BC351 Lecture 1 Chemical Bonding and Thermodynamics Terms Bond Dissociation energy Hydrogen Bond Ionic Bond Hydrophobic effect Change in free energy Electronegativity Equilibrium constant Covalent Bond Entropy Enthalpy Free energy Spontanity Equilibrium Principles 1 The physical nature and the importance of non covalent interactions 2 Introduction to thermodynamics a The interplay between free energy enthalpy and entropy in chemical biochemical processes b The interplay between free energy and equilibrium I Chemical Bonding MUCH OF THIS SHOULD BE REVIEW a We must consider two major classes of chemical bonds in Biochemistry i Covalent bonds ii Non covalent bonds 1 Non covalent bonds can also be called a Weak forces b Weak interactions 2 These include but are not limited to a Ionic bonds b Hydrogen bonds c van der Waals interactions d Hydrophobic interactions LN01 1 b Covalent Bonds pgs 11 14 i Definition of a covalent bond 1 2 As biochemist we are concerned primarily with covalent bonds between H C O and N a These atoms are the major constituents of the macromolecules of biochemical concern i Lipids ii Polysaccharides iii Proteins iv Nucleic acids LN01 2 b Your book also discusses functional groups and makes a rather large list of these in figure 1 15 page 12 ii Bond Dissociation energy pg 44 1 Definition of Bond Dissociation energy a 2 Covalent bonds are particularly strong bonds with dissociation energies ranging from 250 500kJ mol LN01 3 c Non covalent interactions pgs 43 51 i Why do we talk about these 1 Hydrogen bonds and ionic hydrophobic Greek waterfearing and van der Waals interactions are individually weak but collectively they have a very significant influence on the three dimensional structures of proteins nucleic acids polysaccharides and membrane lipids pg 43 ii The types we will consider 1 Hydrogen bonds a Definition of the hydrogen bond i b Definition of electronegativity i ii Rank of electronegative atoms of biochemical interest 1 H C N O LN01 4 c Water is an excellent example of a molecule that exhibits hydrogen bonding potential LN01 5 d Hydrogen bonding in general e Hydrogen bonds are weak compared to covalent bonds i Bond dissociation energy of hydrogen bonds 1 20 25 kJ mol LN01 6 2 Ionic Bonds aka Salt bridges a Definition of an Ionic Bond i O RCO O H RNH H N b The bond dissociation energy of a ionic bond is dependent upon several factors described by the following equation i F Q1Q2 r2 1 Q charge of the two ions 2 r distance b w the two ions 3 dielectric constant ii The dielectric constant reflects the ability of the solvent to disrupt or shield the bond LN01 7 3 Hydrophobic interactions a Definition of hydrophobic effect interaction i II Thermodynamics a Free energy G pgs 21 24 i Definition of Free energy 1 2 In many ways you can think of G as potential energy ii Definition of the change in free energy G 1 2 There are two types of chemical reactions with respects to G a Exergonic reactions i ii b Endergonic reactions i ii 3 Spontaneous reaction a LN01 8 G G REACTION COORDINATE REACTION COORDINATE R C R C b What determines if a reaction is exergonic or endergonic 1 There are a number of ways to answer this question however we will start with a fundamental thermodynamic equation a G H T S b That is to say that a reactions change in free energy is dependent upon two other thermodynamic parameters enthalpy H and entropy S i So what are these parameters c Enthalpy H The Heat Inside i Definition of Enthalpy 1 ii Heat content is a reflection of the number and types of bonds 1 Enthalpy is best thought of in terms of the number and types of bonds found in any given system Whenever we consider enthalpy in this class we will be thinking of bonds breaking and forming LN01 9 of Covalent Bonds of Covalent Bonds of Hydrogen Bonds of Hydrogen Bonds of Ionic Bonds of Ionic Bonds iii There are two types of chemical reactions with respects to H much like with G 1 Exothermic reactions a 2 Endothermic reactions a d Entropy S i Definition of Entropy 1 a If a systems order increases in the process of a chemical reaction then the change in entropy S will be negative LN01 10 b If a systems order decreases in the process of a chemical reaction then the change in entropy S will be positive 2 A word on the universe a The 2nd law of thermodynamics states that the entropy of the universe is increasing S However we can give many examples of processes that have a S In these cases we are considering only the system and not the system plus its surroundings system surroundings universe e The interplay between these parameters in chemical processes i Water evaporation H 2O l H 2O g G H S 3 DAYS LN01 11 ii The hydrophobic effect f Equilibrium and G i Definition of equilibrium 1 A B TIME 0s A B TIME 2s A B TIME 60s 2 The equilibrium constant a b If the Keq is large then products will predominate once the free energy has been minimized c If the Keq is small then reactants will predominate once the free energy has been minimized LN01 12 3 Once a reaction has reached equilibrium it has minimized its free energy a When a reaction is NOT at equilibrium there remains a driving force to obtain this condition That driving force can be quantified as the change in free energy G LN01 13