Lecture 1 Water And Noncovalent Interactions PDF

Water and Noncovalent Interactions Lecture 1 BCMB 401 Spring 24 Reading: Chapter 1.3, appendix Properties of Water Water is a polar molecule that is capable of hydrogen bond interactions In biological systems water is the predominant solvent. It forms a hydrogen bond network that is cohesive yet dyn...

Water and Noncovalent Interactions Lecture 1 BCMB 401 Spring 24 Reading: Chapter 1.3, appendix Properties of Water Water is a polar molecule that is capable of hydrogen bond interactions In biological systems water is the predominant solvent. It forms a hydrogen bond network that is cohesive yet dynamic. (ps to ns) 3-4 hydrogen bonds per water molecule Important for solubility of hydrophilic biomolecules Also leads to the hydrophobic effect Properties of Water Solubility of Hydrophilic Biomolecules (example: Proteins) When we see a protein in aqueous solution represented like this…. we should be thinking about it like this with H2O molecules interacting with full and partial charges on surface of protein: From Front. Mol. Biosci., 13 July 2018 The Hydrophobic Effect is Responsible for Membrane Formation (Barriers) Covalent Bonds: sharing of electrons Covalent interactions C C 1.54 Å Covalent bonds, formed by electron sharing between two adjacent atoms, are the strongest bonds. Bond energy 355 kJ/mol (In this instance textbook is referring to bond dissociation energy) Considerable energy must be used to break covalent bonds. Double bonds such as C=O are even stronger than C-C single bonds Resonance Structures Molecules that have multiple covalent bonding patterns (resonance structures) are more stable (more energetically favorable) Noncovalent Bonding: Critical in biochemical interactions Non-covalent interactions Weaker and more transient: allow biomolecules to interact reversibly in aqueous media Multiple noncovalent interactions create specificity in binding between biomolecules Four types: 1. Ionic interactions 2. Hydrogen bonds 3. van der Waals interactions 4. Hydrophobic effect Noncovalent Interactions 1. Ionic interactions Attractive interactions between two fixed charge centers of opposite sign or repulsion between charges of same sign Energy of an ionic interaction given by the equation: kq1q2 E= Dr Salt crystal Dielectric constant ‘D’ is determined by medium (solvent) Solvent D *Energy hexane water 2 80 -232 kJ/mol -5.8 kJ/mol *In this instance textbook is referring to bond formation energy (enthalpy) r = 3.0 Å and q1= +1 and q2= -1 used in above calculations Proportionality constant, k= 1389 kJ Å mol-1 High dielectric constant of water allows weakening of ionic interactions and dissolution of salts Noncovalent Interactions 2. Hydrogen Bonds Dipole-dipole/electrostatic interactions between an electronegative atoms and a hydrogen covalently bonded to another electronegative atom In biological systems, typically N or O. Also F (not abundant in biochemistry) or in some cases S (depends on environment) Bond length usually 2.5 to 3.5 Å and is measured electronegative atom to electronegative atom. Bond energy usually 4 to 20 kJ/mol (to break) Hydrogen-bond donor = the group that includes the electronegative atom to which the hydrogen atom is covalently bonded Hydrogen-bond acceptor = the electronegative atom less tightly linked (not covalently bonded) to the hydrogen atom Water weakens hydrogen bonds within or between other molecules Have a bond angle. Strongest hydrogen bonds are (approximately) straight (close to 180°) Noncovalent Interactions 3. van der Waals Interactions Transient asymmetry in electron distribution in one atom induces complementary asymmetry in a neighboring atom → resulting in an attraction between the two atoms Bond energy ~ 2 to 4 kJ/mol at optimal distance Weak but additive Noncovalent Interactions 4. Hydrophobic Effect Direct result of placing hydrophobic nonpolar molecules in an aqueous medium Nonpolar molecules in water cannot form dipole-dipole interactions with water molecules Disruption of the hydrogen bonding network of water and increased ordering Nonpolar molecules driven together, water molecules released to bulk solvent. Increases favorable entropy of water. Resulting interactions between nonpolar surfaces are called hydrophobic interactions Energetic driving force → increasing the favorable entropy of water (minimizing unfavorable entropy of water) The laws of thermodynamics govern the behavior of biochemical systems ΔG = ΔH – TΔS (-) ΔG < 0 → Favorable / spontaneous 0 ΔG = 0 → Equilibrium (+) ΔG > 0 → Unfavorable / not spontaneous H = enthalpy → bonds ΔH = change in heat due to bond making and breaking S = entropy → disorder ΔS = change in randomness S = kB ln Ω (Ω = number of microstates, the more microstates a molecule can exist in → the greater the entropy) T is temperature in Kelvin Visualizing Molecular Structures: Small Molecules Stereochemical Renderings and Fischer Projections Space-filling and Ball-and-Stick Models