Module 2 Chemical Foundations S23 Students PDF

 IUPAC = International Union of Pure and Applied Chemistry IUPAC Common 1,2,3-propanetriol glycerol hydrogen and carbon Hydrocarbon tail  or H H H H H 1 3H 1 3 1 3 5...

 IUPAC = International Union of Pure and Applied Chemistry IUPAC Common 1,2,3-propanetriol glycerol hydrogen and carbon Hydrocarbon tail  or H H H H H 1 3H 1 3 1 3 5 H 2H 2 4 2 4 double bond triple bond  CH3-CH2-CH2-CH3 linear hydrocarbon alkane w/ 1 branch alkane w/ 2 branches (alkane)  prefix # of C’s This table applies to monty monkeys meth 1 the naming of all linear eats eat eth 2 hydrocarbons (alkanes, peanut peeled prop 3 alkenes, and alkynes) butter bananas but 4 pent 5 hex 6 hept 7 1 2 3 oct 8 non 9 dec 10 propane  2 4 6 8 1 3 5 7  → prefix for number of carbons, then suffix… “ane”, “ene”, or “yne” 53 26 71 methane yl 4 3 5 26 17 You do need to be able to name or draw 3-methyl heptane linear and branched alkanes.  8 carbons octane from bottom right → top right (puts CH3 side chain on carbon 4) -CH3 = methane → methyl 4-methyl 4 5 6 7 8 3 2 1 name: 4-methyl octane  5 carbons pentane left → right (puts CH3 side chain on carbon 2) -CH3 = methane → methyl 2-methyl 1 2 3 4 5 (either way it is a 5 carbon parent chain with a 1 carbon side chain) name: 2-methyl pentane  5 carbons pentane number left → right (puts CH3 side chains on carbons 2 and 3) -CH3 → methyl 2-methyl + 3-methyl + pentane New Rule: for multiple side chains of the same type, use 1 2 3 4 5 prefixes such as “di-” and “tri-” and number each one with a comma between numbers name: 2,3-dimethylpentane  2 more Rules: for multiple parent chains of the same length, pick the one with the most branches off of the parent chain multiple branches are listed before parent chain… → alphabetically octane bottom right → top right (puts side chains on carbons 3 and 4) 2 branches 4 5 6 7 8 3 8 carbons 7 carbons 2 1  multiple branches are listed before parent chain… → alphabetically -CH2-CH2-CH3 propyl (on C4) and -CH3 methyl (on C3) 3-methyl, 4-propyl (side chains separated by comma’s) 3 carbons: propane 4 5 6 7 8 3 methyl 2 1 name: 3-methyl, 4-propyl octane  10 carbons decane left → right (puts side chain on carbon 5) problem: sidechain is branched (it has its own sidechain…) solution: treat sidechain as a separate (branched) hydrocarbon name: decane 1 2 3 4 5 6 7 8 9 10  10 carbons decane left → right (puts side chain on carbon 5) problem: sidechain is branched (it has its own sidechain…) → C attached to parent chain is always carbon ‘1’ solution: treat sidechain as a → follow rules to name sidechain as hydrocarbon separate (branched) hydrocarbon → put entire name of branch in brackets, suffix to “yl” → number sidechain name: 5-(2-methylpropyl) decane 1 2 3 4 5 6 7 8 9 10 1 2 yl) ) 5- (2-methyl propane 3  You do not need to be able to name or draw branched alkenes or alkynes You do need to name and draw linear alkenes/alkynes and branched alkanes. 1-pentene (or pent-1-ene) 1 2 3 4 5 2 4 1 3 5 1-pentene or pent-1-ene cyclohexane cyclopentane cyclopropane  Naming Hydrocarbons Summary 1. identify longest chain of carbons 2. name parent chain (1C : meth, 2C’s : eth, 3C’s : prop, etc… ) 3. for multiple parent chains of the same length, pick one with the most branches 4. identify side chains and name them 5. side chains have “-ane” suffix changed to “yl” (methane to methyl, etc…) 6. if side chains have branches of their own, circle whole thing, name with C attached to parent as 1, substitute ‘yl’ for ‘ane’, whole side chain name goes in brackets 7. list side chains before parent, alphabetically 8. if multiple side chains of same type, use “di-” or “tri-” 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 1 2 2 1 1 4- (1-methylethyl) octane 3-ethyl, 2-methylheptane  CH CH22 H2C CH2 H2C CH2 H2C CH2 2-propanol propane  R group is a hydrocarbon of some size and will contain carbon linked to the -OH ‘generic structure’ an R group is a generic label for “the rest of the organic molecule”. →for our purposes, we will be looking at examples in which the R group is a hydrocarbon with no additional functional groups present. You do need to be able to name/draw the generic structures of all the functional groups (using “R” to designate the rest of the molecule). You will also be asked to name and draw linear and branched alkanes with functional groups  - (parent chain name, “e” replaced with “ol”) 2-propanol 1,2-ethanediol 1-methanol (or just: methanol) if the number doesn’t provide any necessary information it is often left out… 1-ethanol or just ethanol 2-methyl-2-propanol R group will contain carbon R’ group will also contain linked to the O atom carbon linked to the O atom The two R groups, R and R’, are not necessarily different but they can be. Because of this, a different designation is used for each (R vs. R’) found in sugars and carbohydrates: (R) carbon ether carbon (R’) alcohol glucose Format for naming Ethers : (name of each R group*, “ane” replaced with yl”) then (suffix ‘ether’) * if different, R groups are named in alphabetical order * if the same, the prefix “di ” will be used → if R groups have branches, number and name them: CH3-CH2-O-CH2-CH3 diethyl ether CH3 CH3-CH2-O-CH2-CH2-CH3 CH3-O-CH2-CH-CH3 ethyl propyl ether methyl 2-methylpropyl ether  Found in amino acids and proteins, and in nucleic acids There are 3 possible types of amine functional groups: 1. Primary: one R group 1. 2. Secondary: two R groups 3. Tertiary: three R groups 2. *R groups must have carbon bound to N 3. just like ethers have the O atom in the middle with C-containing R groups attached to it, amines have the N atom in the middle Format: (name of R group(s)*, “ane” replaced with “yl”) + (suffix ‘amine’) * if different, R groups are named in alphabetical order * if same, the appropriate prefix (e.g. “di “ or “tri “) is used CH3 – CH2 – CH2 – N – CH3 – CH2 –CH3 methyl amine ethyl methyl propyl amine dimethyl amine  note: there is a carbon atom right here! Because the functional group itself contains a carbon atom, the R group does not have to contain carbon, although it often does.  + (suffix “al “ in place of “e“) or ethanal propanal methanal  Found in amino acids and proteins, and fatty acids aldehyde carboxylic acid note: there is a carbon atom right here Because the functional group itself contains a carbon atom, the R group does not have to contain carbon, although it often does. found in amino acids and proteins, and fatty acid Format: (parent chain name*) + (suffix “oic acid” in place of “e“) *total # of carbons includes the C in the carboxylic acid group Note: carboxylic acid groups are always at the end of molecules and always contain carbon #1, so it’s unnecessary to indicate carboxylic acid location hexanoic acid butanoic acid methanoic acid  aldehyde carboxylic acid note: there is a carbon atom right here Even though the functional group contains a carbon, in this case both R groups must contain carbon. If this wasn’t the case, it could be an ALDEHYDE (i.e. if R2 = –H) or an CARBOXYLIC ACID (i.e. if R2 = –OH). Format: (# of C with ketone*) + (parent name) + (suffix “one” replacing “e”) *like all hydrocarbons with functional groups, the carbon of the ketone gets lowest number possible 3-pentanone 2-butanone (or just: butanone ?) esters are like a combination of a ketone and an ether Also called: carboxylic acid esters carboxylic acid note: there is a carbon atom right here Because the functional group itself contains a carbon atom, the: R group does not have to contain carbon (but it usually does) The R’ group does have to contain carbon, otherwise: → it could be a… carboxylic acid if R’ were an H). carboxylic acid + alcohol ester + water  carboxylic acid H– + HO–CH2–CH3 H– alcohol + H2O H CH2-CH3 ethanol methanoic acid Name: ethyl methanoate also called: sulfhydryl group found in amino acids and proteins, and neurotransmitters R group will contain carbon thiol group contains sulfur two sulfhydryl groups can join, forming a special type of bond called a disulfide bridge (more on this later in the proteins section…)  + (suffix “thiol”) CH3CH2CH2-SH 1-propanethiol ethanethiol CH3-SH methanethiol Found in nucleotides and nucleic acids, and often seen modifying certain amino acids in proteins R group will contain carbon + (suffix “phosphate”) CH3 methyl phosphate  n.b. functional group takes priority over (contains C=0 double bond) side chains for determining carbon 1 Carbonyl compounds? R’s must contain C? naming number C with OH group and a ‘-’ yes replace hydrocarbon “-e” with an “-ol” suffix e.g. 3-octanol name of both R groups + “ether” yes if R groups same, prefix “di”, if not alphabetical e.g. ethyl pentyl ether 1 R: primary, 2 R’s: secondary, 3 R’s: tertiary amine yes if R groups same, prefix “di/tri”, if not alphabetical Names of R groups plus “amine” e.g. ethyl pentyl propyl amine Aldehyde group always on end so no need to number it no The number of carbons includes the C in aldehyde replace hydrocarbon “-e” with an “-al” suffix e.g. pentanal Carboxylic group always on end so no need to number no The number of carbons includes the C in carboxylic acid replace hydrocarbon “-e” with an “-oic acid” suffix e.g. pentanoic adic number C with ketone =O group and a ‘-’ yes The number of carbons includes the C with ketone replace hydrocarbon “-e” with an “-one” suffix e.g. 2-pentanone no but…. (R’ does have C) yes number C with thiol group and a ‘-’ Parent hydrocarbon chain plus “thiol” suffix e.g. 2-propanethiol number C with phosphate group and a ‘-’ yes Parent hydrocarbon chain plus “phosphate” If multiple phosphates thru P-O-P links use “di/tri” e.g. 3-hexane diphosphate Functional Group Side group Name suffix Example Elements and Atomic Number  Atomic structure Atoms have a central nucleus with protons (positive charge) and neutrons (neutral charge) each having mass of 1u Circling the nucleus are negatively charged electrons, having a mass of essentially 0u The number of protons, neutrons and electrons is usually equal to the atomic number of the atom (i.e. H1, C6, P15)  Electron orbitals Electrons are arranged in ‘orbitals’ filled from the inner most first The first orbital can contain 2 e- the second and third, 8 e- each Atoms attempt to have their outermost 3rd orbital electron orbital filled 2nd orbital 1st orbital When the orbital is half filled or more, the atom attempts to gain electrons, nucleus when less than half filled, it attempts to lose electrons 2 e- 8 e- 8 e- Number of bonds formed by the bioelements (elements in the biomolecules) # bonds Element: formed: Carbon 4 Hydrogen 1 Oxygen 2 Nitrogen 3 (4*) Phosphorous 3 (5*) Sulfur 2 *extra bonds possible in case of ions **extra bonds due to special orbital arrangement  think INTRAmural sports (games between teams within the same university 1) Covalent 2) Ionic think INTERstate highways, roads that connect different states 3) Hydrogen 4) Van Der Waals 5) Hydrophobic  Relative chemical bond strengths more energy stored in bond, greater energy required to form it, greater Covalent energy released when bond is broken Bonds (within molecules) INTRAMOLECULAR bonds are Increasing strength Ionic stronger than INTERMOLECULAR Bonds (between molecules) Hydrogen Bonds Van Der Waals Forces Hydrophobic Forces  INTRAMOLECULAR BOND: atomic number = 1 atomic number = 17  INTRAMOLECULAR BOND: outer shell is closed here also: atomic number = 11 electrons are not shared but are transferred from one atom to the other atomic one atom fills its outer shell number = 12 by gaining electrons while the atomic other fills its outer shell by number = 8 losing electrons  INTERMOLECULAR BOND: (low “electronegativity”) (high “electronegativity”) molecule 1 molecule 2 δ+ δ– δ– δ+ ---- hydrogen bond  T A C G INTERMOLECULAR BOND: Possible scenarios: repulsion between negative electron clouds repulsion between positive nuclei attraction between positive nucleus and negative electron cloud  s -ve INTERMOLECULAR BOND:.. hydrophobic molecule s +ve s +ve water e.g. benzene *explained later on… Hydrophobic molecules: e.g. waxes, fatty acids, oils, alkanes (greasy things) INTRAMOLECULAR BONDS: Covalent Ionic  Atomic number electronegativity  Bonding between atoms with similar electronegativities ½ way between atoms electronegativity 4.0 FF electronegativity 4.0 electron pair forming covalent bond Electronegativity Electron Bond type: difference: attraction: 0 →