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Atoms, Orbitals,
Bonding & Molecules
Emphasizing the Chemistry in Space Science
Glenn R. Morello
Postdoctoral Research Fellow
Centre for Theoretical and Computational Chemistry
[email protected]
Molecules in Astrophysics and
Astrobiology
13-17 February 2017
Outline
Atomic Structure
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Early work on the theory of atomic structure
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Brief look at quantum mechanical descriptions
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Orbitals and occupation in atoms
Bonding in Atoms
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Aspects of bonding; forces and electron density interactions
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From AOs to MOs
Molecules in Space
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Types of molecules in space
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How can these form?
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Solid and liquid phase reactions
Detecting Molecules
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Problems encountered with detecting molecules
Atomic Structure
Atomic Structure (Early)
Important Experiments that Solved Structure
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JJ Thompson – discovers charged particle (electron)
(1897)
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Marie & Pierre Curie – radioactivity (1898)
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Rutherford – alpha and beta particles (1898)
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Rutherford – nuclear model of atom (1911)*
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Bohr – new atomic structure (1913)*
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Rutherford – proton (1920)
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Plank, Bohr, Heisenberg – quantum mechanics (1925)
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Chadwick – neutron (1932)
Atomic Structure (Early)
Proving Structure
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Bohr’s atomic picture fit hydrogen’s emission spectrum
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The key was discrete circular energy levels of electrons
H2 emission spectrum (top)
H2 absorption spectrum (bottom)
Although this electron picture was wrong, the discrete energy values was
correct.
Atomic Structure (Quantum)
Wave Mechanics
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Electrons are both a wave and a particle!?!?
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Uses wave mechanics to give complete description of atoms and molecules
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Schrödinger’s wave equation is the lifeblood of Quantum Mechanics
Atomic Orbitals
Orbitals
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Generally, quantum mechanics relies on electron probability density (P = ψ2)
•
These densities are the “orbitals” we learn early on in general chemistry
Radial distribution
function, ψ2 multiplied by
4πr2
This is spherical in all space
These are the orbitals we
learned in basic chemistry
Atomic Orbitals
Orbitals
•
Generally, quantum mechanics relies on electron probability density (P = ψ2)
•
These densities are the “orbitals” we learn early on in general chemistry
Shapes of orbitals are governed by the
quantum numbers
n – principle quantum number
l – angular momentum
ml – magnetic quantum number
Filling Atomic Orbitals
Orbital Occupation Rules
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Pauli Exclusion Principle: electrons cannot occupy the same quantum state within a
quantum system simultaneously
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All quantum numbers cannot be the same (n, l, ml, s)
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Electrons can only be paired if they have opposite spins
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Electrons are fermions – the wavefunction is required to be antisymmetric
Filling Atomic Orbitals
Orbital Occupation Rules
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Pauli Exclusion Principle: electrons cannot occupy the same quantum state within a
quantum system simultaneously
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All quantum numbers cannot be the same (n, l, ml, s)
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Electrons can only be paired if they have opposite spins
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Electrons are fermions – the wavefunction is required to be antisymmetric
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This is derived mathematically (naturally) in quantum mechanics
Filling Atomic Orbitals
Orbital Occupation Rules
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Hund’s Rule: the state with maximum multiplicity lies lowest in energy
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Electrons do not pair until the orbitals of that level are filled with one electron first
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Unpaired, same spin electrons “see” each other less
Bonding in Atoms
Forces in Bonding
Attractive Forces
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Atoms attract each other at small distances
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Electronegativity (ionic vs. covalent bond)
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Electron (-) attraction towards nucleus (+)
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van der Waals (London and dipoles)
Repulsive Forces
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Pauli repulsion
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Nuclei overlap
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Shrinking ‘space’ for electrons and nucleus
Describing Bonding Forces
Lennard-Jones Potential
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Mathematical description of bonding
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Repulsion is given positive value
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Attraction is given negative value
Why?
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Atoms alone are “zero”
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Formation of bonds creates a more stable
state – negative energy
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It looks better too
When we talk about bond strength, we talk about energy required to break a bond
energy in  positive energy
Quantum Bonding Description
Ψ of same sign overlap
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Electrons have a bigger area to
move
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Most of the electron density is
between the atoms
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Result: Lower energy orbital
Ψ of opposite sign do not overlap
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Most of the electron density would be
found around the individual nuclei
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Result: Higher energy orbital
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These orbitals are typically not
occupied (not in a ground state)
Molecular Orbitals
anti-bonding
bonding
Two atomic orbitals (AO) create two molecular orbitals (MO) when
bonding occurs
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Example here shows the MO diagram for H2
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Electrons will pair with opposite spin and reside in the low energy bonding orbital (σ1s)
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Anti-bonding orbital (σ*1s) is accessible for excited electrons.
Molecular Orbitals
Example MO diagram: N2
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One on axis pz-orbital interacts with the 2s orbital and is a σ-type MO
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Remaining p-orbital electrons combines in π-orbitals
Molecular Orbitals
Example MO diagram: CO
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Similar to N2 diagram with shifted energy levels of the AOs
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σ orbitals have their typical spherical shape
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5σ is the lone pair on carbon
Molecular Orbitals
Example MO diagram: O2
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2s orbitals are very low in energy and do not interact with p-orbitals
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The pz orbital forms the lower energy σ MO
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The px and py combine to make the π and π* orbitals
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Here we have enough electrons to populate the anti-bonding π*!
Astrophysics Consequence
White Dwarfs do not collapse to form black
holes…why?
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At extremely high densities all electrons are free
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So they will all want to be in a minimum energy state
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But what did we just learn?
Electrons are fermions
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No two electrons can occupy the same state
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They arrange in bands of energy levels
Bands in a normal solid
Astrophysics Consequence
White Dwarfs do not collapse to form black
holes…why?
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At extremely high densities all electrons are free
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So they will all want to be in a minimum energy state
•
But what did we just learn?
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Energy
Electrons are fermions
No two electrons can occupy the same state
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They arrange in bands of energy levels
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Compression of electron gas increases electrons per volume
element
•
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Maximum energy level of electron gas increases with pressure
Can not overcome electron degeneracy pressure to collapse!
+
pressure
Normal solid
electron band
White dwarf
electron gas
Molecules in Space
Molecules in Space
Why do atoms react in space?
•
What atoms are in space?
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How do we know?
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What forces govern reactivity?
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How can we use knowledge of space molecules to predict things?
Diatomic
Two atom molecules
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Simple molecules and can be highly
abundant. (H2, N2, O2, CO, etc…)
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Detected through spectroscopic methods:
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Emission lines
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Infrared
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Radiowaves
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Microwaves
Polyatomic
Multi-atom molecules
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Water is one of the the most abundant in
space (atmospheres, interstellar clouds,
moons and planets)
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If these small molecules containing H2O, S,
P, N, O, C are able to react in space or on a
surface (planet or moon), is this how life
began?
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Amino acid building blocks have observed in
space
Molecule Formation in Space
How are molecules formed in space?
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Gas phase reactions are typically performed through excitations or collisions (or both)
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Interstellar matter is not dense (compared to terrestrial densities)
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However, attractions of atoms and molecules to each other for dust particles.
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These are typically made of carbon and silicon
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As grains grow, more reactions can take place
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Surface chemistry very important
Surface Chemistry
Surfaces can be extremely reactive
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Surface atom rearrangement allows access to reactive surface areas
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Space provide all the tool necessary for chemistry…
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Electromagnetic radiation as energy source
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Small molecules
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Dust particles with varying elemental composition
Surface Chemistry
Surfaces can be extremely reactive
•
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Oxygen terminated surface are very reactive
Can form –OH groups, or react with water, H2, small molecules
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Surfaces can perform catalytic reactions (transition metals, oxides, etc..)
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Transition metals can accept electron density
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Polymers, cyclization, and more reactions accessible
Titanium dioxide
Silicon dioxide
Importance of Dust
H2 and O2 and dust….ingredients for life
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Study of dust particles shows absorption and desorption of molecules on dust particle
surfaces.
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O2 deposited on silicate surfaces generate H2O
Importance of Dust
H2 and O2 and dust….ingredients for life!
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Study of dust particles shows absorption and desorption of molecules on dust particle
surfaces.
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O2 deposited on silicate surfaces generate H2O
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Surface is acting as a catalyst for the reaction (energy barrier is reduced)
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New MOs created for the absorbing species, making new bond formation possible
(creation of H2O on the surface)
Remember orbital energies
change when bonds (MOs)
are formed!
CO molecule on Ni surface
Terrestrial Formation
Generation of small molecules (water and more)
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Surface chemistry can favor the formation of certain molecules
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Computational studies using quantum mechanical methodologies can accurately predict
reaction energies at surfaces
Terrestrial Formation
Generation of small molecules (water and more)
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Surface chemistry can favor the formation of certain molecules
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Computational studies using quantum mechanical methodologies can accurately predict
reaction energies at surfaces
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Here, CH4 and C2H4 are not strongly interacting with the surface, but others are
Solution Chemistry
On terrestrial surfaces liquids can influence chemistry
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Oceans on planets and moons
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H2O, liquid methane, ethanol, methanol, …
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Solvent-molecule interactions
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Changes in reaction energies
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Changes properties
How
Solution Effects on Reactivity
Water effects
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Hydrogen bonding is very important
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Can alter reaction energies
Solution Effects on Reactivity
Water effects
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Hydrogen bonding is very important
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Can alter reaction energies
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Dipoles change
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Stabilizes intermediates and products
Life on Enceladus?
Enceladus
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Moon of Saturn
Liquid ocean under a thick layer of ice
Thermal heating
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Tidal effects from Saturn
Geysers spews water and organic
molecules into space
Thought to have deep water geysers
like the Lost City
Can life exist here?
H2O Based Life…or Something Else?
Are there more ways to generate life?
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We think water is the key to life (at least OUR life)
•
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Water penetrates the rock (serpentinization) and creates different minerals and active sites
Can other solvent molecules replace water?
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Alcohols hydrogen bond (weaker)
H2O Based Life…or Something Else?
Are there more ways to generate life?
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We think water is the key to life (at least OUR life)
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Can other solvent molecules replace water?
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Water penetrates the rock (serpentinization) and creates different minerals and active sites
Alcohols hydrogen bond (weaker)
Thought experiment: what happens if you put a protein in another solvent?
Liquid and Solid Interfaces
All ingredients found in space
Liquid and Solid Interfaces
All ingredients found in space
Detecting Molecules
Reactions And Detection
Detecting molecules and reactions
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Energy sources such as cosmic rays can help formation of dust and induce reactivity of
otherwise inert molecules/atoms
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Energy released from excited molecule can be detected
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Molecule can be detected through spectroscopic methods
Detection Problems
Problems with Detecting Diatomic Molecules
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Can be difficult to “see” with spectroscopic methods as they do not have a dipole moment
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For example; Infrared (FT-IR) detection requires a dipole moment
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H2, N2, O2, etc… are invisible.
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Triatomic molecules are detectable…even CO2
Not IR active
Problems
Problems with Detecting Diatomic Molecules
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UV detection required some sort of chromophore (typically a π system)
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However UV rays can break bonds…’good’ for reactivity
Luckily space provides the UV, we just supply the detector
Summary
What you learn in a first-year chemistry course is everything…just not defined in depth.
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Orbitals are not pretty circles
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Electrons are not just a tiny particle
Understanding orbitals and electron behavior gives us a lot of insight into reaction energies,
behavior, and properties.
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Surface-molecule interactions
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Solvent-molecule interactions
A fundamental understanding of chemistry can give you an even greater understanding of what
you find (or might find) in space.
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Often forgotten by astrophysicists!