red22
Bluelighter
- Joined
- Nov 23, 2009
- Messages
- 2,206
Video: https://www.youtube.com/watch?v=lCJEr5bnjUU I embedded the video below.
Transcript: Hi everyone. If you're a chemist, you know the drill. You need to synthesize a specific molecule, but the biggest challenge isn't the lab work. It's finding a reliable protocol. Sure, you can try googling it, but that only works if you have a precise name. And even then, results are often hit or miss.
Today, I'm going to share my secret weapon with you, a massive searchable database of over 50,000 synthesis methods that I use every single day. It runs on Data Warrior, a powerful open-source program, and it's going to change how you do research. Here's how it looks. I use Data Warrior to open it. It's completely free. To find what you need, use the filter panel on the right.
Let's say we want to find Ditrophenol.
We draw the structure, click okay, and the list filters down.
Notice something. The search didn't just find the exact match. It performed a substructure search. This is a powerhouse feature that Google simply can't replicate. It allows you to find synthesis methods for similar molecules when an exact match isn't available.
However, if you need only denitrofenol, you can use the lasso tool, doubleclick the free atoms, and check prohibit further substitution.
Now only our target molecule remains.
Here is the literature reference. It's not clickable. From here you can open the folder with book. Here you can open specific pages.
You can open the links either from this table view by simply clicking on them or you can open them from right-click menu.
This isn't just a search engine. It's a massive digital library of verified lab manuals and gold standard procedures.
Just look at the list of literature.
Since this database was originally created for the postsviet scientific community, many books are in Russian.
But don't worry. First, about a third of the literature is already in English.
Like for example, this synthesis.
Second, for the Russian parts, you can simply take a screenshot of the page and feed it to Gemini or chat GPT. They will recognize the text and translate the protocol for you perfectly. It's not just for organic chemistry either. You can find inorganic methods too. Here is for example preparation of rainy nickel catalyst. Historically, this database was used in almost every Ukrainian research institute. It looked like this and ran on the now defunct ISIS base. In the original version, you had to manually find the files in folders. I've ported everything to Data Warrior and added clickable links to the PDFs. Just make sure to read the instructions in the description to make the links work.
You can download the whole database from my Google Drive. I will leave a link in the description. You might ask, "This database is 20 years old. Isn't there something newer online?" There are online services, but in my experience, none work as efficiently for finding actual procedures. First of all, you can try Google if you know the name of the substance. I should mention right away that it usually doesn't show the specific methods found in my database.
However, sometimes it might give you something new from recent articles or patents. Sometimes even better than what's in the database, sometimes not.
But it's always worth checking Google just in case. Then there are more specialized websites, but they all share one common problem. They either find nothing at all or they don't find a synthesis specifically, but rather every single article where the substance is mentioned. Finding an actual procedure among all those papers is nearly impossible. Take Chem Spider for example. It's a great tool if you need to find chemical properties. There is a structure search here, but let's go to the articles section. Look at how many there are. Good luck trying to find a synthesis method here. Organic synthesis is a good resource with only verified methods, but there aren't many of them.
It also has a structure search. Here is what it found for me. As you can see, there's no synthesis for what I'm looking for. This happens almost every time, which is why I don't really use it. Nevertheless, it's a noteworthy resource. I found some excellent protocols here in the past. Sure, Cambl is for searching molecules in patents.
Unfortunately, as we can see here, we have the same problem. It just throws in everything where the molecule is mentioned. Perhaps if the structure were more complex, the result would be more relevant. It's worth keeping in mind, but I personally don't use it.
If you need a deep dive for a PhD literature review, you'll need Reaxis or SciFinder, but those are incredibly expensive and usually only available to large universities. If you have access to Reaxis, you probably don't need this video. If you don't have Reaxis access, I'm working on another alternative, the Sprey database. It contains 14 databases and about 2.5 million reactions. It used to be available for download years ago, but now it's a paid service very similar to Reaxis. I'm currently merging these files and converting them into a modern format. When I finish, I'll post it on my Telegram channel. So, make sure to subscribe. If you find my work helpful, you can support me via buy me a coffee or my mono link. That's all for today.
Happy synthesizing and see you in the next
Description: database link in my telegram (google drive): https://t.me/ninja_chemist/17
download everything from telegram + torrent file: https://t.me/ninja_chemist/23
I downloaded the database and re-hosted it on MEGA: https://mega.nz/folder/h4BQhBAa#TrbO9FsdCgeUCuiP05_iWQ
Transcript: Hi everyone. If you're a chemist, you know the drill. You need to synthesize a specific molecule, but the biggest challenge isn't the lab work. It's finding a reliable protocol. Sure, you can try googling it, but that only works if you have a precise name. And even then, results are often hit or miss.
Today, I'm going to share my secret weapon with you, a massive searchable database of over 50,000 synthesis methods that I use every single day. It runs on Data Warrior, a powerful open-source program, and it's going to change how you do research. Here's how it looks. I use Data Warrior to open it. It's completely free. To find what you need, use the filter panel on the right.
Let's say we want to find Ditrophenol.
We draw the structure, click okay, and the list filters down.
Notice something. The search didn't just find the exact match. It performed a substructure search. This is a powerhouse feature that Google simply can't replicate. It allows you to find synthesis methods for similar molecules when an exact match isn't available.
However, if you need only denitrofenol, you can use the lasso tool, doubleclick the free atoms, and check prohibit further substitution.
Now only our target molecule remains.
Here is the literature reference. It's not clickable. From here you can open the folder with book. Here you can open specific pages.
You can open the links either from this table view by simply clicking on them or you can open them from right-click menu.
This isn't just a search engine. It's a massive digital library of verified lab manuals and gold standard procedures.
Just look at the list of literature.
Since this database was originally created for the postsviet scientific community, many books are in Russian.
But don't worry. First, about a third of the literature is already in English.
Like for example, this synthesis.
Second, for the Russian parts, you can simply take a screenshot of the page and feed it to Gemini or chat GPT. They will recognize the text and translate the protocol for you perfectly. It's not just for organic chemistry either. You can find inorganic methods too. Here is for example preparation of rainy nickel catalyst. Historically, this database was used in almost every Ukrainian research institute. It looked like this and ran on the now defunct ISIS base. In the original version, you had to manually find the files in folders. I've ported everything to Data Warrior and added clickable links to the PDFs. Just make sure to read the instructions in the description to make the links work.
You can download the whole database from my Google Drive. I will leave a link in the description. You might ask, "This database is 20 years old. Isn't there something newer online?" There are online services, but in my experience, none work as efficiently for finding actual procedures. First of all, you can try Google if you know the name of the substance. I should mention right away that it usually doesn't show the specific methods found in my database.
However, sometimes it might give you something new from recent articles or patents. Sometimes even better than what's in the database, sometimes not.
But it's always worth checking Google just in case. Then there are more specialized websites, but they all share one common problem. They either find nothing at all or they don't find a synthesis specifically, but rather every single article where the substance is mentioned. Finding an actual procedure among all those papers is nearly impossible. Take Chem Spider for example. It's a great tool if you need to find chemical properties. There is a structure search here, but let's go to the articles section. Look at how many there are. Good luck trying to find a synthesis method here. Organic synthesis is a good resource with only verified methods, but there aren't many of them.
It also has a structure search. Here is what it found for me. As you can see, there's no synthesis for what I'm looking for. This happens almost every time, which is why I don't really use it. Nevertheless, it's a noteworthy resource. I found some excellent protocols here in the past. Sure, Cambl is for searching molecules in patents.
Unfortunately, as we can see here, we have the same problem. It just throws in everything where the molecule is mentioned. Perhaps if the structure were more complex, the result would be more relevant. It's worth keeping in mind, but I personally don't use it.
If you need a deep dive for a PhD literature review, you'll need Reaxis or SciFinder, but those are incredibly expensive and usually only available to large universities. If you have access to Reaxis, you probably don't need this video. If you don't have Reaxis access, I'm working on another alternative, the Sprey database. It contains 14 databases and about 2.5 million reactions. It used to be available for download years ago, but now it's a paid service very similar to Reaxis. I'm currently merging these files and converting them into a modern format. When I finish, I'll post it on my Telegram channel. So, make sure to subscribe. If you find my work helpful, you can support me via buy me a coffee or my mono link. That's all for today.
Happy synthesizing and see you in the next
Description: database link in my telegram (google drive): https://t.me/ninja_chemist/17
download everything from telegram + torrent file: https://t.me/ninja_chemist/23
I downloaded the database and re-hosted it on MEGA: https://mega.nz/folder/h4BQhBAa#TrbO9FsdCgeUCuiP05_iWQ
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