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(teaching-articles)=

# Educational Publications Using Avogadro

A variety of activities and resources using Avogadro have been published in journals such as *J. Chem. Ed.*

## Yes We Chem

The website ["Yes We Chem"](https://yeswechem.org) includes English and Italian tutorials and exercises for teaching chemistry with Avogadro.

> The team of **YesWeChem®** is formed by teachers, authors of text- and coursebooks, chemists and enthusiasts of this wonderful science.

## Computational Chemistry

* [Computational Chemistry Activities with Avogadro and ORCA](https://doi.org/10.1021/acs.jchemed.0c00959)
* [$\ce{Ph2Te2}$: An Accessible Main Group Organometallic Target for Spectral Characterization and Modeling](https://doi.org/10.1021/acs.jchemed.2c01039)
* [$\ce{Cp2TiCl2}$: Synthesis, Characterization, Modeling and Catalysis](https://doi.org/10.1021/acs.jchemed.1c01272)
* [A Computational Chemistry Course for Teachers: From Research Laboratories to High-School Chemistry Teaching](https://doi.org/10.1021/acs.jchemed.3c00645)
* [Antioxidant Potential of Anthocyanidins: A *Healthy* Computational Activity for High School and Undergraduate Students](https://doi.org/10.1021/acs.jchemed.2c01070)

## Spectra / Spectroscopy

* [Computation of Chemical Shifts for Paramagnetic Molecules: A Laboratory Experiment for the Undergraduate Curriculum](https://doi.org/10.1021/ed400902c)
* [Computational Modeling of the Optical Rotation of Amino Acids: An ‘in Silico’ Experiment for Physical Chemistry](https://doi.org/10.1021/ed300680g)

## Chemical Reactions and Mechanisms

* [Investigating first-year undergraduate chemistry students’ reasoning with reaction coordinate diagrams when choosing among particulate-level reaction mechanisms](https://doi.org/10.1039/D0RP00193G)

## Materials / Nano

* [Think Outside the Lab: Modeling Graphene Quantum Dots in Pandemic Times](https://doi.org/10.1021/acs.jchemed.1c00879)
* [Extended Hückel Calculations on Solids Using the Avogadro Molecular Editor and Visualizer](https://pubs.acs.org/doi/full/10.1021/acs.jchemed.7b00698)
* [A Computational Experiment on Single-Walled Carbon Nanotubes](https://doi.org/10.1021/ed3006067)
* [The Computational Design of Two-Dimensional Materials](https://doi.org/10.1021/acs.jchemed.9b00485)

## Cheminformatics

* [Possibilities and Challenges of Using Educational Cheminformatics for STEM Education: A SWOT Analysis of a Molecular Visualization Engineering Project](https://doi.org/10.1021/acs.jchemed.1c00683)
* [Basic Cheminformatics Course for First-Year Chemistry Students](https://doi.org/10.1021/acs.jchemed.2c00175)

## 3D Printing and VR

* [Accessible 3D Printing: Multicolor Molecular Models from Consumer-Grade, Single Filament 3D Printers](https://doi.org/10.1021/acs.jchemed.3c00686)
* [A Simplified Method for the 3D Printing of Molecular Models for Chemical Education](https://doi.org/10.1021/acs.jchemed.7b00533)
* [Development and Evaluation of the H NMR MoleculAR Application](https://doi.org/10.1021/acs.jchemed.0c01068)

## Remote Teaching

* [Strategies, Practice and Lessons Learned from Remote Teaching of the General Chemistry Laboratory Course at Brown University](https://doi.org/10.1021/acs.jchemed.0c00746)
65 changes: 17 additions & 48 deletions _sources/teach/index.md.txt
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Expand Up @@ -10,50 +10,33 @@ Avogadro is intended not only for molecular modeling research, but also for educ

## Publications

A variety of activities and resources using Avogadro have been published in journals such as *J. Chem. Ed.*
A variety of web resources and journal articles have been published for using Avogadro, ranging from computational chemistry and cheminformatics, to materials, spectroscopy, reaction mechanisms, and 3D printing.

### Computational Chemistry:
For ideas, see the list of [articles](teaching-articles)

* [Computational Chemistry Activities with Avogadro and ORCA](https://doi.org/10.1021/acs.jchemed.0c00959)
* [$\ce{Ph2Te2}$: An Accessible Main Group Organometallic Target for Spectral Characterization and Modeling](https://doi.org/10.1021/acs.jchemed.2c01039)
* [$\ce{Cp2TiCl2}$: Synthesis, Characterization, Modeling and Catalysis](https://doi.org/10.1021/acs.jchemed.1c01272)
* [A Computational Chemistry Course for Teachers: From Research Laboratories to High-School Chemistry Teaching](https://doi.org/10.1021/acs.jchemed.3c00645)
* [Antioxidant Potential of Anthocyanidins: A *Healthy* Computational Activity for High School and Undergraduate Students](https://doi.org/10.1021/acs.jchemed.2c01070)

### Spectra / Spectroscopy:

* [Computation of Chemical Shifts for Paramagnetic Molecules: A Laboratory Experiment for the Undergraduate Curriculum](https://doi.org/10.1021/ed400902c)
* [Computational Modeling of the Optical Rotation of Amino Acids: An ‘in Silico’ Experiment for Physical Chemistry](https://doi.org/10.1021/ed300680g)

### Chemical Reactions and Mechanisms:
## Activities

* [Investigating first-year undergraduate chemistry students’ reasoning with reaction coordinate diagrams when choosing among particulate-level reaction mechanisms](https://doi.org/10.1039/D0RP00193G)
Beyond published articles, we include a variety of activities contributed by the Avogadro community.

### Materials / Nano:
### General Chemistry

* [Think Outside the Lab: Modeling Graphene Quantum Dots in Pandemic Times](https://doi.org/10.1021/acs.jchemed.1c00879)
* [Extended Hückel Calculations on Solids Using the Avogadro Molecular Editor and Visualizer](https://pubs.acs.org/doi/full/10.1021/acs.jchemed.7b00698)
* [A Computational Experiment on Single-Walled Carbon Nanotubes](https://doi.org/10.1021/ed3006067)
* [The Computational Design of Two-Dimensional Materials](https://doi.org/10.1021/acs.jchemed.9b00485)
[*Basic VSEPR*](basic_vsepr)

### Cheminformatics:
* Investigate molecular geometries using VSEPR rules.

* [Possibilities and Challenges of Using Educational Cheminformatics for STEM Education: A SWOT Analysis of a Molecular Visualization Engineering Project](https://doi.org/10.1021/acs.jchemed.1c00683)
* [Basic Cheminformatics Course for First-Year Chemistry Students](https://doi.org/10.1021/acs.jchemed.2c00175)
[*Hydrogen Clusters*](hydrogen_clusters)

### 3D Printing and VR:
* Investigate the intermolecular interactions of solid hydrogen.

* [Accessible 3D Printing: Multicolor Molecular Models from Consumer-Grade, Single Filament 3D Printers](https://doi.org/10.1021/acs.jchemed.3c00686)
* [A Simplified Method for the 3D Printing of Molecular Models for Chemical Education](https://doi.org/10.1021/acs.jchemed.7b00533)
* [Development and Evaluation of the H NMR MoleculAR Application](https://doi.org/10.1021/acs.jchemed.0c01068)
[*Hydrogen Molecule*](hydrogen_molecule)

### Remote Teaching:
* Investigate the hydrogen molecule and its bond length using different force fields.

* [Strategies, Practice and Lessons Learned from Remote Teaching of the General Chemistry Laboratory Course at Brown University](https://doi.org/10.1021/acs.jchemed.0c00746)
[*Water*](water)

## Activities
* Investigate the geometry of water and hydrogen bonding between molecules.

Beyond published articles, we include a variety of activities contributed by the Avogadro community.
### Organic Chemistry

[*1,3-diaxial interactions*](diaxial_interactions)

Expand All @@ -63,22 +46,10 @@ Beyond published articles, we include a variety of activities contributed by the

* 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.
Expand All @@ -87,9 +58,7 @@ Beyond published articles, we include a variety of activities contributed by the

* 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.
### Biochemistry:

[*Acid-Base Properties of Amino Acids*](acid_base)

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hidden: true
---

articles
diaxial_interactions
acid_base
alkene_isomers
basic_vsepr
hcn_dipole
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markovnikovs_rule
organic_hybridization
water
acid_base

```

[avogadro forum]: https://discuss.avogadro.cc
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<link rel="canonical" href="https://two.avogadro.cc/teach/acid_base.html" />
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="prev" title="Water" href="water.html" />
<link rel="next" title="Alkene Isomers" href="alkene_isomers.html" />
<link rel="prev" title="1,3-diaxial interactions" href="diaxial_interactions.html" />
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
</head>
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><p aria-level="2" class="caption" role="heading"><span class="caption-text">Teach</span></p>
<ul class="current nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="articles.html">Educational Publications Using Avogadro</a></li>
<li class="toctree-l1"><a class="reference internal" href="diaxial_interactions.html">1,3-diaxial interactions</a></li>
<li class="toctree-l1 current active"><a class="current reference internal" href="#">Acid-Base Properties of Amino Acids</a></li>
<li class="toctree-l1"><a class="reference internal" href="alkene_isomers.html">Alkene Isomers</a></li>
<li class="toctree-l1"><a class="reference internal" href="basic_vsepr.html">Basic VSEPR</a></li>
<li class="toctree-l1"><a class="reference internal" href="hcn_dipole.html">HCN dipole</a></li>
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<li class="toctree-l1"><a class="reference internal" href="markovnikovs_rule.html">Markovnikov’s Rule</a></li>
<li class="toctree-l1"><a class="reference internal" href="organic_hybridization.html">Organic Hybridization</a></li>
<li class="toctree-l1"><a class="reference internal" href="water.html">Water</a></li>
<li class="toctree-l1 current active"><a class="current reference internal" href="#">Acid-Base Properties of Amino Acids</a></li>
</ul>
</div>
</nav></div>
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<!-- Previous / next buttons -->
<div class="prev-next-area">
<a class="left-prev"
href="water.html"
href="diaxial_interactions.html"
title="previous page">
<i class="fa-solid fa-angle-left"></i>
<div class="prev-next-info">
<p class="prev-next-subtitle">previous</p>
<p class="prev-next-title">Water</p>
<p class="prev-next-title">1,3-diaxial interactions</p>
</div>
</a>
<a class="right-next"
href="alkene_isomers.html"
title="next page">
<div class="prev-next-info">
<p class="prev-next-subtitle">next</p>
<p class="prev-next-title">Alkene Isomers</p>
</div>
<i class="fa-solid fa-angle-right"></i>
</a>
</div>
</footer>
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<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Basic VSEPR" href="basic_vsepr.html" />
<link rel="prev" title="1,3-diaxial interactions" href="diaxial_interactions.html" />
<link rel="prev" title="Acid-Base Properties of Amino Acids" href="acid_base.html" />
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
</head>
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><p aria-level="2" class="caption" role="heading"><span class="caption-text">Teach</span></p>
<ul class="current nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="articles.html">Educational Publications Using Avogadro</a></li>
<li class="toctree-l1"><a class="reference internal" href="diaxial_interactions.html">1,3-diaxial interactions</a></li>
<li class="toctree-l1"><a class="reference internal" href="acid_base.html">Acid-Base Properties of Amino Acids</a></li>
<li class="toctree-l1 current active"><a class="current reference internal" href="#">Alkene Isomers</a></li>
<li class="toctree-l1"><a class="reference internal" href="basic_vsepr.html">Basic VSEPR</a></li>
<li class="toctree-l1"><a class="reference internal" href="hcn_dipole.html">HCN dipole</a></li>
Expand All @@ -439,7 +441,6 @@
<li class="toctree-l1"><a class="reference internal" href="markovnikovs_rule.html">Markovnikov’s Rule</a></li>
<li class="toctree-l1"><a class="reference internal" href="organic_hybridization.html">Organic Hybridization</a></li>
<li class="toctree-l1"><a class="reference internal" href="water.html">Water</a></li>
<li class="toctree-l1"><a class="reference internal" href="acid_base.html">Acid-Base Properties of Amino Acids</a></li>
</ul>
</div>
</nav></div>
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<!-- Previous / next buttons -->
<div class="prev-next-area">
<a class="left-prev"
href="diaxial_interactions.html"
href="acid_base.html"
title="previous page">
<i class="fa-solid fa-angle-left"></i>
<div class="prev-next-info">
<p class="prev-next-subtitle">previous</p>
<p class="prev-next-title">1,3-diaxial interactions</p>
<p class="prev-next-title">Acid-Base Properties of Amino Acids</p>
</div>
</a>
<a class="right-next"
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