Molecular interactions

Molecular interactions

1. Molecular interactions

   • Electrostatic
     • ion-ion
       • Long range
       • coloumbic interaction
       • Non-directional
       • Many receptors use electrostatics to hold guests in place
     • ion-dipole
       • Directional
         • Dipole aligned for optimal binding
       • not as long ranged as ion-ion
     • dipole- dipole
       • brought on by inherent bond polarity
       • strong orientation dependence
       • Produces attractive or repulsive forces
     • Quadrupole- Quadrupole
       • Charge separation over four sites gives a quadrupole
         • In an aromatic ring, the quadrupole passes through the centre vertically
       • Strong distance dependence (1/r^5)
       • Strong directional dependence
   • Induction
     • Arises from the distortion of a molecule in the electric field of its neighbours
       • Permenant dipole induces a dipole
   • Dispersion
     • induced- induced dipole
     • Dispersion is attractive everywhere and at all distances and orientations
     • Not strongly orientation dependent
     • Short ranged (1/r^6)
   • Repulsion
     • electron-electron repulsion
     • e.g. Lennard-Jones potential
   • Lead to
     • Hydrogen bonding
     • pi-pi interactions
     • cation- pi interactions
     • Van der Waals interactions
     • Results in preferences for particular orientations and reactivity and properties
       • Depend on solvent, temperature and other solutes

2. Quantification

   • Gas phase to solution
     • The changes in the electron cloud repulsion ethalpy can be ignored for molecules in VdW's contact or complexed
     • The effects of induced polarisation are small
     • Dispersion inteactions can be estimated using the Slater-Kirkwood method
       • For two atoms, the disperion interaction depends on atomic polarisability, the number of valence electrons and separation distance
       • Larger and softer atoms give larger dispersion interactions
       • If the atoms are further apart and in solution there are competitive interactions with the solvent so the numerical value is less than expected
       • When measured per unit surface area of contact there is little variation with atom type (cancels out)
     • Electrostatics
       • Can be quantified as pairwise hydrogen bonding interactions where the association constant is found experimentally by fitting to a linear free energy relationship
         • log K = cα2 Hβ2 H + c1
           • c increases for decreasing solvent polarity and c1=-1 and does not vary much
           • + 6 KJ mol-1 for cost of restricting molecular motion
           • Normalisaton of a and b gives acceptor and donor values
             • • HB interactions in blue regions lead to supramolecular complexes
   • 3D plots show interactions in different solvents
     • No solvophobic zone good for weak HB acceptors
     • Disfavoured solute-solute interactions gives good solvents
     • Can use linear free energy relationship and gibbs free energy equations to find association constant in any solvent
     • Solvaphobic interactions
       • For a solution of nonpolar solute in a polar solvent, the solvent can interaction weakly with the solute of strongly with another solvent.
         • Therefore, solute-solvent interaction equilibrium is not 100% towards bound state
         • The limiting situation in water is the formation of a solvent cage around a hydrocarbon to minimise unfavourable solvent-solute interactions
           • Results in a squashed hydrophobic zone, the hydrophobe is less sensitive to the nature of functional group but proportional to surface area
         • In the solvophic quadrant, the size of deltaG is reduced because solvent interactions are already formed in free state
   • Structural effects of alpha and beta
     • Acceptor increases with less s character
       • Acceptor ability increases as effective nuclear charge decreases
       • Acceptor increases down the periodic table (VdW radius)
     • Donor ability increases and electronegativity of substituents increases
       • Donor ability increases as s character increases
       • Configuration: exposure of N l.p. makes it a better acceptor
     • Delocalisation can enhance or reduce donor or acceptor ability
     • Through space repulsion or attraction can alter ability

3. Hydrogen bonding

   • Detection
     • Spectroscopy
       • IR : Curve becomes broader and shift to smaller frequency
       • NMR: Downfield shift
     • Diffraction
       • X-ray molecular diffraction: bond lengths
       • Neutron diffraction: Position of Hs
     • Thermal
       • Increase in M.P.
       • Isothermal titration calorimetry
   • Moderate H-bonds
     • Between neutral donor groups and neutral atoms containing lone pairs
     • Strength depends on surrounding and solvent environment
   • Secondary electrostatic interactions
     • Interactions between neighbouring hydrogen partners can be attractive or repulsive

4. pi-pi interactions

   • Aromatic- aromatic interactions described as charge transfer (weak covalent bond formation)
   • Seen in UV absorption at long wavelengths
   • More complete description involving quadrupoles , which for benzene passes through the centre of the ring
     • Substituent effects can increase of decrease the magnitude of the quadrupole
   • Biological structures predominantly T-shaped, interactions affect stability and folding

5. Electrcstatic interactions

   • ion-ion
     • crown structures and cryptands can detect cations
       • Spherands have higher degree of preorganisation so higher association constants with cations
       • Podand ionophores have over 1000 conformations of which two can bind metal ions octahedrally
     • Salt bridges
       • A salt bring is an ion pair between side chains in a protein in contact with an ammonium ion
         • Considerable variation in strength depending on whether buried of exposed on the protein surface
         • Further reinforcement can be gained by position over a pi surface
     • Channels can selectively only let some ion pass through
     • Anions can be defined and recognised by their charge, size and shape
       • Hofmeister series indicates degree of solvation by water. Expresses the ability to stabilise protein structure
         • Small anions can precipitate protein- protein structure maker
         • Large anions solubilise but do not denature- protein structure breaker
         • Chemical role: catalysis, separation
         • Biological role: signalling, protein stabilisation, phosphate recognition
           • Salt bridges in proteins, transmembrane protassium chanells and transmembrane chloride and anion channels
         • Carboxylates allow neutral receptor to undergo structural reorganisation so no need for solvated anions

6. Hydrophobic effect

   • Polar solvent molecules around a non-polar molecule have to be more ordered than in bulk phase
     • By moving to an organic phase, this hydration sphere can become less ordered and entropy is regained
   • Effect is proportional to the surface area of the molecule being transferred to non-polar environment
   • TdeltaS dominates
   • Crucial in biological processes including assembly of phospholipid bilayer structures, protein folding and recognition events
   • Measured macroscopically for functional groups using the Hansch relationship for substituents on a parent compount
     • Lipophiilicity and other electronic factors are responsible for a drugs interaction with an active site
       • Use QSAR to determine IC50 etc.
   • Amphiphilic molecules have both hydrophilic polar and hydrophobic non-polar groups
   • Call membranes are made up of peoteins, phospholipids and cholesterol
     • Bulky cholesterol disrupts the packing and so prevents freezing a low temps.
     • Cholesterol is rigid and prevents excess chain motion when heated

7. Protein folding

   • Partly driven by desire of poorly solvated non-polar sidechains to avoid water molecules
   • Information for protein folding encoded in the sequence, dihedral angles can only occupy certain combinations
   • Cooperativity speeds up folding as the probability of forming a contact is much higher is another contact is already formed
   • Proteins travel across the energy landscape towards more energetically favourable conformations
     • Hydrophobic effect contributes significantly to the folding of soluble proteins (entropically driven)
     • Hydrogen bonding and pi interactions contribute significantly via secondary structure formation and is enthalpically driven
   • Denatured by heating as TdeltaS increases relative to contribution of H bonds and other favourable interactions. Hydrophobic sidechains are exposed
   • Chaperone-assisted protein folding use ATP to assemble and assist by reducing the energy barriers to folding
     • No use of chaperones can lead to misfolding and genetic diseases

8. Isothermal titration calorimetry

   • Method of choice for studying molecular recognition, protein-protein interactions and protein-ligand interactions
   • Can measure change in free energy, enthalpy and entropy
     • Free energy can provide information about the strength of interactions
     • Enthalpy and entropy reveals the driving forces for complex formation and mechanisms
     • Method 1: titrant is titrated into reaction cell containing titrand. The reference cell and reaction cell are maintained at the same temp and measure temp difference between sample and reference and cells and jacket
       • Method 2: titrant is injected stepwise. For each injection, the reaction between ligand and host emits/absorbs heat in the sample cell. The power needed to keep the cells at constant temp. is measured.
         • The heat released upon binding the ligand is monitored over time.
           • A peak is observed upon heat change, due to injection of ligand into cell
             • Heat change is proportional to amount of binding and decreases over time due to saturation
         • Binding curve obtained from plot of enthalpy vs. ligand:host ratio and fit curve to determine Ka, stoichiometry, enthalpy and total head of reaction
   • Can express heat of reaction with total concentration of ligand and total concentration of macromolecule
     • Use non-linear least squares analysis
       • Best fit will represent the sigmoidal curve
     • A plot of ethalpy vs. T to check linearity and obtain heat capacity change (gradient)
       • A large negative change in capacity suggests a change in surface hydration
         • Water is removed from the solute surface and returned to the bulk solvent
   • Limitations
     • Ligand and host will need to be in the same buffer and salt
     • 5-60C
     • Works for c=10-100 and k=10^8 - 10^9
       • Requires relatively large quantities of protein and ligand
         • Weak association constant makes this worse
     • Remember to measure and account for self-association
     • Coupled and complex equilibria requires more sophisticated algorithms
   • Systems with large c values can be measured by using competition assays
   • Apparent change in enthalpy
     • May not be a direct measure of the interactions between the molecules in a complex
     • e.g. may be a change in confomation
       • Can be deduced from the crystal structures
     • e.g. may be a proton transfer
       • Run experiments at the same pH but in different buffers
         • A change in enthalpy with different buffers is a sign on proton transfer

9. Physical methods

   • To determine Ka and stoichiometry
     • ITC
     • Solution NMR
     • UV/ Fluorescence
     • Quartz Crystal Microbalance
     • Vapour pressure osmometry
     • Choice of method depends on concentration
       • Work between 20-80% for best accuracy
   • Vapour pressure osmometry
     • Depends on colligative properties
       • Vapour pressure and colligative properties depend on the number of particles in solutions
       • The van't Hoff factor is the ratio between the actual concentration of particles in a mixture and the concentration calculated from its molecular mass
         • Less than 1 if associate
     • Vapour pressure above a solution depends on the number of particles in solution, a molecular of weight m which aggregates in solution will give an apparent molecular weight on nm
     • Measure different in resistance between two thermistors with a drop of solution on one and solvent on the other via a wheatstone bridge
   • Gel permeatation
     • Smaller particles have longer retention time
       • Sharper preak means more stable so can determine number of particles in aggregate and number of hydrogen bonds
   • NMR
     • Shifts due to complexation
     • Followed by titration and can measure concentration and shift
       • Shift moves more downfield as concentration increases
       • Peak on Job's plot gives maximum stoichiometry
   • Can calculate enthalpy and entropy from variable temperature binding experiments
   • nOe NMR shows where hydrogens are in space relative to each other
   • UV-Vis: titrate one component into another
     • Number of isobestic points corresponds to number of species present

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