June 27, 2011

How to purchase 150 screening compounds

Have you ever purchased 50, 100 or 1000 screening compounds? Usually such purchases involve from 10 to as many as 30 suppliers. At first, the biggest challenge seems to be understanding which supplier sells which compound, but during the process you encounter a series of various unexpected obstacles and complications that you initially did not even consider.

Since Molport serves numerous clients who have not previously purchased large quantities of screening compounds, we decided to share our experience. We have compiled a daily journal of the problems we have encountered not in one specific instance, but rather in the many situations in which we have found ourselves. Some of the problems were suggested by our clients. In your attempt to purchase screening compounds you may encounter only some of these problems. If your order is placed by your purchasing department, they take on the responsibility of resolving these problems and you will never even know about them.

With this I would like you to understand that we know the details and nuances of purchasing screening compounds. We know that these procedures are often very time consuming especially if you desire to purchase a greater variety of molecules. That is precisely why we created Molport – to make purchasing compounds as easy as purchasing books in Amazon.

We invite you to read our daily „Purchasing 150 screening compounds” journal. We will not publish it in its entirety all at once, but rather by day – the way things happen in reality.

See also: http://blog.molport.com/2015/09/find-compounds-choose-suppliers-and_10.html
Use List Search as one option for search by text or SMILES and more!

The „Purchasing 150 screening compounds” journal

Day 1

We have completed a virtual screening project and have identified a slew of compounds we would like to test – 150 structures. I have an SD file of structures that I convert to the SMILES format and upload it on the ZINC database search form. I like ZINC – this database allows me to quickly find suppliers for an extensive list of compounds and to save the information for further use in Excel. Today I found suppliers for only 125 of the 150 compounds on my list and they are available from 11 different suppliers: one supplier sells 23 compounds, another – 39. Many compounds are offered by more than one supplier and in total there are 243 different catalogue numbers. My colleagues and I discuss which suppliers to use. In the end we decide to contact all the suppliers. The catalogue information databases tend to be outdated – some compounds have already been sold out since being entered into the database. By contacting the suppliers directly we will receive the latest information. I compile lists of each suppliers compounds and will get in touch with all of them tomorrow.

Day 2

I will start my day by quickly contacting all the suppliers. I found each supplier’s home page with information on how to request prices and in-stock status. I found the email address for seven of the suppliers and sent them the list of compounds I was interested in. For one supplier it was necessary to search each compound online in their home page – I found the price as well as the quantity available. I started to enter this information in an Excel table. Two suppliers offer the option of submitting catalogue numbers in their home page, but I will have to contact them nevertheless, because shipping charges do not appear in their home page. In order for us to purchase the maximum number of compounds for the money we have available for this purpose, I will have to contact them for the complete total cost of the order. For one supplier the only way of getting in touch is a contact form in their home page. I wrote them that I wanted to purchase their compounds, but did not know how to do so. Unfortunately, while I was writing I did not notice I had lost my WIFI connection and all I had written was simply lost. Too bad! I wrote everything a second time.

That was a bit of a chore! To get this done took me all morning!

My Excel table already contains the data from those suppliers whose information was available in their home page. By the end of the day I received the first two offers by email. I also entered this data in the Excel table. I am not sure how to correctly save the shipping costs. Each compound has its price, but each order has its total costs that do not depend on the number of compounds ordered! It will be a bit more complicated than I thought to compute the true cost of each compound.

Day 3

I received one more offer. It seems that I will be able to order about one half of the compounds very soon. I am sure I will receive the remaining offers today. Unfortunately, one supplier did not include shipping charges, so I had to write him again. One supplier responded that they would not be able to submit an offer since they service a different region. At least he gave the information to the right contact person! I send the email that I wrote yesterday again, this time to our regional representative. I received an answer along with an offer within one hour. Now that’s what I call service!

I continued to compile offers, but I was really getting tired of this little job. I chose two suppliers and sent them an email requesting offers for the four compounds they sell. To avoid confusion, I started to group these emails in a separate file.

In the afternoon I received an email from the supplier who had not included shipping charge information. Now things are starting to happen! One more supplier sent his offer. But the supplier I contacted using the contact form still has not answered. I reviewed what had been done so far in order to understand exactly what we had managed to find to date: I have offers for 62 products – 40 molecules. Now we understand that 21 molecules will not be available from any of the suppliers – they are sold out!

Day 4

I received three more offers. Now 10 of 11 suppliers have answered. I compiled all the information, but even without the last supplier, it was evident that 35 molecules had already been sold out. A colleague from another group told me over lunch that compounds can also be searched in www.chemspider.com. I checked my 35 missing structures there and found 16 more compounds from 4 suppliers. Two of these compounds are very expensive – 2000 USD each! No! We cannot buy anything that expensive.

Seems like a major hassle for just a few compounds, but some of them have a fairly unique structure and I would really like to test them! And I have to request price information again. I will contact only two suppliers – that way I will be able to get 10 compounds. The other four compounds would have to be purchased two from each supplier – that would be both expensive and complicated and what’s more, I have never heard of these suppliers before. I note that these compounds are not purchasable.

I am still waiting for precise costs and delivery times from one supplier. In order to speed up the process, we could already order products from 9 suppliers. I spend quite a bit of time trying to figure out the most advantageous way to order. 103 compounds can be purchased in several ways, because they are in fact 162 different products. Ok. We decide to purchase all the compounds from the supplier that offers the greatest number of compounds at the lowest price. Next we will purchase the maximum number available from the supplier with the second lowest price. And I processed the entire list. Why are there such differences in price? In the end it turned out I would buy only 2 compounds from the supplier I had requested information on 23 compounds from, because the other compounds can be ordered from other suppliers. Interesting, isn’t it? At the end of the day I filled out the order forms and submitted them to our purchasing division.

Before heading home I decided to make another attempt to contact the supplier who can be reached only by the form in his home page. This is my third try. Upon carefully searching all parts of his home page I found a telephone number and a fax number. I called, but got the answering machine, because this business is in another part of the world and it is now nighttime. I left a message on the answering machine and sent a fax as well. While doing this, I received an email from the supplier whose compounds I found in ChemSpider. He needed to know the quantity and delivery location of the compound in question. I had apparently forgotten to include that in my original purchase request! I sent the requested information and also wrote an email to the supplier I had requested two compounds from. The supplier responded with his offer late in the evening.

Day 5

Today is Saturday! And tomorrow is a day off as well! My friends and I decide to go whitewater rafting!

Day 7

Today we received a response from the two remaining suppliers and we were able to order 10 more compounds from them. In total we have now ordered 125 compounds from 11 suppliers. We were unable to purchase only 25 compounds. Of course, it would be better if we had been able to purchase all 150. Perhaps we should have started with 175 or 200 compounds giving us a greater likelihood that in the end 150 would be purchased?

I also talked to our purchasing department about the orders. It turns out that we had no previous transaction history with 4 of the 11 suppliers. Accounts will have to be opened for them, but the purchasing department will handle all of that – I just have to send them the contact information.

In the evening I checked our purchasing system and saw that orders had already been placed with 7 of the suppliers. Super!

Day 8

The system shows that orders have been placed with 10 suppliers.

Day 9

An order has still not been placed with one supplier. It seems that they have to fill in a great number of documents in order to open an account and they have not yet done so.

Day 10

A purchase order has still not been placed with the last supplier. I sent an email to the purchasing department asking them to put a rush on this. In the meantime the courier service delivered a package from the first supplier (Supplier 1). That is great service! I will check into the possibility of leaving a comment on their home page.

Day 11

Finally all purchase orders have been placed! I received emails from FedEx saying that two more packages (from Supplier 2 and Supplier 3) are on their way.

It is once again the weekend. It is hard to believe that two weeks have passed and we have just finished placing purchase orders.

Day 14

I am still waiting for delivery.

Day 15

I received a phone call from a colleague at the laboratory next to mine. The courier service had left a package addressed to me at his lab because my door had been locked. He had almost forgotten about the package. I also received the bill from Supplier 1.

Day 16

I received a package from Supplier 5 – the invoice showed totally different compounds than those which had been ordered and the bill was only 5 USD. I wrote to the supplier asking for the correct compounds. I received notification from Supplier 6 that their order was on its way.

Day 17

UPS called to say that the shipment from Supplier 3 needs to go through customs and they requested prepayment for this procedure. Our bookkeeper refused since it is not our policy to do so.

Day 18

Supplier 3 wrote to say that UPS had informed them that we refused to accept delivery. We did not refuse delivery, we simply could not prepay the customs fees. Supplier 3 offered to pay for customs and include the fee in our bill. That is good, otherwise we probably would never receive this shipment.

Day 21

We received the shipment from Supplier 7 and Supplier 8, but customs requested additional information about the shipment from Supplier 6. They did not understand why the package was coming from the Ukraine, but the bill from the US. We needed to submit an explanation of how we placed this order.

Day 23

We finally received the shipment from Supplier 6.

Day 24

NMR spectra for three compounds from two suppliers do not match their structure. We sent the results to the supplier.

Day 28

I received a phone call from a very distraught Supplier 9 asking why we had refused delivery of their shipment – it was about to be returned. But I had received no information about this shipment! It turns out that because DHL had been unable to reach the addressee by phone, they did not deliver the shipment. It seems odd that they had not been able to reach anyone – someone is usually at the laboratory!? I called DHL and finally took care of the situation. Although the shipment was on its way back, they would return it to us. The supplier agreed with the compound analyses and will remove these compounds from our bill.

Day 29

We received the shipment from Supplier 9 with 3 fewer compounds than we had ordered. These compounds had not passed their quality control. I do not understand why they did not notify me earlier! I could have ordered these compounds from another supplier had I known!

Day 30

Two weeks have passed and I finally received a response from Supplier 5. It seems that the compounds in the package with the strange invoice are those we had ordered, but the invoice did not match the contents of the shipment because it had been easier for the supplier to send the shipment that way. But where are the compounds now? Were they destroyed? Returned? We found them in the refrigerator.

Day 31

We should have received the shipment from Supplier 10 by now. I inquired about the status of my order and the supplier responded that the compounds would be sent in a few days. First efforts to synthesize these compounds had not been successful and they were awaiting results of the second synthesis. Synthesis!?! They said they had these compounds in their warehouse!?! This information leads me to suspicions about the shipment from Supplier 11 which was also late. I wrote to this supplier as well inquiring about the status of my order.

A month has passed since we started ordering these compounds.

Day 32

Supplier 11 responded. The synthesis of the compounds in question was taking longer than expected and thus, they were requesting a two-week extension on the order. I agreed with the stipulation that we must receive the compounds by day 60. That is the project deadline and the supplier agreed to this stipulation.

Day 35

I received an angry email from Supplier 1 who complained that we had missed the deadline for payment by 14 days and asked that we take care of this. Where to find the time to deal with all of this!

Day 36

I received word from SUP10 that 3 of 5 compounds had been successfully synthesized and the shipment was on its way.

Day 37

We received information from FedEx that they had received a shipment from Supplier 10 that needed to go through customs. The supplier had not sent the necessary bill so we sent an email requesting them to forward the bill.

Day 38

We received the bill from the supplier, we forwarded it to FedEx. Customs was unable to clear our shipment the same day and now we have to wait an additional two days (national holiday).

Day 43

The shipment from Supplier 10 cleared customs but it could not be delivered today.

Day 44

The shipment from Supplier 10 was delivered! We are still awaiting information from Supplier 11 regarding the results of the synthesis of our compounds. I sent an email. They responded that they are still awaiting the last results and then they will send the shipment.

Day 46

Supplier 11 wrote that 16 of 21 compounds had been successfully synthesized. The shipment was on its way.

Day 51

UPS requested the bill for the shipment from Supplier 11 it could clear customs. We forwarded the bill.

Day 52

Customs detained the shipment because they needed a statement from the import authority, which requested a COA, MSDS and other documentation regarding the origin of the compound. We did not have such documentation and asked that the supplier rush the necessary documents to us.

Day 57

We received the documents from the supplier, we forwarded them to the import authority.

Day 60

We started testing. Supplier 11 had not met the deadline for delivery

Day 65

The shipment from Supplier 11 cleared customs and was delivered


For the 150 compounds we had selected, we found 11 suppliers for 125 molecules, but only 112 compounds were actually delivered.

The process of searching for these compounds was so complicated and time consuming that we finally decided not to order several compounds to decrease the number of suppliers we would have to communicated with. The ordering process was as follows: in order to contact 13 suppliers, 12 emails were sent, the CONTACT US form was filled out three times, a fax was sent, messages were left on the answering machine and four hours were spent in the home pages of the suppliers checking on prices and availability. Finally, compounds were ordered from only 11 suppliers.

The ordering procedure itself took a total of 6 days because 5 of the 11 suppliers needed to complete new account documentation.

Shipment delivery required tremendous patience! Delivery took 41 days during which time 11 shipments were received. During this period we received 24 different emails from suppliers, courier services and customs; we sent 15 emails. Several phone calls were made, statements and explanations were written, documentation and compounds were tracked.

After this 2 month long process, the price of these compounds can not only be expressed in monetary terms – it now includes our time and frazzled nerves!

June 20, 2011

A quick way to programmatically check compound availability

If you work in virtual compound screening, you need a compound database. Of course, testing a compound is a lot easier if you can select compounds that can be quickly ordered, that are in stock. You can collect and regularly update supplier catalogs, but to do so comprehensively is a full time job. There are several ready to use commercial, academic and government databases, example, ZINC, CoCoCo. A number of our partners are using the Molport database of commercially available compounds in their in-house chemical databases. But no matter which database you use, by the time you download it, it is out of date.

Choose a database that is regularly updated. I already wrote on the importance of supplier catalog update previously. While building blocks may be sold by a supplier for many years, screening compounds sell out often in a year or two. So if you work with a database that hasn’t updated a supplier’s catalog in over a year – expect that a significant fraction of compounds will no longer be available. No matter which database you use, however, by the time you download it, it is out of date. Of course, if you carefully select 100 compounds for testing, you would prefer for most of them  to be in stock. What to do then?

We have been thinking about this problem for a while and have discussed it with several of you. Besides updating our database frequently, we are now providing monthly incremental database updates: newly added compounds and no longer available compounds. We are also testing a tool that will enable you to programmatically and instantly check the latest compound availability information in the Molport database. In a special URL you can specify the Molport compound ID and get back XML data from the database:

  • The status field returns values shop (compound can be ordered online), source (compound can be ordered by requesting a quote) or unavailable (it is sold out).
  • The type filed returns values stock (supplier has already made this compound and it is in  his warehouse) or virtual (these are compounds that can be made on your request).
  • The field available_mg lists the largest amount of a  compound available (in miligrams).

It works similarly to NCI Chemical Identifier Resolver. You can write a simple code that goes through the list of compounds and checks which of them are available in the needed quantity. So if you need  10 miligrams each of 100 compounds, maybe out of the first 100 only 84 will be available. You can immediately add more compounds until you have 100.

This can even be done without programming in Google Spreadsheet. Here is an example of a table that uses ImportXML function and parses two fields from the XML data:

The syntax to get the value sourced in the cell B2 is as follows:
where molportURL is an abbreviation of the full URL of this service.

Can this be potentially useful to you?
If you would like to know more about this new Molport service or the available compound database, write me through Molport contact us form.

June 14, 2011

Chrome users now can more easily search the Molport available compound database

Have you noticed that in Google Chrome you can search many websites directly from the address bar? This neat tab-to-search feature is available already for some time. Unlike typing the search query in the address bar and pressing enter, this search method uses the search engine of the target site, not the search engine of Google. Instead of going first to the website, finding the search box, entering keywords and pressing the search button, you can simply perform the search directly from the address bar of the web browser. While not all websites support this feature, it is handy when available.

Tab-to-search now works with the Molport website as well.

Type “molport” in the address bar and press tab:

Now type your search query and press enter: 

And see search results in Molport (example: difluoro methylbenzene): 

How about structure search?
You still need to use the chemical structure search form.


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