Chemical Phenomena¶

Abstract

Definitions

Condensed Phase: The scientific study of the properties of matter, as in its solid and liquid phases, in which atoms or particles adhere to each other or are highly concentrated.

Isotropic: (of an object or substance) having a physical property which has the same value when measured in different directions. Often contrasted with

Exergonic vs Exothermic Exothemric relates to the heat transfer $\Delta H$, while Exergonic refers to the overall enegy transfer $\Delta G$ (which includes entropy)

Important condensed phases¶

Homogeneous liquid solutions are the most common condensed phase in chemistry (solvation)
Solids (particularly crystalline)
Surfaces - interfaces between phases
Liquid crystal solutions - solutions that have non-homogeneous properties - typically non isotropic
Supercritical fluids - taking a substance beyond it’s critical temperature
Membranes - seperate two other phases

Sometimes the boundaries between the condensed phase and the component of interest is not so clear.

e.g. hydrated metal ions.

Why is solvation important¶

Condensed-phase properties depend on the condensed-phase wavefunction. This may be very different from the gas phase properties.

For systems that interact within a condensed phase, the interaction also requires a partial desolvation step to be able to interact

The PES will likely be very different in and out of the condensed phased

E.g. 1. Solvatochromism of Dye $\ce{E_T30}\:(S_1-S_0)$ (excited state 1 $\to$ excited state 0)¶

Solvent	Colour	$\lambda_{max}, nm$
anisole	yellow	769
acetone	green	677
2-pentanol	blue	608
ethanol	violet	550
methanol	red	515

E.g. 2. Enzyme-substrate binding¶

One way to approach this would be to use a thermodynamic cycle (since $\Delta E$ is a state function). This is an example of desolvation used in molecular recognition

\[ \Delta G^\circ_{aq}=-(\Delta G^\circ_{aq}(E)+\Delta G^\circ_{aq}(S))+\Delta G^\circ_g+\Delta G^\circ_{aq}(E\cdot S) \]

Taking the first negative ($-(\Delta G^\circ_{aq}(E)+\Delta G^\circ_{aq}(S))$)is the equivalent of desolvating the components

The PES¶

The solvated energy of a system will not be continuous over all point son the PES. Some solvated geometries will end up with lower minima relative to each other than their gas phase counterparts

E.g. 3. $S_N2$ reaction

This reaction is significantly stabilised by the solvent, since there are charged species involved. In the gas phase, there doesn’t even seem to be a definite transition structure

General reaction coordinate¶

In this particular figure, the primary points of the reaction trajectory are very similar, however the transition structure has moved along the PES ($\ce{<->}$) and the product has been significantly stabilised by the effect of the solvent. This particular representation would allow us to better calculate/plot the reaction free energy cycles involved.

¶

Explicit and Implicit solvent modelling¶

Explicit¶

Add in physical solvent molecules around the system of interest
This will likely make finding the reaction coordinate incredibly difficult, due to the sheer number of degrees of freedom involved in the solvent molecules

Implicit¶

Start by computing the gas phase reaction curve with one method
Then compute the free energies of solvation at specific points of interest, using another method.

Equilibrium - Free energy of solvation¶

These properties are NOT explicitly observable properties of the solvent

\[ \Delta G_S^\circ = \Delta G_{ENP}+G^\circ_{CDS} \]

Where:

The dielectric is represented by (electrostatic):

$E=$ electronic energy - The atomic charges pulling the solvent and solute together
$N=$ nuclear repulsion - The proton-proton forces pushing the solvent and solute apart
$P=$ solute-solvent polarisation - The ability for the solvent to orient itself and for the electrons to disperse around the molecules in reaction to electronic stimuli

Other solvent properties are represented by(non-electrostatic):

$C=$ cavitation energy - The energy required to displace the solvent to form the cavity
$D=$ dispersion forces - “The induced dipole-induced dipole favourable interaction, associated with electron correlation” - not electrostatic since it’s fundamental and the dipoles are non permanent
$S=$ structural - concequences of solvating a molcule that could be favourable or unfavourable, e.g. H-bonding is favourable, non-polar molecules in a polar solvent, is unfavourable (reduces the water’s entropy, because the hydrogen bonding opportunities are lost)