deploy: 56f8227

_sources/docs/optimizing-geometry/enabling-ff.md.txt

@@ -0,0 +1,37 @@
+# Enabling additional force fields
+
+Avogadro2 comes equipped with a Lennard-Jones (LJ) force field, but you may wish to use a [different force field](force-fields) that is more suitable for your chemical system. These force fields are only enabled through interfaces to other programs. This includes:
+
+- The UFF and MMFF94 force fields via openbabel.
+- The GFN-FF force field via xtb-python.
+
+One of the easiest ways to do this is to create a conda environment that includes the external program(s) you require.
+
+## Creating an avogadro conda environment
+
+Assuming conda is already installed on your system, the following will create a new environment named avogadro that contains both the openbabel and xtb-python packages.
+
+	conda create -c conda-forge --name avogadro openbabel xtb-python
+
+When desired, this environment can then be activated as:
+
+	conda activate avogadro
+
+```{warning}
+Additional packages may need to be added to your conda environment in order for the force field scripts to run. For example, xtb-python may require the typing_extensions package.
+```
+
+## Setting the Python path
+
+It is also necessary to set the Python path correctly for Avogadro to be able to interface with the Python modules. To do this, go to the "Extensions" menu and select "Set Python Path...". 
+
+![](../../_static/python-path.png)
+
+In the dialogue box, browse to (or copy and paste) the Python executable from the corresponding conda environment. Assuming a Linux or macOS system, you can find this by typing `which python` from a terminal (with the conda environment active). Once this is set, select OK.
+
+![](../../_static/set-path.png)
+
+You must now restart Avogadro for changes to take effect. If you now go to the "Extensions" menu, and under "Calculate", select "Setup Force Field..." you should be able to select the additional force fields.
+
+![](../../_static/ff-selector.png)
+

_sources/docs/optimizing-geometry/index.md.txt

@@ -7,6 +7,7 @@
 caption: Optimization
 ---
 
+enabling-ff
 constraints
 conformers
 force-fields

_sources/index.md.txt

@@ -141,6 +141,7 @@ install/index
 docs/index
 develop/index
 contrib/index
+teach/index
 ```
 
 [avogadro discussion]: https://discuss.avogadro.cc/

_sources/teach/acid_base.md.txt

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+# Acid-Base Properties of Amino Acids
+
+Investigate the pH-dependent protonation of amino acids.
+
+## Tasks
+
+1. Create and optimize the geometry of a glycine molecule (H<sub>2</sub>NCH<sub>2</sub>COOH). Open the "Build" menu and select "Add Hydrogens for pH...". Choose different values of pH (1, 2, 3, ..., 13) and note the effect of pH shift on the electrical charge of glycine.
+2. In a new View, create a (glutamic acid - lysine) dipeptide using the "Build" menu, then "Insert", then "Peptides...". Set the pH to 3 and calculate the corresponding electrical charge of the dipeptide. Do the same for pH 7 and pH 13.
+
+When performing a paper electrophoresis at these pHs, in which direction will the dipeptide move (towards the anode or cathode)?
+
+## Solution
+
+1. Glycine electrical charge according to pH shift:
+	- pH < 5: NH<sub>3</sub><sup>+</sup>-CH<sub>2</sub>-COO<sup>-</sup>H<sup>+</sup>; net charge = +1.
+	- 5 ≤ pH < 10: NH<sub>3</sub><sup>+</sup>-CH<sub>2</sub>-COO<sup>-</sup>; net charge = 0.
+	- 10 ≤ pH ≤ 13: NH<sub>2</sub>-CH<sub>2</sub>-COO<sup>-</sup>; net charge = -1.
+2. Glu-Lys dipeptide:
+
+| pH          | ![](../_static/Glu-Lys_dipeptideatph3.png) | ![](../_static/Glu-Lys_dipeptideatph7.png) | ![](../_static/Glu-Lys_dipeptideatph13.png) |
+| ----------- | ----------- | ------------- | ---------- |
+| Net charge  | +1 | -1  | -2    |
+| Electrophoresis | → cathode (-)   | → anode (+)     | →→ anode (+)  |
+
+
+## Further reading
+
+- [The acid-base behaviour of amino acids (chemguide.co.uk)](https://www.chemguide.co.uk/organicprops/aminoacids/acidbase.html)
+- [Isoelectric point (wikipedia)](https://en.wikipedia.org/wiki/Isoelectric_point)

_sources/teach/alkene_isomers.md.txt

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+# Alkene Isomers
+
+Investigate the stability of alkene isomers due to steric interactions.
+
+## Task
+
+Build and optimize the geometry of isomeric alkenes and compare their relative energies to confirm empirical rules for evaluating alkene stability: Zaitsef’s rule, cis- vs trans-, isolate vs conjugated dienes.
+
+Examples:
+- Compare: 1-hexene, 2-hexene (cis and trans), 2-methyl-2-pentene, 2,3-dimethyl-2-butene.
+- Compare: 1,4-pentadiene and 1,3-pentadiene.
+
+## See also
+
+[Markovnikov's Rule](markovnikovs_rule)

_sources/teach/basic_vsepr.md.txt

@@ -0,0 +1,33 @@
+# Basic VSEPR
+
+Investigate molecular geometries using VSEPR rules.
+
+## Task
+
+Build and optimize the geometry of simple molecules to illustrate VSEPR theory.
+
+- For organic-type molecules, use the MMFF94 forcefield.
+
+Examples: methane, water, ammonia, etc.
+
+- For octahedral-based geometries, use the UFF forcefield which is optimized for all elements.
+
+Examples: SF<sub>6</sub>, IF<sub>5</sub>, XeF<sub>4</sub>, etc.
+
+- Try even 7, 8, or 9 atoms around a central metal - how do the VSEPR rules extend beyond octahedral molecules?
+
+## See also
+
+[Organic Hybridization](organic_hybridization)
+
+## Further reading
+
+[VSEPR theory (wikipedia)](https://en.wikipedia.org/wiki/VSEPR_theory)
+
+```{warning}
+Geometries derived from the trigonal bipyramidal geometry are not currently reliable.
+```
+
+```{tip}
+When using the Draw tool, you may wish to uncheck the “Adjust Hydrogens” box.
+```

_sources/teach/diaxial_interactions.md.txt

@@ -0,0 +1,17 @@
+# 1,3-diaxial interactions
+
+Investigate steric interactions in cyclohexane derivatives.
+
+## Tasks
+
+1. Create and optimize the geometry of a cyclohexane molecule.
+2. Add methyl substituents to the 1 and 3 positions in a diequatorial arrangement, optimize the geometry and note the energy.
+3. Delete the diequatorial substituents to return to cyclohexane, and optimize the geometry again.
+4. Place methyl substituents in 1,3-diaxial positions, optimize the geometry and note the movement of the groups and the energy.
+
+## Solution
+
+|             | ![](../_static/TeachDiaxial_cyclohexane.png) | ![](../_static/TeachDiaxial_diequatorial.png) | ![](../_static/TeachDiaxial_diaxial.png) |
+| ----------- | ----------- | ------------- | ---------- |
+| Molecule    | Cyclohexane | Diequatorial  | Diaxial    |
+| Energy      | 30 kJ/mol   | 40 kJ/mol     | 98 kJ/mol  |

_sources/teach/hcn_dipole.md.txt

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+# HCN dipole
+
+Investigate polar intermolecular interactions using HCN.
+
+## Task
+
+Create two molecules of HCN, run a force field geometry optimization. Check the orientation of the molecules, note the energy of interaction. Find primary dipoles, compare length of interatomic and intermolecular bonds.
+
+## See also
+
+[Water](water)

_sources/teach/hydrogen_clusters.md.txt

@@ -0,0 +1,35 @@
+# Hydrogen Clusters
+
+Investigate the intermolecular interactions of solid hydrogen.
+
+## Task
+
+Create 7 molecules of hydrogen. Optimize the geometry using the UFF forcefield and correct figure until all molecules are standing in a flat hexagonal order. Check the energy of interaction and distance between molecules.
+
+## Solution
+
+
+
+| Cell parameters            | a | b | c | α | β | γ |
+| ----------- | ----------- | ------------- | ---------- | ------- | ------- | ------- |
+| Webelements | 470 pm      | 470 pm        | 340 pm     | 90.0° | 90.0° | 120.0° |
+| UFF         | 486-496 pm  | 486-496 pm    | 324 pm     | 90.0° | 90.0° | 120.0° |
+
+- Space group: P63/mmc (Space group number: 194).
+- Structure: hcp (hexagonal close-packed).
+
+## Issues
+
+Melting of this cluster is poorly controllable.
+
+Cluster is a bit deformed, with long optimization some molecules tend to rotate and stand skew to neighbours.
+
+Since UFF does not properly include quantum mechanical effects and hydrogen bonding, the configuration and size of the unit cell are somewhat different than the experimental configuration.
+
+## See also
+
+[Hydrogen Molecule](hydrogen_molecule)
+
+## Sources
+
+[Webelements data on hydrogen clusters](https://www.webelements.com/hydrogen/crystal_structure.html)

_sources/teach/hydrogen_molecule.md.txt

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+# Hydrogen Molecule
+
+Investigate the hydrogen molecule and its bond length using different force fields.
+
+## Task
+
+- Create the H<sub>2</sub> molecule using the drawing tool.
+- Optimize the geometry with a variety of force fields and tabulate the resulting bond lengths.
+- Enable display of its orbitals (?)
+
+## Solution
+
+![](../_static/Hydrogen_molecule.png)
+
+| Force field | Bond length (Å) | 
+| ----------- | ----------- | 
+| GAFF        | 1.10  | 
+| Ghemical    | 1.01  | 
+| MMFF        | Error |
+| UFF         | 0.71  |
+
+An accurate bond length (see sources) for the molecule is 0.074 nm, so the UFF force field should be used.
+
+## See also
+
+[Hydrogen Clusters](hydrogen_clusters)
+
+## Sources
+
+[Hyperphysics data on the hydrogen molecule](http://hyperphysics.phy-astr.gsu.edu/hbase/molecule/hmol.html)
+

_sources/teach/index.md.txt

@@ -0,0 +1,71 @@
+(teach)=
+
+# Teach
+
+```{warning}
+This section is in the process of being migrated from the original Avogadro documentation. Some instructions and screenshots may be out of date.
+```
+
+Avogadro is intended not only for molecular modeling research, but also for educational use. This category is intended to help educators around the world find lessons and tips for using Avogadro 2 in teaching chemistry. If you have an exercise or article that you would like to list here, please get in touch via [Avogadro Discussion](https://discuss.avogadro.cc).
+
+[1,3-diaxial interactions](diaxial_interactions)
+
+Investigate steric interactions in cyclohexane derivatives.
+
+[Alkene Isomers](alkene_isomers)
+
+Investigate the stability of alkene isomers due to steric interactions.
+
+[Basic VSEPR](basic_vsepr)
+
+Investigate molecular geometries using VSEPR rules.
+
+[HCN dipole](hcn_dipole)
+
+Investigate polar intermolecular interactions using HCN.
+
+[Hydrogen Clusters](hydrogen_clusters)
+
+Investigate the intermolecular interactions of solid hydrogen.
+
+[Hydrogen Molecule](hydrogen_molecule)
+
+Investigate the hydrogen molecule and its bond length using different force fields.
+
+[Markovnikov's Rule](markovnikovs_rule)
+
+Investigate the stability of reactions using Markovnikov's rule.
+
+[Organic Hybridization](organic_hybridization)
+
+Illustrate the geometry and bond lengths in sp<sup>3</sup>, sp<sup>2</sup> and sp hybridized carbons.
+
+[Water](water)
+
+Investigate the geometry of water and hydrogen bonding between molecules.
+
+[Acid-Base Properties of Amino Acids](acid_base)
+
+Investigate the pH-dependent protonation of amino acids.
+
+```{toctree}
+---
+caption: Teach
+hidden: true
+---
+
+diaxial_interactions
+alkene_isomers
+basic_vsepr
+hcn_dipole
+hydrogen_clusters
+hydrogen_molecule
+markovnikovs_rule
+organic_hybridization
+water
+acid_base
+
+```
+
+[avogadro forum]: https://discuss.avogadro.cc
+[github tracker]: https://github.com/OpenChemistry/avogadrolibs/issues

_sources/teach/markovnikovs_rule.md.txt

@@ -0,0 +1,31 @@
+# Markovnikov's Rule
+
+Investigate the stability of reactions using Markovnikov's rule.
+
+## Task
+
+Build a propene molecule and optimize its geometry. Compare the relative energy of bromine-hydrogen substitution at either the 1-carbon or 2-carbon of the carbon-carbon double bond. Which of these two bromopropane compounds will be the major product of a propene bromination reaction?
+
+![](../_static/Markovnikovs_rule.png)
+
+## Solution
+
+![](../_static/Markovnikovs_rule_mechanistic.png)
+
+Results of relative energies expressed in kJ/mol (need confirmation in literature).
+
+| Force field | Intermediate primary carbocation (1') | Intermediate secondary carbocation (2') | 1-bromopropane (1) | 2-bromopropane (2) |
+| ----------- | ----------- | ------------- | ---------- | ---------- | 
+| Ghemical    | -2.24       | -2.06         | -2.39      | -1.87 |
+| MMFF94      | -9.88       | -3.84         | -8.96      | +2.70 |
+| UFF         | +4.05       | +3.63         | +4.15      | +4.86 |
+
+UFF data is considered in this case, the secondary carbocation intermediate requires less energy (2') than the primary carbocation intermediate (1') (resp. 3.6 vs 4 kJ/mol). So compound (2) will be the major form. This is called the Markovnikov’s rule: “the major product of the addition of HX (where X is some atom more electronegative than H, the bromine in our case) to an alkene (here the propene) has the hydrogen atom in the less substituted position and X in the more substituted position”. Mechanisms which avoid the carbocation intermediate such as the presence of dialkyl peroxides will reverse the reaction result and compound (1) becomes the major product (Anti-Markovnikov rule).
+
+## See also
+
+[Alkene Isomers](alkene_isomers)
+
+## Further reading
+
+[Markovnikov's rule (wikipedia)](https://en.wikipedia.org/wiki/Markovnikov's_rule)

_sources/teach/organic_hybridization.md.txt

@@ -0,0 +1,27 @@
+# Organic Hybridization
+
+Illustrate the geometry and bond lengths in sp<sup>3</sup>, sp<sup>2</sup> and sp hybridized carbons.
+
+## Task
+
+For each of ethane, ethylene and ethyne, build the molecule and optimize the geometry. Use the measurement tool to examine bond lengths and bond angles.
+
+## Solution
+
+![](../_static/Hybridisation.png)
+
+![](../_static/Molecular_hybridisation.png)
+
+Results using the MMFF94 forcefield:
+
+- sp<sup>3</sup> - ethane bond angle: 110°; C-C bond length: 1.5 Å.
+- sp<sup>2</sup> - ethylene bond angle: 121°; C-C bond length: 1.336 Å.
+- sp - ethyne bond angle: 180°; C-C bond length: 1.200 Å.
+
+## See also
+
+[Basic VSEPR](basic_vsepr)
+
+## Further reading
+
+[Orbital hybridization (wikipedia)](https://en.wikipedia.org/wiki/Orbital_hybridisation)