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Monkeys and Calcium Carbonate. Should ChemZoo Close its Gates?

29 Apr

In a recent blog post we were asked to CLOSE the ChemSpider site based on a judgment made around our handling of calcium carbonate. The following comments were made regarding the fact that a logP value was calculated for Calcium Carbonate inside the ChemSpider database. Specifically:

 Here is  the entry 

Chemical Structure CCaO3

Molecular Weight 62.02

logP -0.809

hydrogen bond donors 2

Well, they got the chemical formula right. Calcium carbonate is marble, limestone, chalk. It’s hard and does not dissolve in water. You calculate its molecular weight as follows:

Ca=40 + C=12 + 3 (O=16)

and your child will tell you that it comes to 100. (I’ve missed the decimal point). The monkeys only get to 62 before they give up. I have no idea how they get this. The monkeys also tell us how many hydrogen atoms can be used to bind to other molecules. I can’t see any hydrogen atoms, nor can you but the monkeys found 2.

In a later blog  the comments included:

There are several broken parts.

1) for CaCO3 the system created H2CO3 and calculated that

2) What is the point of calculating logP for a sodium Ion?

3) there is no point in calculating logP for calcium carbonate. It’s insoluble in water and octanol

In our world of “Please Provide Feedback” as requested on this beta site this information would have been great to receive via the Feedback link on the ChemSpider pages. We receive lots of daily feedback…some of it celebratory in nature: Thanks! Cool! Tried it.worked great! The majority of it is constructive in nature.  Some is highly critical – “You don’t have structure X on your database..what type of service is that!”  BUT..I’m not aware of a resource having every structure.

The blog posting was brought to my attention by a ChemSpider user. So, a blogged response here seems appropriate.

1) The Molecular Weight of CCaO3 is, indeed, NOT 62. That’s the molecular weight of the doubly protonated carbonate ion. Known bug – listed on our bug page. It also states on the prediction page now some of the properties presented are calculated for the main component only”. The algorithms calculate the weight for the “primary ion” that we use to feed the LogP prediction algorithm engine. Known bug and it has been fixed. Now we need to recalculate for 10 million compounds.

2) Calcium carbonate certainly does exist in various forms as listed. But it IS soluble. The measured solubility of CaCO3 is 1mg/100 mL. Ask anyone who lives in a limestone area if calcium carbonate is soluble. . Boil a kettle dry and see what deposits on the element. Cut a copper pipe open and check for the furring from hard water. Check out wikipedia  details about solubility. It might not be highly soluble but many compounds can be highly insoluble but still have a measured octanol-water partition coefficient. But I do get the point.it’s not what you would call an organic molecule so why calculate a logP value?

3) The number of hydrogen bond donors is two. Ah-ha. Now the meat of the problem. There are three issues here really.1) it is not easy to communicate the details of all prediction algorithms before people click a button (and most people don’t care anyways), 2) We need to continue to expand the FAQ list for such issues and 3) The provider of the algorithm for logP prediction needs to consider whether they would want to change what they report for ions such as carbonate or not. Based on feedback the answer is it’s fine as is.

To explain, when carbonate is dissolved in water it protonates. logP is the partition of any species between 2 solvents, specifically logP generally refers to octanol-water partitioning. So for carbonate ion there would be 3 logP’s (CO3–, HCO3-, H2CO3) in competition, to account for that overall distribution of species.

 Calciium Carbonate Species

Carbonate ion, under the measurement conditions of octanol-water partitioning, likely does actually partition. It may exist in the literature as as an experimental value. I don’t know. However, I think it is valid to list predicted values. I can find such predicted values in the International Safety Cards for the National Institute of Occupational Safety and Health for other carbonates (Barium Carbonate, there are no predicted values for calcium carbonate but it does say it is insoluble and we already know that isn’t true!).

The number of hydrogen donors is the sum of OHs and NHs. One of the forms of carbonate in the multi-species is the doubly protonated form and the number of hydrogen bond donors is actually two.

Clearly, logP is not so simple as everyone thinks! In fact an industry has been built around logP algorithms while the fact is that there has been an increasing shift to logD as the parameter of choice, especially for the pharmaceutical scientists. Why? The majority of compounds are not neutral in the body and they experience different pHs as they migrate through the system. While logP is a very important parameter in many ways it is now overshadowed by logD as an important parameter. ACD/Labs provided ChemSpider with their ACD/LogP batch product as part of our collaboration. They also provide a free add-in for the Freeware ChemSketch package to allow anyone to download and predict logP values. ACD/LogD is their tool providing logD calculations.

As commented by PMR, “I cannot let garbage science go uncommented. That is what peer-review is about. And it can be painful.”

Indeed. It was painful to get the criticism this way…we’d prefer the Leave Feedback since it is beta. However, it appears that prediction is valid. So it’s listed. That said, we welcome feedback from the community about whether to remove this value from the database. Or, simply curate the data yourself!

 

About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database (www.chemspider.com). Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (http://www.openphacts.org), a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service (http://cds.rsc.org/) and the RSC lead for the PharmaSea project (http://www.pharma-sea.eu/) attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at https://comptox.epa.gov, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.
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Posted by on April 29, 2007 in ChemSpider Chemistry

 

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