Calcium Carbonate, logP predictions and Chris Lipinski

30 Apr

Recently I posted a response to a comment to the judgment that ChemSpider should not list the logP value associated with Calcium Carbonate. Our belief is that the ACD/LogP product is appropriately predicting a logP value for carbonate. 

That said we thought it appropriate to consult with an expert. Who better than Chris Lipinski. Chris is the author of the “Rule of Five” a simple algorithm for predicting drug compounds likely to show oral activity. At Pfizer, from 1970 to 1990, he supervised medicinal chemistry drug discovery laboratories discovering multiple gastrointestinal and diabetic clinical candidates. In this process he became interested in the design of bioisosteres and in drug physical chemical properties and quantitative structure activity relationships, especially as they related to problems of oral activity.  The comments below are an excerpt from an email exchange with Chris: “Carbonate anion is distinctly different than other inorganic anions in that it is only stable at base pH. The reported first acidic pKa of around 6.1 for H2CO3 is actually a composite of two numbers; the true pKa which is around 4 and the equilibrium constant between CO2 dissolved in water and true H2CO3 which favors the dissolved CO2 by a factor of about 100. It takes a distinct period of time for the equilibrium to occur on the orders of 10’s of seconds at 37 deg C. Hence carbonic anhydrase in human physiology. The stability of H2CO3 is tremendously dependent on pH, on stabilizing cations and by anything with a transient tendency to form an anhydride or mixed ester with H2CO3, eg. orthophosphoric acid in soda pop. So a complex answer to a simple question. My position would be that since universally the complex equilibria is rolled into the pKa (and presumably log P of H2CO3) I would simply list your calculated LOG P for CaCO3.” 

With Chris’ comments we will be leaving the logP value for Calcium Carbonate in place. We do welcome any further feedback though. We know there are errors on ChemSpider as they are being curated now by ChemSpider users as shown here. There are > 10 million records..we do need your feedback!


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 ( 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 (, 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 ( and the RSC lead for the PharmaSea project ( 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, 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.
Leave a comment

Posted by on April 30, 2007 in ChemSpider Chemistry


0 Responses to Calcium Carbonate, logP predictions and Chris Lipinski

Leave a Reply

Your email address will not be published.

This site uses Akismet to reduce spam. Learn how your comment data is processed.