)

What are Geometric Isomers?

GEOMETRIC ISOMERS are diastereomers cis/trans: are groups are on the same side or different. There is no difference in atoms or connectivity only place in space cis and trans or follow E/Z convention prioritize numbering based on molecular weight (FOLLOWS Cahn Ingold Prelog Molecular weight priority assignment) if highest priority on same side = Z if highest priority on opposite sides = E cis=same side trans=opposite side usually used for double bonds that can't rotate, triple bonds have one partner and are linear anyway REMEMBER: Cis isomers often HAVE DIPOLE moment Trans isomers usually do NOT have dipole moment (Cis can have intermolecular attraction) Cis isomers HAVE STERIC HINDRANCE Trans isomers DON'T have steric hindrance (Trans are more stable/ harder to break down)

What are the 3 types of Diastereomers?

Geometric Isomer (cis/trans and E/Z) Epimer (only one stereocenter is different/opposite in two different molecules) Anomer (same Carbon can switch between two diastereomers forming R but then reverting back and forming S another time)

What is the percent "s" character of the hybrid oxygen orbital in water?

H-O-H 2 sigma bonds and 2 lone pairs steric number of 4 (or 4 potential partners) sp3 s is 1/4 of this hybridization p is 3/4 so 25% s character

Hydrazine

H2N-NH2 focus on N-N H can be substituted to R Very reactive (explosive) wants to react to shed Hydrogens and form elemental Nitrogen makes it powerful reducing agent (gives its electrons. reduction is the receiving of electrons so the agent gives)

WHICH VERSION of 2,3-dibromo-2-butene would have higher heat of combustion? higher boiling point?

HEAT OF COMBUSTION depends on the thermodynamics of reactant vs product it is heat released when combusting (Hydrocarbon + O2 -> CO2 + H2O) whichever CIS or TRANS has the highest energy or least stable will have the higher heat of combustion CIS has steric hindrance where highest priority is on same side they are closer together increasing their energy level. BOILING POINT depends on strength of intermolecular forces. Cis does have molecular dipole moment while trans version would be neutral the dipole moment gives + and - ends increasing intermolecular interaction Cis BP > Trans BP NOTE that this is different in Melting Point. Melting point (Solid -> Liquid) depends on intermolecular interaction sure, but the larger factor is STACKING ability or how close can two molecules be. trans molecules can stack on top easily and closely cis molecules are limited in how closely they can stack. THE CLOSER MOLECULES ARE TO EACH OTHER AS SOLIDS, THE HIGHER THE VAN DER WAALS FORCES = MORE ENERGY REQUIRED TO DISRUPT/PUSH APART therefore Trans MP > Cis MP

What is molecular shape and bond angles determined by?

Hybridization (different orbitals mix together) Valence Shell Electron Pair Repulsion: electron pairs try to be as far away as possible lone pairs unbonded are closer to nucleus and give greater repulsion to partners this means l.p push partners closer together decreasing their angle

Alkanes, Alkenes, Alkynes, (Alky)

Hydrocarbons -ane: single bond -ene: double bond -yne: triple bond alkys are just Carbon and Hydrogen

MCAT exceptions to octet

Hydrogen and Helium: stable with 2 e- in valence shell Boron and Aluminum: stable with 6e- in valence shell Atoms in THIRD PERIOD or higher can accept more than 8 electrons common ex: PCl5, SF6, PO4-3, SO4-2 10, 12, 10, 12

Imine (and Enamine)

Imine: C=NR instead of C=O start with C=O, Acid makes Carbon more electrophilic/more reactive (by donating H to nucleophilic O making O+ which attracts electrons in double bond to lone pair on O making single bond OH, but C will be + and unstable) therefore acid is a catalyst to make Carbonyl more reactive then to make resulting OH into better leaving group amines (RNH2) are nucleophilic (Nitrogen with lone pair wants positive) donates lone pair to C and C=OH becomes single bond OH takes another H becoming -OH2+ (excellent leaving group) Amine lone pair moves to form double bond between N and C. Enamine: C=C-NRR if HNRR (secondary amine) then after attacking carbonyl carbon, lone pair from N comes down to form double bond and N+ alpha carbon (c adjacent to carbonyl carbon, will be very stable thanks to resonance: double bond can move back to lone pair on N making carbonyl C positive) therefore a nucleophile can take away H and lone pair forms on alpha C making it negative. the lone pair on alpha carbon forms the double bond between Carbons https://www.masterorganicchemistry.com/2011/09/24/reagent-friday-hydrazine-nh2nh2/#comment-395365

Formulas, Depictions and 3D representations

LEWIS DOT LINE-BOND WEDGE-DASH CONDENSED FORMULA FISCHER PROJECTION NEWMAN PROJECTION BALL AND STICK SPACE FILLING MODEL

IUPAC Nomenclature

MCAT doesn't require to name complex organic compounds, neither will the answer be select the correct drawing. Need to be able to draw structure given name to answer question about reactivity. NAMING IS NOT THE FOCUS, INTERPRETING AND DRAWING OUT IS prefixes: meth- 1C eth- 2C prop- 3C but- 4C pent- 5C hex- 6C hept- 7C oct- 8C non- 9C dec- 10C ring means cyclo- Parenthesis around side chains (if using systematic) instead of isobutyl cyclopentane, (2-methyl propyl) cylopentane note in side chains, C bonded to parent is always #1 RULES: 1. longest Carbon chain (if tie most substituted is parent, lowest number sub is preferred) 2. terminal C closest to substituent/functional group is #1 3. substituents are ALPHABETICALLY named, with number identifying C attached to 4. if more than one of same substituent is present, use prefixes di, tri, tetra, etc (also repeat the number: 4,5-di isopropyl-2,2 dimethyl octane) or 4,5-bis(1-methyl ethyl) - 5. hyphens are before and after subs/functional group numbers. Not between standard prefixes 6. do not consider prefix of number (di,tri) or if it includes hyphen(sec- tert-) when alphabetizing do alphabetize other prefixes for common names (isopropyl, isobutyl) https://www.khanacademy.org/science/organic-chemistry/bond-line-structures-alkanes-cycloalkanes/naming-alkanes/v/common-and-systematic-naming-iso-sec-and-tert-prefixes PRACTICE https://www.khanacademy.org/science/organic-chemistry/bond-line-structures-alkanes-cycloalkanes/naming-alkanes/v/organic-chemistry-naming-examples-2

Amine

N with 3 partners (derived from ammonia NH3) can be H or R groups participate in hydrogen bonding act as bases the more substituted = higher inductive effect = higher basicity

What are Enantiomers? (stereoisomer)

Non-Identical, Non superimposable mirror images must have one chiral center otherwise the 3D space will not matter or be different CHIRALITY: "handedness" any atom to four different GROUPS (not always atoms, if group is different but first atom is same = still chiral) are chiral and can result in different molecule depending on arrangement in 3D space mirror image = no matter how much I turn or rotate I can never get it to look like its mirror image (because the fingers of the hand are unique. I can put 5 on 5 easily but never get it to be identical (top=top) in a 4 partner molecule, no matter how we rotate or conform, at least 2 partners will be out of place (that means we can switch 2 partners to make a different enantiomer) chirality means it is different molecule achirality means it is the same molecule in a flipped conformation PRINCIPLE OF CHIRALITY https://www.khanacademy.org/science/organic-chemistry/stereochemistry-topic/chirality-r-s-system/v/chiral-achiral-jay https://www.khanacademy.org/science/organic-chemistry/stereochemistry-topic/chirality-r-s-system/v/introduction-to-chirality PRACTICE https://www.khanacademy.org/science/organic-chemistry/stereochemistry-topic/chirality-r-s-system/v/chiral-examples-1 https://www.khanacademy.org/science/organic-chemistry/stereochemistry-topic/chirality-r-s-system/v/chiral-examples-2

What is: observed rotation specific rotation plane polarized light optically active vs inoptically active racemic mixture

OBSERVED ROTATION is what is experimentally seen. It is the rotation caused by a stated concentration and path length. (not comparable with other substances) SPECIFIC ROTATION is specific/intrinsic to the compound. It equalizes concentration and path length allowing comparison with other substances altuis observed is simply degree to which a sample rotates plane polarized light. however that rotation is not a universal constant for a particular molecule. It varies depending on concentration and length of tube chosen. specific takes factors of concentration and tube length into account by dividing observed rotation by tube length and concentration. This is like "observed rotation per length, per concentration unit" PLANE POLARIZED LIGHT: is light that only goes through one plane (up and down or left and right but not both) unpolarized light goes anywhere and everywhere so we take a filter that only lets in a single plane. this lets us measure any rotation that occurs to it as it passes through compound OPTICAL ACTIVITY: chiral = rotate light achiral = no rotation Any molecule that is chiral and not symmetrical will rotate light but if there is symmetry, the molecule will be achiral and not rotate light even if it has opposing chiral centers (where D and L cancel out). (Consider the whole molecule) enantiomers are optically active. and will rotate light with the same magnitude but in opposite directions RACEMIC MIXTURES: when both enantiomers are present in solution they oppose each other's rotation. D enantiomer is rotating light by 60 to right L enantiomer is rotating light by 60 to left racemic mixtures is a 50/50 mix of both enantiomers in absolute configuration (R and S) and will have an observed rotation of 0. CAN AN OPTICALLY INACTIVE COMPOUND ROTATE PLANE-POLARIZED LIGHT? if it has even number of opposing chiral centers (R = S), it can rotate light internally, the net effect of entire molecule however is no rotation optically inactive means no net rotation from plane polarized light before to after the tube.

Mesyl/Tosyl

OH is strong base = bad leaving group convert to good leaving group = need weak base take strong acid and use conjugate H2SO4 is strong acid HSO4- is weak base stabilized by resonance HSO4- is good leaving group but problem cause still an acid (OH) if we swap in methyl (CH3) for acidic portion (MESYLATE) or we sub toluene (6C aromatic ring with methyl) (TOSYLATE) with the same leaving group ability this solves: great leaving group without acidic proton to react with nucleophiles Alcohols: there are times you need to get rid of them. Except there's one problem. They're terrible leaving groups. Remember that good leaving groups are weak bases? Hydroxide ions are strong bases, and therefore very poor leaving groups. LEAVING GROUPS: accept lone pair of electrons as bond between it and neighbor is broken. if stable with extra lone pair, the better it is as leaving group acids accept lone pairs bases donate lone pairs therefore weak bases are good leaving groups WHY weak bases instead of strong acids? H-A into A-, A- is conjugate base that ACCEPTED lone pair and bond is broken it is a base acting in reverse and accurately describes leaving groups. the more stable A- is the greater the equilibrium constant favoring dissociation to make A-. good leaving groups are conjugates of strong acids H3O+ -> H2O HI -> I- HBr -> Br- the stronger the acid the weaker the conjugate base However there's a way to turn the OH group into a good leaving group - if you can convert it into a weaker base. OH is very strong base, H2O is weak base, but turning OH -> H2O involves Sn1 which rearranges and scrambles steroecenters and can mix enantiomers into racemic mixture. So how do we convert alcohols into good leaving groups while keeping arrangment the same (for pure substituition)? One practical way this is done is with the sulfonates p-toluenesulfonylchloride (TsCl) and methanesulfonylchloride (MsCl). Treatment of an alcohol with TsCl or MsCl, usually in the presence of a weak base such as pyridine, results in the sulfonate esters. Conversion to the sulfonate esters does one thing: the conjugate bases - toluenesulfonate and methanesulfonate are now extremely weak bases, since they're heavily stabilized by resonance. Weak bases, you say? That makes them great leaving groups. And you are right. The sulfonate esters participate easily in reactions such as substitution and elimination reactions. AMAZING RESOURCE TO UNDERSTAND LEAVING GROUPS: https://www.masterorganicchemistry.com/2011/04/12/what-makes-a-good-leaving-group/ TOSYLATES AND MESYLATES AS LEAVING GROUPS FOR OH AND WHY https://www.masterorganicchemistry.com/2015/03/10/tosylates-and-mesylates/

Which bond limits Rotation?

Pi bonds are formed above and below the plane, for one to rotate is to break these bonds sigma bonds being directly inbetween nucleuses, allow rotation without disrupting the bond

Nitro

R-NO2+ there is resonance between the 2 Oxygens and N is + attracting electrons to it. this makes R group or CH more acidic

Ether

R-O-R carbon group on "ether" side of Oxygen each R group is named ex diethyl ether ethyl methl ether methyl: 1C-O ethyl: 2C-O isopropyl: 3C-O tert-butyl: 4C-O phenyl: 5C-O https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Supplemental_Modules_(Organic_Chemistry)/Ethers/Nomenclature_of_Ethers

Nitrile

RCN C has TRIPLE BOND to N

What is the Cahn Ingold Prelog system and why is it useful?

Ranks groups or substituents according to molecular weight highest weight = 1 lowest weight = 4 we use this system to distinguish enantiomers into R and S (Absolute Configuration) once we put 4 in the back or into the page so its easier to see if molecule rotates clockwise or to the right (R) or counter-clockwise or to the left (S)

Bonds in Increasing Reactivity

Reactivity is how READILY a species will react in presence of a nucleophile or electrophile (this is in terms of electrostatic forces not acid bases or others) compare not distance, but the actual sigma and pi bonds pi bonds are held above/below sigma bonds are held inbetween it is easier to react with pi bonds then sigma bonds Alkanes (sigma) are very unreactive Alkynes (sigma+pi+pi) are way more reactive than single but slightly less reactive than Alkenes Alkenes (sigma+pi) are most reactive I GOT THIS WRONG SO REVIEW ME alkynes are slightly more stable than alkenes pi bonds in triple are more stable than pi bonds in double WHY ARE TRIPLE BONDS LESS REACTIVE THAN DOUBLE BONDS? triple bonds are sp hybridized (2 partners or a triple bond and single) double bonds are sp2 (3 partners or a double bond and two singles) higher s character pulls more tightly on those pi electrons in pi orbital, making them more centralized and therefore lower energy than pi electrons in sp2 hybridized

Finding Stereocenters (R)/(S)

STEREOCENTERS: all 4 partners are unique CH2 CH3 are NOT stereocenters due to 2 and 3 identical hydrogens all the "cross" points are stereocenters meaning have to be consistent with stereochemistry: what is relationship or else can possible give enantiomer HOW DO WE FIND (R) OR (S)? rank priority groups through ATOMIC NUMBER. highest is 1, lowest atomic number is 4 (usually H) if tie, go to what its bonded to and rank C1 H-C-OH C2 C1 is tied with C2, so look at what they are bonded too. C1 is CH3 (highest to lowest: H,H,H) C2 is CH(OH)C (highest to lowest: O,C,H) go down line until tiebreaker is reached. O>H so C2 is #2 and C1 is #3 H is #4 C (#3) (#4) H-C-OH (#1) C (#2) Draw circle from 1->2->3->4 its a clockwise circle (arrow going to Right) BUT WAIT THERE'S MORE remember that horizontal lines ARE TOWARDS YOU. that means H is towards you. we need to flip everything to put H in back, or merely reverse the direction. RIGHT in FISCHER BECOMES LEFT OR (S) LEFT in FISCHER BECOMES RIGHT OR (R) (because H is towards in fischer projections and needs to be flipped) OR CAN FLIP MOLECULE TO #1 (towards me) and put #4 in back and get correct orientation. (#2 is planar and up) (#3 is away from me and to right) this visualization makes it very easy to see R or S

Condensed Formula

Sequential order of bonding tricky to expand, but remember octet rule and ideal bonding PRACTICE https://www.youtube.com/watch?v=5qFxJsDaRtY

Bonds in Increasing Stability

Stability on MCAT means "THERMODYNAMIC STABILITY" lowest energy to do work is the most stable, strongest weak bonds have higher energy to do something (react/break bond and form something new) strong bonds have lowest energy and it takes more energy to break bond apart the closer atoms are the more stable triple is most stable single is least stable single<double<triple

What is a Stereoisomer

Stereoisomer: differ in spatial arrangement of atoms rather than order of connectivity differs from constituitional isomerism which is just different connectivity (different partners in different places) stereoisomers keep the same connectivity (same 4 partners to same atom) BUT differ in 3D spatial arrangement (how different atomic particles and molecules are situated in space around organic compound) an enantiomer is mirror image non-superimposable stereoisomer Chirality (handedness) is atoms with 4 unique partners that form a mirror image that is non superimposable when we flip a right hand and left hand on to same side they do CANNOT be superimposed, the 4 partners don't match Watch out for symmetry along atoms with 4 different groups. Symmetry would make superimposable and therefore the molecule NOT chiral. (the reason why need 4 unique partners is because symmetry is guaranteed if 2 are identical, but just because have 4 unique partners doesn't mean it's not symmetrical) Even with chiral centers, if I can segment the molecule so that left matches right then the molecule is symmetrical (the chiral centers are identical to each other) https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Supplemental_Modules_(Organic_Chemistry)/Chirality/Chirality_and_Stereoisomers

What are Conformational Isomers?

THESE ARE NOT TRUE ISOMERS because they are the SAME EXACT molecule. when single bonds rotate it technically is in a different orientation (conformation) can be staggered or eclipsed with adjacent NEWMAN PROJECTIONS CAN BE USED TO SHOW CONFORMATIONS AND COMPARE ENERGY whenever a question asks to compare conformational energy, draw a Newman projection strain comes from potential energy of being too close, SIZE MATTERS IN CONFORMATION ENERGY and since isomer is the lowest energy, then only the staggered form is considered and nothing else (no isomers) SINCE ITS THE SAME MOLECULE however if we can change the partners and add a Dueterium we have multiple staggered forms: anti and guache (still conformation) but whether the different conformations can be separated into multiple isomers depends on energy difference between the two. for conformations, the energy is different but not different enough to consider them different isomers

Relative Configuration

TWO MOLECULES HAVE THE SAME RELATIVE CONFIGURATION IF THEIR SPATIAL ARRANGEMENT IS IDENTICAL (R or S), BUT THEY HAVE ONE--AND ONLY ONE-- NON IDENTICAL SUBSTITUENT (Br instead of Cl) position of atoms or groups in space relative to something else in molecule absolute configuration is independent of atoms or groups elsewhere in molecule cis or trans is a relative configuration both D or L is the same relative configuration likewise if two groups are both facing the same direction (both out of the page or both into the page then same relative configuration) in a fisher projection both D or L is the same relative configuration http://www.chem.ucla.edu/~harding/IGOC/R/relative_configuration.html

Ranking Resonance Structures

UNDERSTAND in terms of stability: full octet > least formal charge > electronegative getting - formal charge full octet is most stable The structure that contributes the most is the one that: 1) Allows the most atoms to have a full octet 2) Has the least formal charge (no charge is the best, 1 is better than many) (likewise it is more stable to spread out charge density than have it all on one atom especially among similar electronegative atoms) 3) Places formal charge on atom most receptive to that charge most electronegative has - and least electronegative has + (oxygen with a - instead of Carbon with - Carbon with + instead of Nitrogen with +) the most electronegative is going to attract the most electrons, molecule is unstable otherwise RESONANCE GIVES STABILITY, if pi electrons can move and delocalize = more stability and a great way to predict acidity. Among similar species that both experience resonance, the more stable species will have the most possible resonance structures ClO4- is more stable than ClO3- because ClO4- has 4 resonance structures while ClO3- has 3

Valence bonding

Use periodic table Carbon and family is 4 electrons away from a full shell so it normally forms 4 bonds (tetravalent) Nitrogen and family are 3 electrons away from a full shell so it normally forms 3 bonds (trivalent) Oxygen and family are 2 electrons away from a full shell, so it normally forms 2 bonds (divalent) Chlorine and halogen family are 1 electron from a full shell, so it normally forms 1 bond (monovalent)

Vinyl, Allyl

Vinyl: H2C=CH- Allyl: H2C=CH-CH2- forms vinyl cations a bridge between both carbons to the same Hydrogen and + on H also allows conjugation and resonance (adjacent C can become +)

What is Resonance?

When electrons are delocalized in a molecule. they don't belong to any one molecule, but to seemingly all we best describe this with multiple structures (with delocalized electrons on specific elements) that give weighted avg of the actual resonant structure structures are "snapshot" of different arrangements of electrons that contribute to the "Actual Structure" "Actual Structure" is a WEIGHTED AVERAGE (hybrid) of all contributors and doesn't look like any of the individual resonance structures each snapshot contributes differently most stable = most contribution (looks more like resonant structure) least stable = least contribution stability depends on formal charges of all elements (what is more comfortable having delocalized electrons nearby) KEY UNDERSTANDING: the actual structure does NOT "resonante" back and forth between forms; it is a PERMANENT WEIGHTED HYBRID of all contributing structures How do we know? the bond length of resonant structures is smaller than a single bond but larger than a double bond and all bonds in ion are the same length. bond order is 1.5 instead of 1 or 2. NO3- any 1 of the 3 O are happy to have the double bond (N can't exceed octet, so only 1 O would get double bond) this is resonance as electrons are free and can delocalize from one orbital and be in another. instead of saying NO3- has 3 different structures that revert into each other, there is 1 structure that all 3 contribute to. more stable = where the delocalized electrons likely hang out charge likewise isn't localized to any 1 element but to the molecule as whole RESONANCE can stabilize an intermediate or product making reaction more favorable likewise resonance can make nucleophiles less reactive since electron density is not 100% localized around a single atom but spread out among many (decreasing negative charge)

What is Heat of Combustion?

When molecules are combusted, HydroCarbon + Oxygen -> Carbon Dioxide + Water all bonds are broken and then reformed via a radical reaction (explosive even) THE LESS STABLE BOND = HIGHER POTENTIAL ENERGY = HIGHER HEAT OF COMBUSTION MORE STABLE BOND = LOWER POTENTIAL ENERGY = LOWER HEAT OF COMBUSTION how do we calculate energy released/absorbed? bond energy (enthalpy) or how much energy required to break bond, which is same energy released when bond forms, (because reactant and product thermodynamics is constant). Bond enthalpy (also known as bond energy) is defined as the amount of energy required to break one mole of the stated bond. For example, the bond energy of a O-H single bond is 463 kJ/mol. This means that it requires 463 kJ of energy to break one mole of O-H bonds. H0 (heat of reaction) sum of bond enthalpies of bonds broken and formed by def bond enthalpy values to BREAK (+) (energy required in system) when FORMING bonds (-) energy released from system COMBUSTION OF METHANE CH4 + 2O2 -> CO2 + 2H2O C-H bond enthalpy: 413 kJ/mol 4 C-H bonds broken = 4(413kJ/mol) O=O bond enthalpy: 495 kJ/mol 2 O=O bonds broken = 2(495 kJ/mol) total energy required to break = 1652 + 990 = +2640 kJ/mol C=O bond enthalpy: 799 kJ/mol 2 C=O bonds formed = 2(-799kJ/mol) H-O single bond enthalpy: 463 kJ/mol 4 H-O bonds formed = 4(-463 kJ/mol) total energy released by forming = -3,452 kJ/mol whichever is larger determines if reaction is exothermic or endothermic -808 kJ/mol means exothermic or energy released NOTICE ENTHALPY (H) is the energy difference between reactants and products COOL ARTICLE WITH DIAGRAM http://wiki.chemprime.chemeddl.org/articles/a/t/o/Thermodynamics~_Atoms,_Molecules,_and_Energy_in_the_Environment_e088.html

Lewis Dot Structure

all atoms and valence electrons drawn as dots or lines if shared in bond. count valence electrons for each atom. draw bonds to least electronegative atom. 1 bond = 2 electrons shared subtract electrons in bond from total electrons place remainder as lone pair electrons on surrounding then center atoms. atoms want nobel gas configuration where valence shell is filled H only has s orbital which is filled with 2 e- octet rule for 2nd period (s and p subshells)

Sulphone

an organic compound containing a sulfonyl group linking two organic groups. O=S=O (sulfonyl) S with 2 double bonds to O also bonded to 2 R groups Sulfur can exceed octet rule while Oxygen can't

(R) and (S) Absolute Configuration

assign priority based on molecular weight to all four groups in chiral atom (the first the atom directly bonded, if tie then move to next highest until tie breaker is reached) next rotate #4 or lowest priority to the back we can keep one in place with center (as axis) and move atoms to in same direction until #4 is in back or if #4 is in front, take a circle 1-2-3 and flip R to S or S to R or flip molecule in mind make #1 eclipse chiral center and take the correct configuration R = clockwise to the right S = counterclockwise to the left in a 4 partner molecule, no matter how we rotate or conform, at least 2 partners will be out of place (that means we can switch 2 partners to make a different enantiomer) if we flip 2 = make enantiomer if we flip 4 = make same molecule or we can hold 1 in place, and move 3 in same direction around until #4 is in back VISUALIZE https://www.chemtube3d.com/stchiralcentersrs/ https://www.khanacademy.org/science/organic-chemistry/stereochemistry-topic/optical-activity/v/cahn-ingold-prelog-system-for-naming-enantiomers How KHAN VISUALIZES IT https://www.khanacademy.org/science/organic-chemistry/stereochemistry-topic/optical-activity/v/r-s-cahn-ingold-prelog-naming-system-example-2

What is hybridization?

atoms when bonded hybridize/mix their higher and lower energy valence electron orbitals to form intermediate energy hybrid orbitals HYBRIDIZATION IS REASON FOR SHAPE OF BONDED MOLECULES Carbon has 2 electrons in its valence 2s orbital and 2 electrons in the 2p orbitals if stick with tradational model, Carbon has only two unpaired electrons and would form 2 bonds, this is not what we observe in real life. when bonding, Carbon forms 4 orbitals of equivalent energy called sp3 hybridized orbitals this occurs as Carbon elevates the valence s orbital up in energy and valence p orbitals down in energy to the same level, (hund's rule fill the lowest energy, which means 1 to each of 4 orbitals) here 4 orbitals each with an unpaired electron, want to bond (share electron) to fill orbital the shape of the orbitals are now equal, no longer an s orbital and 3 p orbitals, but each are an sp3 hybridized orbital something that looks inbetween an s and 3 p orbitals long lobe and short lobe s contributes 1/4 of character and p contributes 3/4 of character sp has one p orbital hybridize and 2 pi orbitals for triple bond (sigma+pi+pi) 50% s character and 50% p character sp2 has 2 unpaired p orbitals hybridize and 1 pi orbital for double bond (sigma + pi) SIGMA BONDS ARE MADE BY HYBRIDIZED ORBITALS, Pi BONDS ARE MADE BY Pi ORBITALS KHAN ACADEMY: https://www.khanacademy.org/science/organic-chemistry/gen-chem-review/hybrid-orbitals-jay/v/sp3-hybridized-orbitals-and-sigma-bonds

Forming and Breaking Bonds. Energy is always {insert} when a bond is formed, and {insert} when a bond is broken.

bond is a lower energy state, fulfills valence shell of both partners FORM BOND = RELEASE ENERGY as atoms get closer, their potential energy decreases stability increases BREAK BOND = REQUIRES ENERGY to push atoms away or increase PE requires an input of energy because spontaneously they would rather get closer the higher the PE (distance between) the more energy contained (PE = energy) IN ATP, WHAT RELEASES ENERGY FOR BODY TO USE? it is not the breaking of phosphate bond, this requires energy. it is the formation of bonds in lower energy products, so that the release of energy is more than the energy taken to break initial bonds. Hydrolysis or adding water to triphosphate releases a phosphate now bonded to OH instead of the phosphate chain the new -OH bond releases more energy than was required to break the phosphate bond of ATP therefore net energy release (or spontaneous reaction) to power another nonspontaneous reaction

Geminal and Vicinal (Gem- and Vic-)

both describe two functional groups close together geminal (gem-): means both functional groups are bonded to same atom (1,1 relationship) vicinal (vic-): means the functional groups are bonded to adjacent Carbons (1,2 relationship) usually they describe the same functional group or atom gem-dibromide: Br-C-Br vic-dibromide: Br-C-C-Br

Coordinate Covalent Bonds

both electrons shared are donated by one atom. usually covalent bonds involve both atoms donating 1 electron and accepting 1 then sharing both together Lewis bases donate electrons Lewis acids accept electrons WHY DO COORDINATE BONDS OCCUR? when atom has less than octet/full valence shell but other atom has full octet/full valence shell, full shell atom doesn't need electron but may have electrostatic attraction less than full shell atom needs electrons, and may have electrostatic attraction solution: the full shell atom donates both electrons in a shared covalent bond, full shell gains no electrons unfilled shell becomes filled shell receiving 2 electrons Usually Coordinate Covalent occurs when donor molecules (bases) surround and bind to single "recipient" molecule (acid, usually metal) FOR MCAT, if molecule DOESN'T HAVE LONE PAIR of ELECTRONS = CANNOT PARTICIPATE in COORDINATE COVALENT BOND complex formed by metal and molecules forming coordinate covalent bonds with that metal is called "COORDINATION COMPLEX" Coordinate covalent bonding is central to Lewis theory all metal aquo complexes are coordinate covalent (water has lone pair while metal is cation like ligands each donating electrons to a metal center still most electronegative atom will pull electrons closer exception: Carbon Monoxide CO+ C=O the C has 6 valence e- while O has full octet (and 2 lone pairs) so O will donate 2 e- to C making a coordinate covalent bond C triple bond O this changes the formal charges C has 3 bonds and 1 lone pair 4ve - 5e = -1e O has 3 bonds and 1 lone pair 6ve - 5e = +1e not charge but formal charge ionic charge denotes additional or less electrons in valence shell formal charge denotes how same number of electrons are arranged: how many lone pairs, how many bonds ex Cl- (ionic charge) is Cl with one extra electron so 8ve electrons C (triple) O+ the Oxygen donated its lone pairs to turn double bond into triple, it still has 8ve electrons: didn't lose or gain, the lone pairs became bond Donor -> Acceptor arrow denotes who gives 2 electrons to whom

isobutyl

butyl = 4C iso = all but 1 C forms a continuous chain the 1 C is part of an isopropyl group at end of chain like isopropyl but with an extra CH2 bonded to parent or functional group

Carboxylic acid

carbonyl + alcohol = carboxylic acid all are weak acids that dissociate OH into O- the O- is made stable thanks to resonance as lone pair can form double bond while double bond moves to lone pair on the other oxygen.

What is Formal Charge

compare atom when unbound in ground energy state to atom when bound in molecule. this lets us predict electron distribution and bonding. difference between # of electrons in element in ground state and number of electrons of the element bonded in a molecule. (so need to know dot structure) (dot structure will be the one with lowest possible formal charges) Formal charge = valence - assigned valence comes from periodic table and number of electrons in outer shell assigned comes from lone pair electrons and bonding electrons. Key caveat: assume equal sharing of electrons, so a bond of two electrons assumes that each atom contains 1 of the electrons. because we are trying to account for all elements and all electrons as if they were each not bonded to compare with actual not bonded elemental ground state if the assigned number (element in molecule), has less electrons than valence ground state (element not bonded to anything), then we know the element has lost electrons and is positively charged within molecule if molecular element (assigned number) has more electrons than free element on its own (valence number), then the element gained electrons and is negatively charged within molecule if assigned number = valence number, then element didn't gain or lose electrons and has no charge. Each element would have its own formal charge the entire molecule's charge is the sum of all individual elemental formal charges. THE SUM OF FORMAL CHARGES = IONIC CHARGE see image, will H2SO4 have all single bonds or double bonds? we can use formal charge to find out. A FORMAL CHARGE MEANS ELEMENT IS NOT AT LOWEST POSSIBLE ENERGY, But the electron number doesn't change, so how do we alter formal charge? by choosing how each holds electrons (lone pairs for self or bonds to share, total umber of electrons remains constant) the molecule will adjust, if possible, to lower formal charge AWESOME MCAT KHAN VIDEO https://www.khanacademy.org/science/chemistry/chemical-bonds/copy-of-dot-structures/v/formal-charge-and-dot-structures

Newman Projections

compares CONFORMATION of partners of a C to adjacent C (only valuable for sigma bonds that can rotate) sp3 can rotate sp2 can't rotate thanks to pi bond imagine looking eye level on plane C-C bond so that 1st C eclipses the 2nd C draw point and three lines representing first C. draw larger circle intersecting first three lines and lines coming out of circle for 2nd C (see pic) look at conformation of tetrahedral partners. are partners of C1 staggered to partners of C2 or eclipsing? we can make an energy diagram. REMEMBER electrons want to be as far apart from each other as possible Next consider atoms of different size. most stable is when largest size molecules are farthest apart or 180 PRACTICE https://www.chemtube3d.com/stethanenewman/ https://www.khanacademy.org/science/organic-chemistry/bond-line-structures-alkanes-cycloalkanes/conformations-alkanes-cycloalkanes/v/newman-projections

What is the Octet Rule? Why 8? When is it not 8?

complete outer electron shell is very stable. noble gases have full outer shell halogens are 1 away from filling so very reactive adding electrons to fill shell, releases energy other reactions are possible but less energetically favorable atoms follow octet rule because always seek most stable electron configuration (lowest energy) Octet rule is based on outer valence shell of s (2 e- to fill) and p (6e- to fill) when all 8 electrons present, outermost valence shell is full and that means lowest energy highest stability this means we can predict whether atoms will gain or lose electrons (how they will bond), whichever takes the least energy to arrive at full outer valence shell this only applies to the low atomic weight elements up to #21 (Sc the first element of (3d orbital in 4th period) the 3d orbital starts to be filled in the 4th period after 4s, but exist in 3rd period https://www.thoughtco.com/octet-rule-explanation-in-chemistry-606457

What is Aromaticity?

conjugated, unsaturated ring systems that exhibit greater stability than one would expect based on either resonance or conjugation alone flat, conjugated, cyclic, 4n+2 pi electrons benzene is unsaturated, has 3 double bonds, 2 resonance forms benzene is FAR MORE stable than conjugated straight chain alkene with 3 double bonds and 2 resonance forms CONJUGATION: connected unhybridized p orbitals with delocalized pi electrons that can freely flow throughout HUCKEL's RULE: to exhibit aromaticity, a ring system must have exactly 4n+2 pi electrons meaning if there are 6 pi electrons then aromatic if there are 10 pi electrons then aromatic if there are 2 pi electrons then aromatic (pi electrons as in electrons in unhybridized p orbitals) but if there are 7 or 9 pi electrons then NOT aromatic these electrons do not stabilize the system, but the ring will actually be very unstable 1 double bond = 2 pi electrons 3 double bond = 6 pi electrons 5 double bond = 10 pi electrons WHY 4n+2 pi electrons stable? Molecular Orbital theory: compound is stable if bonding orbitals are filled with paired electrons. in aromatic compounds, 2 electrons fill lowest energy molecular orbital and 4 fill each subsequent energy level. all bonding orbitals are filled and all electrons paired WHICH ELECTRONS ARE PI ELECTRONS? pi electrons lie in p orbitals and sp2 hybridized have 1 p orbital WHAT ABOUT IONS? huckel's rule still applies, electrons from a double bond can move and be a lone pair on the atom. They are still pi electrons. Only electrons participating in sigma bonds can't move. WHAT ABOUT HETEROCYCLIC COMPOUNDS (some elements other than C in ring)? aromaticity comes from pi electrons, so as long as pi electrons are paired and fill the orbital (4n+2) they are aromatic. if atom other than C is attached to sp2 hybridized carbon and has lone pair (to make double bond) then it is sp2. GEOMETRY DEFINES HYBRIDIZATION you can only assign hybridization states to atom if you already know geometry AWESOME KHAN VIDEO EXPLAINING AROMATICITY https://www.youtube.com/watch?v=RaBI3lAACKg BEST ARTICLE TO UNDERSTAND WHY https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Map%3A_Organic_Chemistry_(Wade)/17%3A_Aromatic_Compounds/17.05%3A_Aromatic%2C_Antiaromatic%2C_and_Nonaromatic_Compounds

How to determine Hybridization

count the number of sigma bonds (and lone pairs as these can form sigma bonds). this is known as steric number and determines hybridization (mixing of orbitals, s increases energy and p decreases energy into a middle energy) sp= 2 sigma bonds (s orbital and p orbital) sp2 = 3 sigma bonds (s orbital and 2 p orbitals) sp3 = 4 sigma bonds (s orbital and 3 p orbitals) sp3d = 5 sigma bonds (s orbital, 3 p orbitals and 1 d orbital) sp3d2 = 6 sigma bonds ( s orbital, 3 p orbitals, and 2 d orbitals) hybridization makes the sigma bonds between bonded atoms double and triple bonds are made by left over p orbitals (didn't hybridize) that overlap above and below plane of atoms note: s orbital has to fill with 2 electrons before any p orbital gets 1 when hybridizing, s donates 1 electron to now equivalent hybridized orbital up/down up up s px py pz becomes up up up up sp3 sp3 sp3 sp3 Remember that hybridiaztion is in terms of sigma bonds around central atom not in the entire molecule VERY GOOD KHAN ACADEMY TUTORIAL TO SEE ORBITALS WITH 1 e- AND CALCULATE HYBRIDIZATION https://www.khanacademy.org/science/organic-chemistry/gen-chem-review/hybrid-orbitals-jay/v/sp-hybridization-jay-final

Epoxide

cyclic ether (2C) with O looks like triangle and is very reactive either acid or base will provide a nucleophile that attacks carbonyl carbon

What do chiral centers look like in an Enantiomer?

enantiomers have opposite R/S configurations at EVERY chiral center this is what makes them "mirror images" if one chiral center matches the other, they would be diastereomers NOTE both enantiomers and diastereoemers are Stereoisomers

Draw 2 energy coordinate diagrams demonstrating why the combustion of a less-stable molecule results in higher heat of combustion than combustion of more stable molecule.

energy required or released is determined by difference in energy of products and reactants stability means low energy (lower on diagram) less-stability means more energy (higher on diagram) what are the reactants and products products are the same in all combustions: CO2 and H2O reactants can be different meaning, energy level of product is constant but reactant energy level varies an unstable molecule has higher reactant energy level than more stable molecule HEAT OF COMBUSTION = ENERGY DIFFERENCE BETWEEN REACTANT AND PRODUCT less stable reactants have higher energy levels so the DIFFERENCE is much higher Compare Reactant 1 with Reactant 2 reactant 2 is less stable (higher energy), it therefore releases more energy to get to product than reactant 1. DELTA H is the difference between reactant and product energy levels SIMPLEST ANSWER: higher energy reactants release more energy than lower energy reactants

Quick Recap: how do we draw dot structures?

given molecular formula: check periodic table for total valence electron numbers use group number x number of atoms see if cation or anion and take away or add electrons the least electronegative atom in center (shares the most bonds, most electronegative will hog more electrons than share) like C exception for Hydrogen because it only forms 1 bond draw surrounding bonds and electrons to fill octet see how many valence electrons used from total. Rest are added to central atom. compare formal charges to find best structure

Aliphatic

hydrocarbons are divided into 2 classes 1. aromatic (4n+2 pi electrons full) 2. aliphatic they can be straight chain or cyclic hydrocarbons they can be single, double, triple bonds and other elements beside H can be bonded like O,N,S,Cl

Space-Filling model

instead of ball and stick model draw atom and electron cloud as sphere. nucleus is in center space filling model is useful because shows how much space or volume is occupied, drawback: its harder to establish the bond patterns, have to see overlap which may be hidden on a 2D representation shows the degree of electron cloud overlap which relates bond length AND nonbonding overlap such as H bonding between multiple water molecules BOND = STRONG OVERLAPPING OF SPHERES NONBOND is shown with overlap as well the radius represents van der Waals interactions thanks to space filling model we can SEE how O would attract H (has the space to overlap with H) https://www.reed.edu/chemistry/ROCO/Geometry/space_filling.html

Bond-Line structure

instead of writing each C and H (like in Lewis), use lines to represent bonds in a zigzag pattern. look to formal charge to determine how many Hydrogens to each C C has 4 valence electrons and would make 4 single bonds if neutral C 1 bond = 3Hs C 2 bond = 2Hs C 3 bond = 1 H C 4 bond = 0 H if C formal charge is + ? valence - molecular 4-3=+1 so C is only bonded to 3 partners instead of usual 4 if C formal charge is - ? valence version - molecular version 4-5 = -1 so C is bonded to 5 partners WE TRY TO REPRESENT GEOMETRY sp3 = tetrahedral sp2 = trigonal planar sp = linear

Wedge-Dash Formula

just like line-bond except represent 3D molecule in 2D page SOLID WEDGE = coming out of page towards you DASH = going out of page away from you line = within the plane of page WE TRY TO REPRESENT GEOMETRY sp3 = tetrahedral (partners are 109.5 degrees away from each other) meaning 2 in plane, 1 coming towards, 1 going away sp2 = trigonal planar (just lines) sp = linear (just lines) https://www.khanacademy.org/science/organic-chemistry/gen-chem-review/bond-line-structures/v/three-dimensional-bond-line-structures-new

Review of common names

n = normal: when all carbons form continuous unbranched linear chain iso = all carbons except for last form a continuous chain neo = all but 2 Cs form a continuous chain, the 2Cs are part of tert-butyl group at end of chain sec or s = secondary: when functional group is bonded to secondary Carbon (used in relatively short chains about 4 no more than 5) tert or t = tertiary: when functional group is bonded to a tertiary (C with 3 partners) https://www.chem.ucla.edu/~harding/IGOC/C/common_name.html

How does rotational limitation of pi bonds relate to our previous study of proteins?

peptide bond between amino acids (amino group attacks carbonyl of other acid) thanks to resonance, peptide experiences double bond character and can't rotate- a key characteristic of peptide that gives the backbone planar geometry resonance involves the pi orbitals allowing conjugation, therefore atoms that allow resonance can't rotate, otherwise they prevent their pi orbitals from conjugating together.

Fisher Projections

perspective on stereochemistry need to be able to convert between line diagrams Vertical and Horizontal lines in 90deg cross formation VERTICAL = CARBON BACKBONE (into plane of page/dash) HORIZONTAL = H or OH (projecting out of page/wedge) (R)/(S) method (stereocenter rotate right or left) 1. number Carbons down vertical chain 2. figure out R and S for ALL stereocenters 3. sketch line diagram (don't worry about stereochemistry, just get all Carbons and bonded elements in place) 4. estimate stereochemistry, compare to fischer and swap dash for wedge if got wrong OH is #1 C on side with more stereocenters (crosses in vertical line, if identical) is #2 C on side with less stereocenters or lower atomic number partner is #3 H is #4 2 options: either draw arrow first (1-2-3-4) and flip direction (R becomes S and S becomes R) or flip molecule towards #1 and put #4 in back and draw arrow https://www.youtube.com/watch?v=p2iYv0DXcbc

Aromatic (drawing), Aryl, Benzyl

planar ring with 4n+2 pi electrons (usually all sp2 hybridized) 2, 6, 10, 14 pi electrons ARYL: is a simple aromatic ring where 1 Hydrogen (outdside ring) has been replaced with another atom (halogen, OH, etc) (ARYL: Element bonded to aromatic ring) BENZYL: Benzene ring (6C) with CH2 (will bond to something else) because of aromaticity, ring only performs substituition but not addition reactions

What is Polarimetry and how does it work?

polarimetry is measuring the rotation of polarized light as we pass it through a compound. it depends on temperature and wavelength and concentration and pathlength unpolarized light goes anywhere and everywhere in all directions can't measure any changes pass unpolarized light through a filter that only lets a specific plane of light through (say up and down) the polarized plane of light passes through a tube containing a solution of a chemical compound if compound is an enantiomer, it is optically active and will rotate the up and down plane of light to the left or right (depends on how much and path length and concentration the compound is) DOUBLING PATH LENGTH = DOUBLING ROTATION DOUBLING CONCENTRATION = DOUBLING ROTATION (more interaction with enantiomer = light rotates more) the analyzer is another filter that we look through, and we would adjust the angle from up to down until light passes through filter and into eye. Now concentration and path length determine will determine OBSERVED ROTATION, this is NOT comparable with other results of differing path lengths and concentrations if we wanted to find a standard, we would divide OBSERVED ROTATION by concentration x path length to get SPECIFIC ROTATION SPECIFIC ROTATION = OBSERVED/(concentration)(path length) concentration = g/ml path length = dm or decimeters SPECIFIC ROTATION is unique to the substance itself and allows comparison to different test conditions its standardized. and gives the observed rotation if using a concentration 1 g/ml and path length of 1 dm allowing apples to apples comparison with other substances We can compare specific rotations, but we can't compare observed rotations because they can have differing concentrations and path lengths all specific rotations have the same concentration and path length allowing apples to apples comparison. CONCEPTUAL UNDERSTANDING https://www.youtube.com/watch?v=1LdFePZHAyY

What are Structural Isomers?

same atoms but differ in terms of structure or how they connect to each other how many ways can we draw C5H12? see One Note: Isomers 3 different ways fist single chain of 5 then chain of 4 with 1 as branch then chain of 3 with 2 as branch going any further would make the same molecules how many ways can we draw C3H8O see One Note get 3 C line place OH on middle (C2) can move OH to end (C1) can have O in between C1 and C2 https://www.khanacademy.org/science/organic-chemistry/gen-chem-review/bond-line-structures/v/structural-constitutional-isomers-new

What are Stereoisomers

same formula, same bond-bond connectivity (structural has different bond-bond) but different spatial or 3D arrangements 2 categories: Enantiomers Diastereomers molecule can only have stereoisomers if molecule has chiral centers. atom bonded to 4 unique partners MUST be 4 partners, any less and molecule would be the same just conformational MUST be different, if 2 are identical then molecule would be the same and just conformational

What is an ISOMER (important MCAT)

same molecular formula (same atoms/elements) but different compound isos + meros = equal parts isomers have equal parts but ARE NOT the same timing and energy are important factors an isomer must be an energy minimum; it must lie in an energy well because molecules are dynamic and change all the time, we can't call every small permutation a separate isomer. instead we focus on the lowest energy forms which is where most of time is spent https://www.britannica.com/science/isomerism/Conformational-isomers

How are Enantiomers similar and different?

same physical properties: boiling point, melting point density reactivity, what's different: direction they rotate light (same magnitude) the products made when reacting with ANOTHER chiral compound.

Rank following according to Decreasing bond length: triple bonds double bonds single bonds

single has longest only consisting of a sigma bond > double med of sigma and pi bond > triple has shortest made of sigma and 2 pi bonds MORE BONDS = MORE ELECTRON DENSITY OVERLAP = ATOMS ARE CLOSER TOGETHER

sp, sp2, sp3 sp3d sp3d2: which hybridization has atoms closer together? How can we know?

sp has central atoms closest together thanks to highest amount of s character (50%) (also potential for 2 pi bonds to make triple bond which is the shortest bond length) sp2 has 33% s character, so atoms are further apart (more p character which is more dumbbell than spherical) sp3 has 25% s character sp3d has 20% s character sp3d2 has 17% s character https://www.khanacademy.org/science/organic-chemistry/gen-chem-review/hybrid-orbitals-jay/v/sp2-hybridization-jay-final https://www.khanacademy.org/science/organic-chemistry/gen-chem-review/hybrid-orbitals-jay/v/sp3-hybrid-orbital-jay-final

Which model is the most accurate visual representation of an actual molecule?

space filling model. shows bonds as overlap of orbital space. however the electron clouds will not be nicely color coded. There are only math functions that predict where electrons might be. The first thing we would be able to see is the nucleus, most of the molecule is empty space to see electrons would require magnification many many times that.

What are Diastereomers?

stereoisomers that are not full enantiomers. NON-IDENTICAL, but NOT MIRROR IMAGES they are different compounds, have same atoms, same connectivity, and different arrangement at some chiral centers. S R and R S above are enantiomers having the opposite absolute configuration at EVERY chiral center SR and RR these are stereoisomers. 1 center is opposite, but 1 center is the same. If any center is the same, it CAN'T be a Mirror Image, but still nonsuperimposable KEY though notice the similarities and differences between Diastereomers and Enantiomers: both are different compounds, but only enantiomers can be mirror images, all others are diastereomers

tert-butyl

tertiary = attached to 3 Cs butyl = 4 Carbons C to parent has 3 CH3s

What is Electronegativity and how we can we compare it?

the ability of nucleus to pull an electron within a covalent bond electron affinity is ability to attract a new electron higher electronegativity means more pull determined by size which can be seen on periodic table the smallest atoms, have closest distance between nucleus and valence = more attraction Fluorine has highest electronegativity F = 4.0 (max) Francium has lowest electronegativity Fr = 0.7 (min) Carbon and Hydrogen have similar but not identical values C = 2.5 H = 2.2 so Carbon pulls electrons just a little bit more than Hydrogen for MCAT should have general intuition of common atoms, which comes from periodic table trends

Bonds in Increasing Strength

the more stable, the more strength, or the harder it is to pull atoms away from each other triple is strongest single is weakest single<double<triple

Aromatic Compounds and Resonance

the resonance structure that has 6 pi electrons in the ring (aromatic) will be much more stable than structure that has better electronegativity or less formal charges or than compound with more resonance structures double bond to atom in ring but not in ring contributes 1 pi electron not 2 PRACTICE FULVENE AND TROPONE https://www.youtube.com/watch?v=GXEsl7o6aHM

Evaluating Resonance Structures

to avoid mistakes visualize the movement of electrons and calculate resulting formal charge this way it is easy to see why something is or isn't a resonance structure consistency is key Go through checklist 1. full octet count atoms for formal charge 2. lowest number of formal charge 3. most electronegative gets - formal charge, least gets + OR atom with largest radius is more stable with extra negative charge REMEMBER size trumps electronegativity in terms of stability. while more electronegative can attract better, the greater size can even more stably hold the extra charge (down periodic table) Sulfur is more stable with - than Oxygen is even though O is slightly more electronegative REMEMBER more substituted Carbocation is more stable. having neighbors sharing electrons (electron rich neighbors) increases stability for electron poor atom. electron poor is stabilized by electron rich neighbors tertiary or carbocation with 3 partners is more stable than 2 >> 1 PRACTICE https://www.youtube.com/watch?v=SKHMKP7-qlc https://www.youtube.com/watch?v=vx9fzYPNby0 https://www.youtube.com/watch?v=thwNCDTk6wc https://www.youtube.com/watch?v=OSjO22ZDCCc

Organic Nomenclature: Functional Groups

why do we think about functional groups? because they have predictable behavior. By understanding the trends for each, one can accurately understand many many molecules MUST MEMORIZE ALL, MCAT refers either by name or structure and expects understanding. key is to visualize: alkane alkene alkyne alkyl vinyl allyl aromatic/arene aryl benzyl aliphatic alkoxy hydroxyl alcohol ether mesyl/tosyl amine aldehyde ketone carbonyl acyl acetal ketal hemiacetal hemiketal enamine/imine hydrazine carboxylic acid acetyl anhydride ester amide nitro nitrile gem-/vic- epoxide sulphone KHAN for basic most seen functional groups https://www.khanacademy.org/science/organic-chemistry/bond-line-structures-alkanes-cycloalkanes/functional-groups/v/functional-groups-first https://www.khanacademy.org/science/organic-chemistry/bond-line-structures-alkanes-cycloalkanes/functional-groups/v/more-functional-groups