experimental_data/README.md

# Amide Formation Kinetics Dataset

A comprehensive dataset for studying amide formation reactions through multiple analytical modalities including nuclear magnetic resonance (NMR) spectroscopy, image-based reaction monitoring, and kinetic rate analysis.

## Dataset Overview

This dataset contains experimental data from amide formation reactions between various amines and acyl chlorides. The collection includes raw NMR spectroscopy data, time-series image analysis data, processed rate measurements, and a complete example experiment with analysis tools.

## Dataset Structure

The dataset is organized into four main archives:

### 1. `Amide_Project_NMRs.tar` (~2.9 GB)
**Room temperature NMR spectroscopy data**

Contains raw Bruker NMR data files for various amide formation reactions. The data is organized by:
- Aniline compound (e.g., `4-(4-F-phenoxyaniline)`)
- Acyl chloride reagent
- There are two experiments per reagent pair, the first is before the addition of the second reagent, to get
  a standardization of the integrals. The second experiment is after the addition of the second reagent to monitor the reaction progress.

**Structure:**
```

Room temperature NMRs/

└── [Aniline Compound]/

    └── [Aniline] + [Acyl Chloride]/

        └── [Experiment ID]/

            ├── acqu, acqus, acqu2, acqu2s (acquisition parameters)

            ├── pdata/ (processed data)

            ├── lists/ (pulse program files)

            └── [other Bruker NMR files]

```

**Format:** Bruker TopSpin-compatible raw NMR data

### 2. `Example_Experiment.tar` (~3.6 GB)

**Complete example experiment with analysis tools**



A full example experiment demonstrating the experimental workflow, including:

- YAML configuration file for experiment parameters

- Jupyter notebook (`inflection_finder.ipynb`) for data analysis
- Time-series images captured during the reaction (white light illumination)
- Input data structure for image analysis pipeline

**Structure:**
```

Example_Experiment/

└── 4-30-24-Ninetales/

    ├── 4-30-24-Ninetales.yaml (experiment configuration)

    ├── inflection_finder.ipynb (analysis notebook)

    └── input/

        └── images/

            └── white/ (time-series PNG images)

```

**Use Case:** Reference implementation for setting up and analyzing similar experiments

### 3. `Final_Amide_Image_Analysis_Data.tar` (~169 MB)
**Processed image analysis results**

Contains processed CSV files with quantitative analysis results from image-based reaction monitoring. Data is organized by:
- Experiment date
- Experiment identifier (e.g., Venusaur, Bulbasaur, Ninetales)
- Analysis type (white light, yellow light data)

**Structure:**
```

Final_Amide_Image_Analysis_Data/

└── [Date]-[Experiment ID]/

    ├── white_data.csv

    └── yellow_data.csv

```

**Format:** CSV files with quantitative reaction monitoring data

### 4. `Rates and Rate Plot Points Datasets.tar` (~1.5 MB)
**Kinetic rate measurements**

Excel spreadsheets containing calculated reaction rates and rate plot points for various aniline + acyl chloride combinations.

**Structure:**
```

Rates and Rate Plot Points Datasets/

└── Rates Dataframes/

    ├── group1 + [Acyl Chloride] rates.xlsx

    └── [additional rate data files]

```

**Format:** Excel (.xlsx) files with rate data and plot points

**Coverage:** Includes rates for 1000+ reagent combinations including:
- Substituted benzoyl chlorides (fluoro, chloro, bromo, nitro, etc.)
- Aliphatic acyl chlorides (acetyl, heptanoyl, dodecanoyl, etc.)
### Amines in the Dataset

The amines featured in this dataset are primarily aniline derivatives, serving as nucleophiles in amide coupling reactions. Their diversity enables investigation of electronic and steric effects on reaction rates and product distributions. The collection includes:

- **Parent aniline:** Unsubstituted aniline (C₆H₅NH₂)
- **Electron-donating substituents:** Such as methyl (-CH₃), methoxy (-OCH₃), and tert-butyl groups, affecting nucleophilicity and reactivity
- **Electron-withdrawing substituents:** Including fluoro (-F), chloro (-Cl), bromo (-Br), nitro (-NO₂), and trifluoromethyl (-CF₃)
- **Substituent patterns:** Derivatives with single or multiple substitutions at the ortho, meta, or para positions to systematically probe structure-reactivity relationships

These amines cover a representative portion of commercially accessible aniline derivatives, enabling cross-comparison of chemical behavior across a broad chemical scope. This variety supports detailed kinetic and mechanistic analyses included in the associated datasets.


## Usage

### Extracting the Data

```bash

# Extract all archives

tar -xzf Amide_Project_NMRs.tar

tar -xzf Example_Experiment.tar

tar -xzf Final_Amide_Image_Analysis_Data.tar

tar -xzf "Rates and Rate Plot Points Datasets.tar"

```

### Working with NMR Data

The NMR data is in Bruker format and can be opened with:
- Bruker TopSpin
- MestReNova
- NMRPipe
- Python libraries (nmrglue, nmrpro)

### Working with Image Analysis Data

The processed CSV files can be loaded directly into:
- Python (pandas)
- R
- Excel
- MATLAB

### Example Experiment

Navigate to the `Example_Experiment/4-30-24-Ninetales/` directory and:
1. Review the YAML configuration file for experiment parameters
2. Open `inflection_finder.ipynb` in Jupyter to see the analysis workflow
3. Examine the time-series images in `input/images/white/`

## Data Collection Details

- **Reaction Type:** Amide formation (aniline + acyl chloride)
- **Temperature:** Room temperature (NMR experiments)
- **Monitoring Methods:** 
  - NMR spectroscopy (kinetic time points)
  - Image-based monitoring (white and yellow light)
  - Rate measurements

## Chemical Scope

The dataset covers a diverse range of:
- **Aniline derivatives:** Various substituted anilines
- **Acyl chlorides:** 200+ different reagents including:
  - Aromatic (benzoyl, naphthoyl, substituted benzoyl)
  - Aliphatic (acetyl, alkyl chains)
  - Heteroaromatic (furoyl)
  - Specialized structures (adamantane, cinnamoyl)

## Amine Groupings

The amines in this dataset are organized into three groups for systematic analysis. The rate data files are named according to these groupings (e.g., `group1 + [Acyl Chloride] rates.xlsx`).

### Group 1
1. tertbutylamine
2. blank
3. 4-fluoroaniline
4. p-anisidine
5. aniline
6. 2,4,6-trimethylaniline
7. 4-heptylaniline
8. 2,6-diisopropylaniline
9. dicyclohexylamine
10. 4-hexylaniline
11. 2-methylthioaniline
12. 2-aminobiphenyl

### Group 2
1. 4-tertbutylaniline
2. diisopropylamine
3. 4-bromoaniline
4. 2-methylpiperidine
5. 8-aminoquinoline
6. 3-aminoacetophenone
7. morpholine
8. 2-methoxy-5-CF3-aniline
9. 2-(2-methoxyethoxy)aniline
10. 3 amino pentane
11. 2,6-dimethylpiperidine
12. 4-vinylaniline

### Group 3
1. p-toluidine
2. m-toluidine
3. N-isopropylcyclohexanamine
4. o-anisidine
5. triphenylmethanamine
6. 2,6-dimethylaniline
7. tertbutyl-3,5-dimethylpiperazin-1-carboxylate
8. 3-anilinopropionitrile
9. 2-fluoroaniline
10. 1-Boc-4-cyclopropylaminopiperidine
11. 3-methoxyaniline
12. 4-aminobenzophenone

## Citation

If you use this dataset in your research, please cite:

```bibtex

@dataset{amide_formation_kinetics_2025,

  title={Amide Formation Kinetics Dataset},

  author={Baumer, Mitchell and Kubaney, Andrew and Bernhard, Stefan},

  year={2025},

  institution={Carnegie Mellon University},

  publisher={Hugging Face},

  url={[gomesgroup/prism]}

}

```

## License

Copyright 2025 Bernhard Group (Mitchell Baumer, Andrew Kubaney, Stefan Bernhard), Carnegie Mellon University

This work is licensed under the Apache License 2.0 with Commons Clause License Condition v1.0.

**Commons Clause Condition:** The grant of rights under the License does not include, and the License does not grant to you, the right to Sell the Software. "Sell" means practicing any or all of the rights granted to you under the License to provide to third parties, for a fee or other consideration (including without limitation fees for hosting or consulting/support services related to the Software), a product or service whose value derives, entirely or substantially, from the functionality of the Software.

**Full License:** Apache License, Version 2.0

See the [LICENSE](LICENSE.txt) file for the full license text.

## Contact

For questions or issues regarding this dataset, please contact mbaumer@andrew.cmu.edu.


---

**Note:** This dataset is intended for research purposes in chemical kinetics, reaction monitoring, and method development for amide formation reactions.