Enjoyed SPARQLTHON and weekend #memo

In this week I participated SPARQLTHON #78 where held on national institute of genetics. I am not familiar to SPARQL so it was difficult to develop something with SPARQL, but I tried to use SPARQLWRAPPER which is package for using sparql from python and tried to retrieve information from ChEMBL RDF. It was good opportunity

Generate possible heteroaromatic cores from query molecule #RDKit #chemoinformatics

Hetero shuffling is the approach which replace atoms of scaffold and generate new molecule with atom replaced scaffold. For example benzene as core, examples of shuffled cores will be pyridine, pyrimidine etc. The approach is often used medicinal chemistry project to improve ADMET properties, biological activities and also used for substance patent claim strategy. Native

Efficient site-selective functionalization with TFT #organic_synthesis #organic_chemistry #memo

There are many new functionalization reactions of molecules in these days such as electrochemistry, photo-redox and cross-coupling etc. New reaction will give more choices for synthetic route. Chemists often use cross coupling or another functinalyzation reactions, but these reactions are required foothold such asAr- halogen or ArOTf groups. And the reaction precursor is synthesized by

Draw molecular network on Jupyter notebook with rdkit and cytoscape.js-2 #RDKit #cytoscape

Yesterday, I posted about cyjupyter. And got comment how to render the compound name on each node. I think it is possible to use context attribute in style settings. Let’s try. Code is almost same as yesterday Networkx is easy to make network with many attributes. I set smiles as name attribute. OK let’s draw

Draw molecular network on Jupyter notebook with rdkit and cytoscape.js #RDKit #cytoscape

I use cytsocape and cytoscape.js when I would like to draw molecular network. Molecular network can be made from similarity, matched molecular pair etc. In cytoscape there is a plug in for drawing chemical structures named ‘chemviz‘. There is no plugin for cytoscape.js. So it is needed for drawing function which draw chemical structures as

卒団式に行った話 #diary #dodgeball

日曜は、子供が通っている小学生ドッジボールクラブの卒団式でした。6年生の子供たちを送り出す恒例イベントです。 イベントの最初は親子ドッジです。6年生中心とするオフィシャルチームvs大人チームや、4年生以下のジュニアチームvsママさんチームなど普段は試合することない親子のガチンコ対決が繰り広げられますw。試合に応援に行って上から見てると、もっとパス回しを速くしたりいいのではとか、アタックもっと頑張れとか思っちゃうこともあるんですがいざコートに入ると子供たちのパスは早いこと早いこと、アタックももちろん強烈。普通に小学生にボコボコにされます。 親子ドッジの後はみんなでレストランで打ち上げパーティです。うちの長男はまだ小二なので送り出す側で6年生の子供たちのスピーチや、卒団生のご両親の挨拶を聞いたりするわけですが、一つの競技に打ち込んで成長した6年生はたくましいですね。私も途中でちょっと泣きそうになってしまいました。 きっとこれからも色々あると思うけど、きつい練習に耐えてきた精神力と、そこで培われた体力は、きっとこれからの未来にプラスになることでしょう。 卒団した6年生の皆さんのこれからのより一層の活躍にエールを送りつつ今日の駄文を閉めたいと思います。 さあ、次はさくら杯！4年生のみんなはジュニア最後の試合です。悔いの残らない素晴らしい試合を見せてくれることを楽しみにしています！！

Recent trends of Flow Chemistry #memo #chemistry #technology

I enjoyed reading the article in my lunch break. Researchers at Abbie published nice review about the flow chemistry in the pharmaceutical industry. The URL is below. https://pubs.acs.org/doi/10.1021/acs.jmedchem.8b01760 The review describes wide range of the flow chemistry from large scale synthesis to lab scale synthesis. Flow chemistry can run the reaction under high temperature and

Visualize HOMO LUMO with psi4 #RDKit #psi4 #psikit

Now thin wrapper of psi4 named psikit can generate cube file which has frontier orbital information. After calling getMOview, I would like to check the orbital shape. Psi4 provides vmd_cube.py script which generates cool view on VMD. To run the script on python3, it is needed to change line 332 from ‘for k,v in options.iteritems():’

Calculate atomic charges with psikit #RDKit #psi4

Recently I implemented new function in psikit for atomic charge calculation. Now user can get mulliken charges, RESP charges and Lowdin charges very easily. There is quick example below. At first import libraries. I used methanol and imidazole for demo. And psikit can generate 3D structure from SMILES and optimize the conformer with RDKit. Then

Nano scale parallel compound synthesis #memo #chemistry

Total synthesis of complex natural product named “Taxol” was my master thesis theme when I was in university. Total synthesis of complex molecule, it is required long reaction steps. You know, amount of the material in near the final step is very limited. In my case I had few milli gram of compound but I