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Author Template - 1. Basics

Abstract

Contains examples of all basic MyST markdown syntax

Writing Syntax Section

This file demonstrates all the main syntax of MyST Markdown (MyST v2).
All examples are adapted using the MOF (Metal–Organic Framework) theme,
and the latest recommended ::: fenced directive syntax is adopted throughout.

Authors can directly copy these templates and modify the content. Each section includes an official documentation link with more extensible functions.

0. Document (Frontmatter)

Frontmatter Documents

Place this at the very beginning of each markdown file. Below is a sample for this tutorial.

---
kernelspec:
  name: jupyterbook
  display_name: 'jupyterbook'

title: Author Template - 1. Basics
abstract:
  Contains examples of all basic _MyST markdown_ syntax
---

kernelspec: Specifies the local jupyter execution environment for interactive Python code blocks.

title: The title of the chapter, shown in the table of contents in the left sidebar.

abstract: A brief introduction to the chapter.

1. Typography

Typography Document

1.0

1.1 Emphasis and Inline Formatting

Regular text
**Bold Text** Bold Text
*Italic Text* Italic Text
***Bold Italic*** Bold Italic

Showcase of `inline code`. Example: inline code part.

1.2 Block Quote

> MOF-5 consists of **Zn₄O** secondary building units (SBUs) and *benzene dicarboxylate ligands (BDC)*.

MOF-5 consists of Zn₄O secondary building units (SBUs) and benzene dicarboxylate ligands (BDC).

1.3 Horizontal Rule

---

1.4 Footnotes

As shown in the following reference[1]

As shown in the following reference[^1]

[^1]: This is a review about AI for MOFs.

(The Footnotes section at the bottom will show the footnote content.)

2. Admonitions

Callouts & Admonitions Documents

The latest MyST recommendation is to use:

:::{type}
Content
:::

Available types:

2.1 tip

:::{tip} What is coordination polymerization?
MOFs are essentially crystalline frameworks formed by metal ions and multidentate organic ligands through coordination bonds.
:::

2.2 note

:::{note}
UiO-66 is one of the most stable and widely used Zr-based MOF structures.
:::

2.3 warning

:::{warning}
HKUST-1 is prone to hydrolysis in humid environments, resulting in structural collapse.
:::

2.4 General admonition

:::{admonition} Custom Block Title
Content...
:::

3. Figures

Figures Documents

MyST recommends using the fenced directive:

:::{figure} path/to/image
:name: image-label   
:width: 70%
:align: center
Figure Caption  (If the :name: tag is not added, the caption will not be automatically numbered as Figure N)
:::

3.1 Local Images

Schematic diagram of MOF structure.

Figure 1:Schematic diagram of MOF structure.

3.2 Web Images

Structure diagram of MIL-101 (Wikimedia).

Figure 2:Structure diagram of MIL-101 (Wikimedia).

4. Math

Math and Equation Documents

MyST supports all LaTeX math syntax.

4.1 Inline Formulas

The porosity of a MOF can be written as ϕ=Vvoid/Vcell\phi = V_\text{void} / V_\text{cell}.

$\phi = V_\text{void} / V_\text{cell}$

4.2 Block Formulas

$$
V_\text{cell} = abc\sqrt{
1 + 2\cos\alpha\cos\beta\cos\gamma -
\cos^2\alpha - \cos^2\beta - \cos^2\gamma
}
$$
Vcell=abc1+2cos⁡αcos⁡βcos⁡γ−cos⁡2α−cos⁡2β−cos⁡2γV_\text{cell} = abc\sqrt{ 1 + 2\cos\alpha\cos\beta\cos\gamma - \cos^2\alpha - \cos^2\beta - \cos^2\gamma }
(1)
$$
\begin{aligned}
q(P) &= q_{\max} \frac{bP}{1 + bP} \\
\phi &= \frac{V_\text{void}}{V_\text{cell}}
\end{aligned}
$$
q(P)=qmax⁡bP1+bPϕ=VvoidVcell\begin{aligned} q(P) &= q_{\max} \frac{bP}{1 + bP} \\ \phi &= \frac{V_\text{void}}{V_\text{cell}} \end{aligned}
(2)

5. Tables

Tables Documents

5.1 Standard Markdown Table

| Name | Metal Center | Ligand | Feature |
| :--- | :--- | :--- | :--- |
| MOF-5 | $\mathrm{Zn}^{2+}$ | BDC | Classic MOF |
| UiO-66 | $\mathrm{Zr}^{4+}$ | BDC | Exceptional Stability |
NameMetal CenterLigandFeature
MOF-5Zn2+\mathrm{Zn}^{2+}BDCClassic MOF
UiO-66Zr4+\mathrm{Zr}^{4+}BDCExceptional Stability

5.2 Block Table

:::{table} Table caption
:label: table
:align: center
| head | head |
| --- | --- |
| content | content |
:::
StructureBET Surface Area (m²/g)
MOF-53800
MIL-1014500

6. Cross References

Cross Reference Documents

You can add a :name: to any block and reference it.

In Section2, cite the figure as:

:::{figure} ../images/Figure-1.png
:name: MOF-structure
:width: 70%
:align: center
Schematic diagram of MOF structure.
:::

See [](#MOF-structure).

See Figure 1.

[Section 1.2 Typical Structures and Unit Cells in Chapter 1](./ch1-mof-basics#target-struct).

Section 1.2 Typical Structures and Unit Cells in Chapter 1.

7. External References

Websites like wiki and github can be referenced directly:

<wiki:Metal–organic_framework>

wiki:Metal–organic_framework

Other external references:

[External Reference Documents](https://mystmd.org/guide/external-references)

External Reference Documents

8. Embedding

[Embedding Documents]

You can embed content from this document or other documents. For example, to embed Figure 1 from Chapter 1 of the MOF-book:

:::{embed} ch1-mof-basics.md/#fig-mof-schematic
:::
A schematic diagram of a MOF structure.

Figure 1:A schematic diagram of a MOF structure.

9. Citations

Citation Documents

Use DOI to cite:

Citation example:

[MOF paper](doi.org/10.1038/s41578-025-00772-8)

MOF paper

Repeated citation:

[MOF paper](doi.org/10.1038/s41578-025-00772-8)

MOF paper

As shown in [Yaghi, 2025](https://doi.org/10.1038/s41578-025-00772-8).

As shown in Yaghi, 2025.

(No repeated reference will show in the References section at the end if the same DOI is cited multiple times.)

10. Proofs and Theorems

Theorems Documents

You can add theorems, definitions, proofs, etc. by using {prf:keyword}, where keyword may be theorem, lemma, definition, etc.

:::{prf:theorem} Stability Criterion for MOFs
:label: theorem-1
MOFs are generally more stable if the coordination number of the metal node is sufficiently high.
:::

:::{prf:proof} Proof
:label: proof-theorem-1
A high coordination number restricts the degrees of freedom of the framework structure, thereby increasing its stability.
:::

11. Exercises

Exercise Documents

:::{exercise} 
:label: my-exercise
Porosity Exercise
Calculate the unit cell volume of a simple cubic cell with an edge length of 3 nm and a porosity of 0.5.
:::
:::{solution} my-exercise
$V = 27\text{ nm}^3$.
:::

Note: use a label for exercise, and the corresponding label for solution.

12. Blocks and Comments

Blocks and Comments Documents

12.1 Blocks

Blocks are used to segment formatting:

+++ {"cell": "one"}
cell 1

cell 1

12.2 Comments

Comments are used to add annotations within code.

This next line won't render, but it is in the HTML and LaTeX!
% Markdown comment line

This next line won’t render, but it is in the HTML and LaTeX!

13. Diagrams

Flowcharts and similar structures are supported and it is recommended to use Mermaid diagrams.

Diagram Documents

Mermaid Official Documents

:::{mermaid} 
graph TD
    A[Metal Node] --> B[Ligand]
    B --> C[3D Network]
:::

14. Asides

Asides and Margin Documents

Used for sidenotes, which will appear in the right sidebar:

:::{aside}
ZIF series materials exhibit outstanding performance in gas separation.
:::

15. Dropdowns, Cards, Tabs

Dropdowns, Cards, Tabs Documents

15.1 Dropdown

:::{dropdown} Click to Expand MOF Description
MOFs are porous materials consisting of metal nodes and organic ligands.
:::
Click to Expand MOF Description

MOFs are porous materials consisting of metal nodes and organic ligands.

15.2 Tabs

::::{tab-set}

:::{tab-item} Structure
MOF frameworks rely on metal nodes and organic linkers.
:::

:::{tab-item} Pores
Pore size determines adsorption selectivity.
:::

::::
Structure
Pores

MOF frameworks rely on metal nodes and organic linkers.

16. Glossaries and Terms

Glossaries Documents

:::{glossary}

MOF
: Metal–Organic Framework

SBU
: Secondary Building Unit

:::
MOF
Metal–Organic Framework
SBU
Secondary Building Unit
Footnotes

  1. This is a review about AI for MOFs.

    ↩
References
  1. Zheng, Z., Rampal, N., Inizan, T. J., Borgs, C., Chayes, J. T., & Yaghi, O. M. (2025). Large language models for reticular chemistry. Nature Reviews Materials, 10(5), 369–381. 10.1038/s41578-025-00772-8
English Content (EN)
MOF Book Example Chapter 2 (Advanced)
English Content (EN)
Author Template - 2. Code