Fundamentals of Organic Chemistry PDF

***[Fundamentals of organic chemistry ]*** **What is organic Chemistry:** \- The chemistry of carbon-based molecules more reduced than carbon dioxide Aliphatic molecules - any molecules (chains, rings, branched chains) that are not aromatic. Single, double, and triple bonds are allowed Aromatic...

***[Fundamentals of organic chemistry ]*** **What is organic Chemistry:** \- The chemistry of carbon-based molecules more reduced than carbon dioxide Aliphatic molecules - any molecules (chains, rings, branched chains) that are not aromatic. Single, double, and triple bonds are allowed Aromatic molecules - Any molecules that contain a particular type of **resonance structure** of alternating double and single bonds in rings. E.g Benzene **Carbon:** \- Has a valence of 4 = needs to form 4 single covalent bonds to be uncharged and thus a molecule not an ion. \- Covalent bonds share electrons from each party: \+ C (Valence = 4) bonding with H ( Valence = 1) can only form single bonds (1 electron from each party) \+ Simply put, double bonds and triple bonds form in the same way but have 2 electrons from each party or 3 electrons from each party, respectivly. \- Common valences: C = 4, H = 1, N = 3 or 4 S = 2, P = 5, O = 2 **Finish slide** **Hydrocarbon:** \- Make chain of singly-bonded C atoms and fill all remainling valence positions with hydrogens we get Alkanes (CnH(2n+2)), E.g Butane \- Alkanes are found in viridiplantae waxes/resins and oils of some aves and chondrichthyes \+ If we replace 1 single bond with a double bond between 2 C atoms we get alkenes (CnH(2n)) -Alkenes sensu stricto are relativly rare in life but C\--C double bonds are not \- If we do the same thing but instead adding a triple bond between 2 C atoms we get Alkynes (CnH(2n-2)) **Length of C Chains:** 1 = methyl- e.g. methane \[also formyl- e.g. formate\] 2 = ethyl- e.g. ethanol \[also acetyl- e.g. acetic acid\] 3 = propyl- e.g. propanoate 4 = butyl- e.g. butan-1-ol 5 = pentyl- \[also valeryl- e.g. valeraldehyde\] 6 = hexyl- \[also caproyl- e.g. caproic acid\] 7 = heptyl- \[also enanthyl- e.g. enanthane\] 8 = octyl- \[also caprylyl- e.g. caprylic acid\] 9 = nonyl- \[also pelargonyl- e.g. pelargonic acid\] 10 = decyl- \[also capryl- e.g. capric acid\] **Must know off by heart, Learn the alternative names of C1 and C2** \- For rings we just add \"cyclo\" E.g Cyclopropane **Functional Groups:** \- Things we can plug into a basic skeleton E.g alkane yo give functionally \- Numbers in names relate to positions of double/triple bonds or functional groups and always from end it is closest to **Hydroxyl Group (-OH)** \- Found in Alcohols (names end in ol) E.g Propan-1-ol \- There can be more than 1 pressent: \+ Two = a **diol** E.g Propan-1,2-diol (Slvent used in cosmetics) \+ Three = a **triol** E.g Propan-1,2,3-triol aka Glycerol \+ More = a Polyol E.g meso-xylitol, Pentan-1,2,3,4,5-tetrol = artifitial sweetener **Carbonyl Group (-C=O)** \- If only the **end of a chain** they are **Aldehydes** ( Names end in al but we normally end in - aldehyde to avoid confusion with -ol), E.g Butanal/butyraldehyde \- Aldehydes are important metabolic intermediates, Also used in signalling. Aldehyde moieties are found in reducing sugard E.g D-(+)-glucose \- If in the **middle of the chain** they are called ketones ( and end in one) E.g Butan-2-one. Kentone moieties are found in many non-reducing sugars **Carboxyl/carboxylate groups (-COOH)** **Esters and Their Formation:** \- Reaction of carboxylic acid with an alcohol forms a ester = key formatin of lipid membranes in eukarya E.g CH3CH2OH + C4H9COOH → (CH3CH2)OCO(C4H9) + HHO ethanol + pentanoic acid (valeric acid) → ethyl valerate + water \- Lipids of the Eukarya, bacteria and some Archaea are esters of sugar alcohols E.g Glycerol and fatty acids \- Aromas of many fruits and flowers are esters: \+ Ethyl acetate \+ Bornyl acetate \+ Methyl saalicylate **( Add more info)** **ethers (-O-) and organic sulfides (-S-):** \- Ethers have a bridging oxyge n (-O-) between 2 groups e.g dimethyl ether (H3C-O-CH3) -Ethers are found in double-headed lipids of some Archaea \- Organic sulphides have bridging sulfur (-S-) between 2 groups E.g dimethylsulfide (H3H-S-CH3) \- Organic sulfides are important signalling molecules for Aves ( E.g Larus a P) marine mammalia (E.g Phoca vitulina L.) as well as in some flowers of the Araceae Becc.ex \- Organic disulphides (and trisulfides) are also possible and have bridges of chains of sulfer atoms (-S-S- and -S-S-S-). Important protein folding. And are also found in many Viridiplantae E.g Bulbs **Related groups -** The sulpher homologue of the alcohol is the thiol (mercaptan in old parlance) and has an -SH group E.g Butan-1-Thiol **Aromatic rings:** \- Archetype is the benzene ring (C6H6) but there other aromatic rings \- C6H5 groups are phenyl-groups \- C6H5CH2 groups are benzyl groups \- Delocalised electrons must be pressent, this means alternating C-C and C\--C bonds around the ring that flip back and forth in resonance on a femtosecond scale \- Usually lipophilic molecules ( Some are hydrophobic some are not) \- Important in protein structure such as DNA structure **Aromatic VS Aliphatic** \- Hydroxylated carboxylic acids (Carboxylic acids with an -OH added on) are widly used in skincare products. As they break bonds between dead skin cells and encourage shedding. Top: Salicylic acid (a BHA) has a benzene ring, meaning its fat-soulable and will dissolve in sebum in pores and shed dead cells from inside of pores -- important if you have oily or combination skin. Mandelic acid (an "aromatic AHA") is a good alternative if sensitive to salicylic acid Bottom: Glycolic acid (an "AHA") is a small aliphatic molecule, meaning it's very water-soluble and is small enough to penetrate layers of dead skin, but it won't dissolve in sebum in pores so will only shed surface skin -- important if you have older or dryer skin as it won't strip the oil you need to keep. AHAs are not for use on skins of under-30s! **cis- and trans- and (E)- and (Z)-** \- double bonds, triple bonds and rings cannot rotate. \- as such, arrangements of groups on either side are important and lead to one form of isomerism. \- if two functional groups are on the same side of a double bond (etc), they are cis- and if on opposite sides, trans-. (top) cis-but-2-ene \[(Z)-but-2-ene\] (bottom) trans-but-2-ene \[(E)-but-2-ene\] Largely superseded now by E-Z notation, which is more flexible and allows for groups that aren't the same but are similar to be "paired". You don't need to learn E-Z and I won't be covering it but if you see it, it's the same as cis- /trans- BUT caveat is that (Z)- doesn't always go with cis- **optical isomers -- (D)- and (L)- etc** many molecules important in biochemistry can rotate polarised light. the direction of rotation relative to that of a standard substance gives them a prefix of (D)- or (L)- from dextro (right) and laevo (left). This cannot be determined from looking at a structure, only in vitro! a sample of a substance that contains both e.g. (D)-lactic acid and (L)-lactic acid is written (D/L)-lactic acid and is called racemic lactic acid (or lactic acid racemate). some molecules have an asymmetric C around which groups can be arranged in 2 mirror image arrangements -- this C is a chiral centre. Some chiral molecules rotate polarised light, some don't. In biochemistry, most do! So we use (D)- or (L)- but in wider chemistry, you will see R- and S- used which are a bit like (E)- and (Z)-. typing: type "(d)-" and then format the "d" in "SMALL CAPS" to get a capital that is of the right size! all amino acids found within proteins are (L)-. most natural monosaccharides are (D)-.