# 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¶

1. Start by computing the gas phase reaction curve with one method
2. 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)