Uploaded August 2025 | Updated September 2026, 2 weeks ago
Molecular Geometries
Dr. DeBacco
Molecular Geometries
Molecular Geometries: describe how atoms are arranged around a central atom in a molecule.
These shapes are predicted using the Valence Shell Electron Pair Repulsion (VSEPR) theory, which says that electron pairs repel each other and will arrange themselves to be as far apart as possible.
How Lone Pairs Affect Shape
Lone pairs take up more space than bonding pairs, so they distort bond angles and change the shape:
VSEPR Notation (AXE Method)
AX₃ type in VSEPR notation:
A = central atom
X₃ = three bonded atoms
E₀ = no lone pairs on the central atom
Linear
A molecule is linear when its atoms are arranged in a straight line.
The bond angle between atoms is exactly 180°.
This shape minimizes repulsion between electron groups around the central atom.
Linear geometry occurs when the central atom has two electron groups.
These groups can be:
Two bonding pairs (AX₂ type)
Or two bonding pairs and three lone pairs (AX₂E₃ type)
Trigonal Planar
A molecule is trigonal planar when a central atom is bonded to three surrounding atoms arranged in a flat triangle.
All atoms lie in the same plane, and the bond angles between them are 120°.
VSEPR notation: AX₃
Bent (Angular)
A molecule is bent when the central atom is bonded to two other atoms, but lone pairs on the central atom distort the shape.
Lone pairs repel more strongly than bonding pairs causing compression of the bond angle
The result is a V-shaped or angular structure.
Bond angles typically range from 104.5° to 120°, depending on the number of lone pairs.
Common VSEPR types:
AX₂E₁: One lone pair → bond angle ~120°
SO₂
AX₂E₂: Two lone pairs → bond angle ~104.5°
H₂O
Tetrahedral
A molecule is tetrahedral when a central atom is bonded to four surrounding atoms.
These atoms are positioned at the corners of a tetrahedron, with the central atom at the center.
The bond angles are approximately 109.5°, which allows for maximum separation and minimal repulsion between electron pairs.
VSEPR notation: AX₄
Trigonal Pyramidal
A molecule is trigonal pyramidal when a central atom is bonded to three surrounding atoms and has one lone pair of electrons.
The lone pair pushes the bonded atoms downward, creating a non-planar, pyramid-like shape.
The bond angles are slightly less than 109.5°, typically around 107°, due to lone pair repulsion.
The electron geometry is tetrahedral, but the molecular geometry is trigonal pyramidal.
VSEPR notation: AX₃E₁
Trigonal Bipyramidal
The molecule has five electron groups around the central atom.
These groups arrange themselves to minimize repulsion:
Three atoms lie in a flat triangle (the equatorial plane) at 120° angles.
Two atoms are positioned above and below this plane (the axial positions) at 90° angles to the equatorial atoms.
The result is a trigonal bipyramid, like two pyramids sharing a triangular base.
VSEPR notation: AX₅
See-Saw
Named for its resemblance to a playground seesaw, this geometry is a distorted trigonal bipyramid.
It occurs when one of the five electron domains is a lone pair, which shifts the shape from symmetrical to asymmetrical.
The lone pair typically occupies an equatorial position
The electron geometry is trigonal bipyramidal, but the molecular geometry becomes seesaw
VSEPR notation: AX₄E₁
T-Shaped
A molecule is T-shaped when the central atom is bonded to three surrounding atoms and has two lone pairs.
The atoms form a shape that resembles the letter T:
Two atoms are positioned vertically (axial)
One atom is placed horizontally (equatorial)
The bond angles are typically 90° and 180°, but lone pair repulsion can distort these slightly.
The electron geometry is trigonal bipyramidal, but the molecular geometry becomes T-shaped.
VSEPR notation: AX₃E₂
Octahedral
Atoms are positioned at the six corners of an octahedron with 6 bonding pairs, no lone pairs
All are 90° between adjacent atoms and 180° between opposite atoms
VSEPR notation: AX₆
Square Pyramidal
Electron groups: 6 total
5 bonding pairs + 1 lone pair
Base atoms:
~90° between adjacent atoms
Apex atom:
~90° to each base atom
The lone pair slightly distorts the geometry, making it less symmetrical than a perfect octahedron
VSEPR notation: AX₅E1
Square Planar
The two lone pairs occupy opposite axial positions in the octahedral arrangement, leaving the four bonded atoms in a flat square around the central atom.
6 total electron groups (4 bonding pairs + 2 lone pairs)
All bond angles are 90°
Shape: Flat and symmetrical, like a square drawn on a plane with a high symmetry.
VSEPR notation: AX₄E₂
Link to Lecture Slides: drive.google.com/file/d/1ZGpqCwhAgU73EfjDtRAYEXaWpgicIE_r/view?usp=drive_link
*Due to the description character limit the full work cited for "Molecular Geometries" can be viewed at... docs.google.com/document/d/1q19JW9Qb4pNKJS4C96PAKRs--Z75nCvl/edit?usp=drive_link&ouid=104237452697237972847&rtpof=true&sd=true
Molecular Geometries
Dr. DeBacco
Molecular Geometries
Molecular Geometries: describe how atoms are arranged around a central atom in a molecule.
These shapes are predicted using the Valence Shell Electron Pair Repulsion (VSEPR) theory, which says that electron pairs repel each other and will arrange themselves to be as far apart as possible.
How Lone Pairs Affect Shape
Lone pairs take up more space than bonding pairs, so they distort bond angles and change the shape:
VSEPR Notation (AXE Method)
AX₃ type in VSEPR notation:
A = central atom
X₃ = three bonded atoms
E₀ = no lone pairs on the central atom
Linear
A molecule is linear when its atoms are arranged in a straight line.
The bond angle between atoms is exactly 180°.
This shape minimizes repulsion between electron groups around the central atom.
Linear geometry occurs when the central atom has two electron groups.
These groups can be:
Two bonding pairs (AX₂ type)
Or two bonding pairs and three lone pairs (AX₂E₃ type)
Trigonal Planar
A molecule is trigonal planar when a central atom is bonded to three surrounding atoms arranged in a flat triangle.
All atoms lie in the same plane, and the bond angles between them are 120°.
VSEPR notation: AX₃
Bent (Angular)
A molecule is bent when the central atom is bonded to two other atoms, but lone pairs on the central atom distort the shape.
Lone pairs repel more strongly than bonding pairs causing compression of the bond angle
The result is a V-shaped or angular structure.
Bond angles typically range from 104.5° to 120°, depending on the number of lone pairs.
Common VSEPR types:
AX₂E₁: One lone pair → bond angle ~120°
SO₂
AX₂E₂: Two lone pairs → bond angle ~104.5°
H₂O
Tetrahedral
A molecule is tetrahedral when a central atom is bonded to four surrounding atoms.
These atoms are positioned at the corners of a tetrahedron, with the central atom at the center.
The bond angles are approximately 109.5°, which allows for maximum separation and minimal repulsion between electron pairs.
VSEPR notation: AX₄
Trigonal Pyramidal
A molecule is trigonal pyramidal when a central atom is bonded to three surrounding atoms and has one lone pair of electrons.
The lone pair pushes the bonded atoms downward, creating a non-planar, pyramid-like shape.
The bond angles are slightly less than 109.5°, typically around 107°, due to lone pair repulsion.
The electron geometry is tetrahedral, but the molecular geometry is trigonal pyramidal.
VSEPR notation: AX₃E₁
Trigonal Bipyramidal
The molecule has five electron groups around the central atom.
These groups arrange themselves to minimize repulsion:
Three atoms lie in a flat triangle (the equatorial plane) at 120° angles.
Two atoms are positioned above and below this plane (the axial positions) at 90° angles to the equatorial atoms.
The result is a trigonal bipyramid, like two pyramids sharing a triangular base.
VSEPR notation: AX₅
See-Saw
Named for its resemblance to a playground seesaw, this geometry is a distorted trigonal bipyramid.
It occurs when one of the five electron domains is a lone pair, which shifts the shape from symmetrical to asymmetrical.
The lone pair typically occupies an equatorial position
The electron geometry is trigonal bipyramidal, but the molecular geometry becomes seesaw
VSEPR notation: AX₄E₁
T-Shaped
A molecule is T-shaped when the central atom is bonded to three surrounding atoms and has two lone pairs.
The atoms form a shape that resembles the letter T:
Two atoms are positioned vertically (axial)
One atom is placed horizontally (equatorial)
The bond angles are typically 90° and 180°, but lone pair repulsion can distort these slightly.
The electron geometry is trigonal bipyramidal, but the molecular geometry becomes T-shaped.
VSEPR notation: AX₃E₂
Octahedral
Atoms are positioned at the six corners of an octahedron with 6 bonding pairs, no lone pairs
All are 90° between adjacent atoms and 180° between opposite atoms
VSEPR notation: AX₆
Square Pyramidal
Electron groups: 6 total
5 bonding pairs + 1 lone pair
Base atoms:
~90° between adjacent atoms
Apex atom:
~90° to each base atom
The lone pair slightly distorts the geometry, making it less symmetrical than a perfect octahedron
VSEPR notation: AX₅E1
Square Planar
The two lone pairs occupy opposite axial positions in the octahedral arrangement, leaving the four bonded atoms in a flat square around the central atom.
6 total electron groups (4 bonding pairs + 2 lone pairs)
All bond angles are 90°
Shape: Flat and symmetrical, like a square drawn on a plane with a high symmetry.
VSEPR notation: AX₄E₂
Link to Lecture Slides: drive.google.com/file/d/1ZGpqCwhAgU73EfjDtRAYEXaWpgicIE_r/view?usp=drive_link
*Due to the description character limit the full work cited for "Molecular Geometries" can be viewed at... docs.google.com/document/d/1q19JW9Qb4pNKJS4C96PAKRs--Z75nCvl/edit?usp=drive_link&ouid=104237452697237972847&rtpof=true&sd=true


![Nitrogen Fertilizers Impact on CBD and THC Concentrations in Cannabis
Nitrogen Fertilizers Impact on CBD and THC Concentrations in Cannabis
Professor DeBacco
Research Article
Dilena, E., Close, D. C., Hunt, I., & Garland, S. M. (2023). Investigating how nitrogen nutrition and pruning impacts on CBD and THC concentration and plant biomass of Cannabis sativa. Scientific Reports, 13(1), 19533.
https://www.nature.com/articles/s41598-023-46369-5
Total Biomass and Total Cannabinoid Concentrations
Total biomass and total cannabinoid concentrations in % DW (on the y-axis) versus measured N concentrations in % DW (on each x-axis).
Treatment group labels are indicated by different colors.
The shape of the points (circle or triangle) indicates whether or not the plant associated with the data point was on the sun edge.
For each regression n = 20.
Inverse Relationship of [N] to [Cannabinoid]
The increase in biomass as N concentration increased from 3 to 6 was approximately 100%
Note the y-axis scale
However, the corresponding decrease in cannabinoid concentrations was approximately 67%
This entails a net decline in yield in terms of grams as N concentration increases
Three Key Points
1. Biomass was strongly and positively related to N
2. Cannabinoid concentrations were strongly and negatively related to N
3. Plants on the sun-edge tended to have higher biomass levels and cannabinoid concentrations
High Nitrogen Levels
Higher nitrogen nutrition raised the concentration of N in both inflorescence and leaf plant matter.
For very high levels of N nutrition (500 mg/mL), inflorescence cannabinoid concentrations decreased significantly (with little change in biomass) and leaf biomass increased significantly.
With higher N supply stem diameter also increased.
The net effect of increasing nitrogen nutrition on the total yield of cannabinoids was negative because the increase in biomass (which was only significant in leaves) was not enough to offset the consequent decrease in cannabinoid concentrations.
Take Home Message…
Cannabinoid concentration, as well as cannabinoid yield per plant were decreased with the increase in N supply.
Target Nitrogen Levels
Very high concentrations of fertilizer are not advisable because of lower cannabinoid concentration and yield, and that the optimal N nutrition is likely to be between 60 and 210 mg/L.
0.008-0.028 ounces per gallon
Prunings Impact
Double stem pruning was applied as an additional treatment to investigate efficacy on biomass increase.
Pruning treatment did not increase cannabinoid concentrations or affect biomass when measured at the final harvest.
Study Also Evaluate Sun Edge Plants
Across all treatments, as an artefact of this trial, sun-edge plants that were more directly exposed to sunlight showed a trend towards more biomass and higher cannabinoid concentrations
According to the statistical model developed for this study.
Self-shading of plants can limit the production of cannabinoids, so it is important to consider plant density and light intensity/spectrum.
*However, these results can only be considered preliminary and does warrants further research.
Link to Lecture Slides: https://drive.google.com/file/d/1lgV_46bDoXmPwXrAQAhfs7b04vcFISMU/view?usp=drive_link
*Due to the description character limit the full work cited for Nitrogen Fertilizers Impact on CBD and THC Concentrations in Cannabis can be viewed at... https://docs.google.com/document/d/1PAyFcsjILnKWvikPChNQmrt3hFAgH5Vh/edit?usp=drive_link&ouid=104237452697237972847&rtpof=true&sd=true Nitrogen Fertilizers Impact on CBD and THC Concentrations in Cannabis](https://i.ytimg.com/vi/gRAM9e2otLg/mqdefault.jpg)







![Calculating Net Energy Change of a Reaction
Calculating Net Energy Change of a Reaction
Dr. DeBacco
How Its Calculated Using Bond Enthalpies
If you know the bond enthalpies of all bonds broken and formed:
ΔH = Σ (Bond energies of bonds broken) − Σ (Bond energies of bonds formed)
In other words:
Breaking bonds = energy absorbed/input (endothermic)
Forming bonds = energy released/output (exothermic)
Higher bond energy = stronger bond
So the heat of reaction tells you the net energy flow for the whole process.
Net Energy Change
To calculate the net energy change of a chemical reaction, you are essentially figuring out how much energy is absorbed or released when bonds are broken and formed.
Formula for Net Energy Change (ΔH)
ΔH = Σ(Bond energies of bonds broken) − Σ(Bond energies of bonds formed)
Breaking bonds → requires energy (positive values)
Forming bonds → releases energy (negative values)
Step-by-Step Guide
Write the balanced chemical equation.
Make sure all reactants and products are accounted for.
List all bonds broken in the reactants.
Count how many of each type of bond is broken.
List all bonds formed in the products.
Count how many of each type of bond is formed.
Use average bond energies
These are typically found in tables (e.g., C–H ≈ 413 kJ/mol, O=O ≈ 495 kJ/mol).
Plug into the formula.
Add up the energy for all bonds broken and subtract the energy for all bonds formed.
Example: Combustion of Methane
CH₄ + 2O₂ → CO₂ + 2H₂O
Bonds broken:
4 × C–H (413 kJ/mol)
2 × O=O (495 kJ/mol)
Bonds formed:
2 × C=O (799 kJ/mol)
4 × O–H (463 kJ/mol)
ΔH = [4×413 + 2×495] − [2×799 + 4×463] ΔH = [1652 + 990] − [1598 + 1852] ΔH = 2642 − 3450 = −808 kJ/mol
This reaction is exothermic, releasing 808 kJ/mol of energy.
Link to Lecture Slides: https://drive.google.com/file/d/1RVZ77V5Vt6CWEoUCQJ9D9PV3Ds_sefFR/view?usp=drive_link
*Due to the description character limit the full work cited for Calculating Net Energy Change of a Reaction can be viewed at... https://docs.google.com/document/d/1o4ZSu6akSk xD_8q9gyRspC_EypGy-b/edit?usp=drive_link&ouid=104237452697237972847&rtpof=true&sd=true Calculating Net Energy Change of a Reaction](https://i.ytimg.com/vi/iHWwrt6rrWU/mqdefault.jpg)