The ChemConnector Blog by Antony Williams

This particular feature might have been around for a while for authors in Elsevier publications but it is the first time that I have received a CiteAlert. I know that many of my other Elsevier publications have been cited, some quite highly, so I assume it is a new service. It’s a great idea and is something I would encourage other publishers to consider.

I’m on the agenda to speak at the Bio-IT meeting in Boston next year (April 27-29 2009) to present on “Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry.” In case you are assembling your calendar for next year here’s the announcement…

“Join the life sciences community in Boston, MA next April 27-29, 2009 for the 7^th Annual Bio-IT World Conference & Expo (www.bio-itworldexpo.com).  Since its debut in 2002, Bio-IT has established itself as a premier event showcasing the myriad applications of IT and informatics to biomedical research and the drug discovery enterprise.  The 2009 program will feature best practice case studies and joint partner presentations relevant to the technologies, research, and regulatory issues of life science, pharmaceutical, clinical, health, and IT professionals. “

I’ll be giving three papers at the ACS meeting in Salt Lake City in Spring of next year. It seems way in the distance but as usual that time will come way too quickly. I’ve accepted invitations to write four papers before the end of January so it will be the usual crunch. See you in Salt Lake City!?

PAPER ID: 1212659
PAPER TITLE: “Going a mile InChI by InChI: Enabling online chemistry at ChemSpider”

DIVISION: Division of Chemical Information
SESSION: The Adoption and Use of the IUPAC InChI/InChIKey SESSION START TIME: Sunday, March 22, 2009, 9:00 AM

PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Sunday, March 22, 2009 from 9:35 AM to 10:05 AM

PAPER ID: 1238487
PAPER TITLE: “Text mining for chemistry and building a public platform for document markup”

DIVISION: Division of Chemical Information
SESSION: General Papers
SESSION START TIME: Wednesday, March 25, 2009, 2:00 PM

PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Wednesday, March 25, 2009 from 2:05 PM to 2:30 PM
PAPER ID: 1243060
PAPER TITLE: “Cleaning up chemistry for the pharma industry: Delivering a flexible platform for interrogating the FDA DailyMed website”

DIVISION: Division of Chemical Information
SESSION: General Papers
SESSION START TIME: Wednesday, March 25, 2009, 2:00 PM

PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Wednesday, March 25, 2009 from 3:55 PM to 4:20 PM

I am a week behind on submitting a Chapter for publication in the Second Edition of the Encyclopedia of Spectroscopy. Too much work…not enough time. In the meantime I’ve co-authored a couple of publications with friends from ACD/Labs…one of these addresses an issue discussed on the ChemSpider Blog…a longstanding wish to compare empirical and quantum-mechanical NMR prediction approaches.

A Systematic Approach for the Generation and Verification of Structural Hypotheses.

During the process of molecular structure elucidation, selection of the most probable structural hypothesis may be based on chemical shift prediction. The prediction is carried out either by empirical or quantum-mechanical (QM) methods. When QM methods are used NMR prediction commonly utilizes the GIAO option of the DFT approximation. In this approach the structural hypotheses are expected to be investigated by the scientist. In this article we hope to show that the most rational manner by which to create structural hypotheses is actually by the application of an expert system capable of deducing all potential structures consistent with the experimental spectral data and specifically using 2D NMR data. When an expert system is used the best structure(s) can be distinguished using chemical shift prediction using either incremental or neural net algorithm. The time-consuming quantum-mechanical calculations can then be applied, if necessary, to one or more of the “best” structures to confirm the suggested solution.

The Application of Empirical Methods of NMR Chemical Shift Prediction to Determine Relative Stereochemistry.

The reliable determination of stereostructures contained within chemical structures usually requires utilization of NMR data, chemical derivatization, molecular modeling, quantum-mechanical calculations and, if available, X-ray analysis. In this article we show that the number of stereoisomers which need to be thoroughly verified can be significantly reduced by the application of NMR chemical shift calculation to the full stereoisomer set of possibilities using a fragmental approach based on HOSE codes. The usefulness of suggested method is illustrated using experimental data published for artarborol.

I’ve had the pleasure of working with my close friend Gary Martin and my old colleagues from ACD/Labs for the past couple of years on a processing technique for NMR called indirect covariance. Our latest publication was just accepted to the Journal of Heterocyclic Chemistry.

Unsymmetrical Indirect Covariance Processing of Hyphenated and Long-?Range Heteronuclear 2D NMR Spectra – Enhanced Visualization of ²J_CH and ⁴J_CH Correlation Responses

Abstract

Recent reports have demonstrated the unsymmetrical indirect covariance combination of discretely acquired 2D NMR experiments into spectra that provide an alternative means of accessing the information content of these spectra. The method can be thought of as being analogous to the Fourier transform conversion of time domain data into the more readily interpreted frequency domain. Hyphenated 2D-?NMR spectra such as GHSQC-?TOCSY, when available, provide an investigator with the means of sorting proton-?proton homonuclear connectivity networks as a function of the ¹³C chemical shift of the carbon directly bound to the proton from which propagation begins. Long-?range heteronuclear chemical shift correlation experiments establish proton-?carbon correlations via heteronuclear coupling pathways, most commonly across three bonds (³J_CH), but in more general terms across two (²J_CH) to four bonds (⁴J_CH). In many instances ³J_CH correlations dominate GHMBC spectra. We demonstrate in this report the improved visualization of ²J_CH and ⁴J_CH correlations through the unsymmetrical indirect covariance processing of GHSQC-?TOCSY and GHMBC 2D spectra.

It’s also one of the most colorful publications, with the most correlation arrows (!) I’ve ever been involved with.

Welcome to the ChemConnector Blog. This blog will be a chemmunication vehicle for the website www.chemconnector.com, to go online shortly. As many of you will  know me from the ChemSpider blog you will likely be aware that I took a sabbatical after 10 years working a company and have taken a few months down. For the time-being my intention is to spend some time consulting for groups and organizations interested in utilizing my skills and growing the business of ChemConnector - Connecting Scientists to Problem Solvers. This, of course, in parallel to the ongoing work on ChemSpider.  More on this will come shortly but essentially I hope to work with my extended network of friends, colleagues, partners and contacts in science to help solve problems for chemists. It may be in the cheminformatics domain utilizing the ChemSpider team, commercial service providers or Open Source proponents. It may be in the world of chemical synthesis by connecting chemists to custom synthesis houses or vendors (you will see an increasing trend towards social networking for chemists on ChemSpider in the future). It may be in the realm of the application of analytical science to solving structure elucidation problems or setting up an analytical facility. It may be in the authoring of reports and materials of scientific interest. It’s an exciting opportunity and very invigorating - I’ll get to work with people I respect, work on solving problems of interest and, I believe, stay connected to the multiple facets of a changing environment.

For the past 8 months I’ve been running two blogs associated with ChemSpider…the ChemSpider blog and the ChemSpider News blog. These had different intents - the ChemSpider blog was to cover the general directions, vision, activities, challenges and community conversations about the ChemSpider service. The ChemSpider News was to cover details of new functionality as it was rolled out. What has happened is that the postings on ChemSpider News regarding new functionality have been missed by the readers of the blog as a result of the readership being different (and different subscriptions to Feedburner being in place). This has not been good for the ChemSpider users since they have not been getting the latest and greatest news about new functionality. It’s a great shame to deliver new functionality and not have people use it for weeks on end because they don’t know about it.

What I’ve also been posting on the ChemSpider blog are my own personal views regarding a whole variety of issues…none of them ChemSpider related. For example, my views on vaccines, on fluoride, on drugs, and on my views of various research undertakings. Recently John Doe took me to task in a recent response on the ChemSpider blog. While I vehemently disagree with his comment regarding the reasons behind my posting I have decided to separate news regarding ChemSpider and its mission, direction and new functionality from my own personal commentaries, pleas, musings and, once in a while, thigh-slapping fun exchanges (especially the ones about erectile dysfunction drugs and how the drug industry can learn from the golfing industry).

So, the ChemSpider News site, while it will remain online for past references it will be discontinued and all new functionality comments will be posted to the ChemSpider Blog. The ChemSpider blog will become just that…all about ChemSpider. Once in a while I’ll put a list of what’s been discussed here on ChemConnector in case any of the readers want to click over for a browse of a particular post. This blog, ChemConnector, is going to be for me to chemunicate…