all 2004 Supplemental notes Acids and Bases Curved Arrow ormalism or Pushing Electrons Carbon and other second row elements such as B,,, and follow the octet rule, i.e. they try to have the sum of bonding electrons and electrons in lone pairs around them equal to 8. or the first row, hydrogen tries to have 2 electrons. In general, E of these elements will have more than an octet (or duet for hydrogen). Electron Deficient Compounds Sometimes molecules have atoms that are short of an octet by one or more electron pairs they tend to be very reactive. or example: 1. + has 0 electrons and it needs 2, thus it is deficient by 2. 2. B 3 is an electron deficient compound. The boron atom in boron tri-fluoride has 6 electrons, and it needs 8. Thus it is deficient by 2 electrons. ne additional lone pair is needed to fill its octet. B B B 3. Methyl cation has 6 electrons, and it needs 8, thus is deficient by 2. C C C -1-
all 2004 Supplemental notes Lewis Acids and Lewis Bases + B B B 8 Electron Lewis Base Lewis Acid Tetrafluoroborate ion Electron deficient compounds, which can behave a electron pair acceptors are Lewis acids. A species that donates an electron pair is a Lewis base. The reaction above is called Lewis acid/ Lewis base association reaction. Lewis acid electrophile ( loves electrons ) Lewis base nucleophile (why??) We will see many Lewis acid-lewis base reactions in coming months. IT IS VERY IMPRTAT to be able to identify Lewis acids and Lewis bases. Another example (simplified): lone pair + ammonium ion 8 e - Lewis Base 0 e - Lewis Acid 8 e- -2-
all 2004 Supplemental notes What Do Curved Arrows Mean? source of electrons destination of electrons new bond, electrons shared B 3 B 3 The curved arrow indicates the flow of electrons. The arrow always starts at the electron donor and ends at the electron acceptor. ere the arrow starts at the Lewis base end and ends at the electron deficient species (the Lewis acid). **ote that charge is conserved. What about the reverse reaction? B B + -3-
all 2004 Supplemental notes + Conjugate Acid-Base Pairs Br Base Acid Conjugate acid + Br Conjugate base Conjugate Acid-Base Pairs 1. ote that the -Br bond is broken and 3 - bond is formed. 2. Why is the -Br bond broken? Because the in Br already had a duet and if it is to accept two electrons from ammonia, it must also lose two. 3. When a lone pair is contributed, the formal charge on the atom contributing the lone pair becomes more positive by one integer, and when a lone pair is gained, the formal charge on the atom receiving the lone pair becomes more negative by one integer. Example: 0 0 +1-1 + Br itrogen contributes a lone pair to form a new bond, so the charge increases by 1. Bromine gains a lone pair when the bond is broken, so the charge decreases by one. ote that the net charge on both side of the arrow should be the same (charge is conserved). + Br -4-
all 2004 Supplemental notes Examples Drawn to show tetrahedral geometry with lone pairs occupying sites. Base Acid C 3 C 3 Conjugate acid + C 3 C 3 Conjugate base Conjugate Acid-Base Pairs ote the charges, bonds formed and bonds broken. ote the conjugate Lewis acid pair and Lewis base pair. ote that the arrows indicate flow of electrons. What about: Base Acid C 3 C 3 Conjugate acid + C 3 C 3 Conjugate base Conjugate Acid-Base Pairs Wrong Reaction is not wrong, BUT use of the curved arrow is incorrect. REMEMBER: Electrons flow from tail to head!! Also note BrØnsted-Lowry Acid and Bases: BrØnsted Acid A species which reacts by donating a proton ( + ). BrØnsted Base A species that can accept a proton. BrØnsted-Lowry summary: m n m-1 n+1 X + B X + B Bronsted Acid Bronsted Base -5- Conjugate Base Conjugate Acid So BrØnsted-Lowry Acid-Base definition is a more limited definition than Lewis acid base.
all 2004 Supplemental notes Use of Curved Arrow ormalism to Derive Resonance Structures ot all molecules can be described well by one Lewis structure. In many cases another structure can be derived by a shift of one or more electron pairs. Both structures for benzene are equal in energy. Which structure is correct? Actually, neither is correct. The real structure of benzene is in between the two structures above. The two structures shown above are called two limiting resonance structures. ** Extremely important: Resonance does T imply rapid interchange between structures, but rather that the actual structure is a weighted average of the two (or more) limiting resonance structures. Curved arrows can help one draw resonance structures. ere the arrow describes flow in the loose sense of the word. circle impies 1.5 bonds between carbons -6-
all 2004 Supplemental notes ther Examples 3 C 3 C 3 C curve implies 1.5 bonds between carbons ote, like in the case of Lewis acids-lewis bases: The arrow represents flow of electron pair. low "in", means formation of new bond; low "out", means breaking a bond. Atoms should not violate octet rule. The overall charge is conserved. 3 C C 3 3 C C 3 C C 3 3 Left structure, no charge separation. Right structure +,- so right structure is higher energy and contributes less. 2 C C 3 2 C C 3 Right structure has the minus charge on more electronegative atom. So, the right structure is lower in energy and contributes more to the actual structure of the molecule. -7-
all 2004 Supplemental notes Stability of Resonance Structures and Summary for Deriving Them: Try to satisfy octet. Maximize the number of covalent bonds. Minimize charge separation. Try to place negative charges (electrons) on most electronegative atom. Positive charge on halogens is really bad (because they are highly electronegative). ewer than four bonds to carbon is quite bad. Charges on carbon are quite bad. More than 8 electrons on carbon, nitrogen, or oxygen, is unacceptable. -8-
all 2004 Supplemental notes BrØnsted -Lowry Acid Base Equilibria Equilibrium constants: n m n-1 m+1 X + B X + B e.g. Cl + Cl + ne can write an equilibrium expression: K eq = X n-1 B m+1 n m X B Molarity of species K eq > 1 implies reaction goes to the right K eq < 1 implies reaction goes to the left K eq > 1 implies that X- n is a stronger acid than -B m+1 and that :B m is a stronger base than X n-1-9-
all 2004 Supplemental notes Acid-Base Equilibria in Water In the case below where water is the solvent: X + 2 X - + 3 + then: X 3 K eq = X 2 In this case concentration of 2 = 55 M and is effectively unchanged since it is present in such a large excess. Then, K a = K eq [ 2 ] = X 3 X K a = dissociation constant and is a measure of acid strength. Larger K a implies stronger acid. Range of K a we may see is from 10-55 up to 10 7 ; 62! orders of magnitude. Chemists use inverse log scale: pk a = -logk a the lower the pk a, the stronger the acid p = -log[ 3 + ] the lower the p, more acidic the solution ote for: n m K eq n-1 m+1 X + Y X + Y -([pka (X)]-[pKa (Y)]) K eq = 10-10-
all 2004 Supplemental notes pk a values Examples 2 3 C 4 3 16 33 50-60 + + 2 pka 3 16 K eq = 10 -(3-16) = 10 +13 So this reaction goes towards the right. 2 + C 3 + C 4 pka 16 ~50 K eq = 10 -(16-50) = 10 34!! So, pk a 's are quantitative measures of acidity and allows one to make predictions about reactions. Example: Conjgate Base: C - 3 > - 2 > - > : 3 > 2 Ö: > >>>> Acid + C 4 < : 3 < 2 Ö: < 4 < 3 + <<< 2 + pk a : >50 33 16 10 2 << 10 otice that both 3 and 2 can be both acid and base. Such compounds are said to be amphoteric. -11-
all 2004 Supplemental notes Strengths of BrØnsted-Lowry Acids and Bases Proton transfer reactions: Proton transfer reactions can generate ions hydroxide ion 2 + 2 + 3 hydronium ion ydronium ion as acid: length of arrow indicates approximate position of equilibrium 3 + 3 2 + 4 ydroxide ion as base: + 2 + 3 2 + C 4 2 + C 3 + 2 + -12-
all 2004 Supplemental notes Rules for Charge Stability of Ions with a ull ctet Element effect 1. egative charge is most stable on most electronegative atom. - > R- - > R 2 - > R 3 C - Increasing Stability 2. or atoms of similar electronegativity, the negative or positive charge is more stable on the larger atom. R-Te - > R-Se - > R-S - > R- - Increasing Stability R 2 S + > R 2 + Increasing Stability Why? Larger atoms distribute charge over a greater volume. 3. Positive charge is most stable on least electronegative atom. R 3 + > R 2 + Increasing Stability These trends in stability can be used to predict directions of the acid-base reaction shown above and others throughout the term. LEAR TIS WELL! -13-
all 2004 Supplemental notes Periodic table of 246a Valence electrons 1 2 3 4 5 6 7 8 Li a K Be Mg Ca B C Al Si P S Electronegativity increases across row Electron affinity increases across row Acidity increases across row Cl Br I e e Ar Kr Xe Acidity increases down column Bond strength to decreases down column Acidity of acids in a row C 4 < 3 < 2 < pk a ~50 ~32 16 3.5 Acidity of acids in a column < Cl < Br < I pk a 3.5 ~ 6 ~ 8 ~ 10-14-
all 2004 Supplemental notes is more electronegative than I. So how do we explain this trend? Consider reaction -A + + A: - We can use ess law of summation to break up reaction into pieces 1. Bond breaking -A + A 2. Electron add to A e - + A A: - 3. Ionization of + + e - Sum -A + + A - -15-
all 2004 Supplemental notes ow for comparison between acids: 1. Bond Breaking a) Energy to break bonds drops dramatically down column Bond - - Cl - Br - I Bond Dissociation Energy (BDE) (kcal/mol): 136 103 88 71 Reason: Lower orbital overlap b) Energy to break bond doesn't vary so much across a row Bond C 3-2 - - - BDE (kcal/mol) 105 107 119 136 2. e - +A A: - is electron affinity, EA a) Electron affinity doesn't vary that much down a column Atom I Br Cl EA(kcal/mol) 70 78 83 78 b) Electron affinity increases dramatically across a row Atom C 3 3 EA(kcal/mol) 1.8 18 42 78 3. Ionization of to + This is the same for each acid so it doesn't enter into comparison. -16-
all 2004 Supplemental notes So, or BDE I (kcal/mol) 136 71 BDE = 65 kcal/mol avors I or EA I (kcal/mol) 78 70 EA = 8 kcal/mol avors But 65 >> 8 thus I must be stronger acid than So, down a column BDE dominates the strength of the acid. In a row EA dominates the strength of the acid. -17-
all 2004 Supplemental notes Polar or Inductive Effects Remember that opposite charges attract -- like charges repel 1) o relative stabilization 2) Charge spread over larger volume-some stabilization 3) Dipole- some significant stablization 4) Two dipoles- more significant stablization 5) Dipole oriented in wrong directiondestablization 6) Remote dipole- weak stablization All other things equal, if molecules have similar conjugate bases which experience these environments then (ignoring entry #2!): pka: 5 > 1 > 6 > 3 > 4-18-
all 2004 Supplemental notes Examples umber of polar groups: Cl Cl Cl Cl Cl Cl pka 4.73 2.86 1.26 0.064 Proximity of polar groups: Cl Cl pka 4.82 4.52 4.06 2.84 Cl Resonance: pka 18 5 13 orders of magnitude Why? but also less important The minus charge is delocalized between the oxygens. The resonance structure on the right inductively stabilizes oxygen (but is a minor contributor). SUMMARY: Three major effects: Element effect (EA and BDE), Inductive effect, and Resonance -19-
all 2004 Supplemental notes Conjugate Acid LEAR TESE VALUES Conjugate Base pka I I - -11 Br Br - -8 Cl Cl - -6 3 + 2-2 S 3 S 3 - -1 3 C 3 C - 0 3 C 3 C - 4.76 2 S S - 7.0 C C - 9.2 4 + 3 9.2 R-S R-S - 10-12 R- R- - 16-20 3 2-32 2-35 C 4 - C 3 Increasing acidity: Increasing basicity: UP in table DW in table A strong acid makes a weak base and vice versa. 48-20-
all 2004 Supplemental notes ydrogen Bonding A hydrogen bond is a particular type of a Lewis acid-lewis base interaction. It can occur between a hydrogen atom attached to a heteroatom such as,, (called the hydrogen bond donor group) and an atom that has a lone pair (typically also,, and ) the hydrogen bond acceptor. More generally any acidic hydrogen can be a hydrogen bond donor and any Lewis base can be a hydrogen bond acceptor. ydrogen bonding is a special case of dipole-dipole interactions, and it is also an example of a weak covalent bonding interaction. donor 0.96Å 1.8-1.9Å acceptor ote that the --- angle is drawn to be 180, I believe that this is the preferred angle for hydrogen bonds. -21-
all 2004 Supplemental notes Effects of ydrogen Bonding ydrogen bonding affects the boiling point of solvents. Thus for water and low molecular weight alcohols, the boiling points are unusually high since in addition to overcoming van der Waals interactions, the hydrogen bonds must be broken in order to vaporize the solvent. If such interactions did not occur it is likely that water would boil below ambient temperature, which would make life on earth rather difficult. As we will see later, solvents capable of hydrogen bonding selectively stabilize anions. -22-
all 2004 Supplemental notes Importance of ydrogen Bonding to Life on Earth ydrogen bonds are critical to defining the base pairing in DA. The specificity of the hydrogen bonding interactions in DA is thought to be central to its ability to replicate with high fidelity. - P - Adenine Thymine - P - - P - Cytosine Guanine P - - -23-
all 2004 Supplemental notes ydrogen Bonding and Proteins ydrogen bonds are critical to the so-called secondary structure of proteins (of which enzymes are a subset). The primary structure is the sequence of amino acids that make up the protein. The secondary structure is predominantly determined through hydrogen bonding interactions. These interactions largely define the threedimensional structure of the protein. The actual sequence of amino acids determines what hydrogen bonds can be formed. Much research is now devoted to understanding how to predict the three-dimensional structure of proteins based upon the amino acid sequence. The three-dimensional structure of a protein determines its physical and chemical properties. As an example, spider silk has a specific secondary structure (known as β pleated sheets) that gives it strength in three dimensions (its strength per unit weight is greater than that of steel!) The reactivity of an enzyme is defined by its three -dimensional structure. -24-