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Chemical Information

BULLETINSpring 2011 Volume 63 No. 1

Anaheim

Chemical Information Bulletin Vol. 63(1) Spring 2011

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Chemical Information Bulletin A Publication of the Division of Chemical Information of the ACS

Volume 63 No. 1 (Spring) 2011 (updated March 24, 2011)

David Martinsen, Editor American Chemical Society

[email protected]

In This Issue

Message from the Chair 3 Letter from the Editor 4 CINF Sponsorship 4 CINF at the ACS National Meeting

Technical Program Highlights 5 Committee Meetings and Social Events 7 CINF Symposia 8 Technical Program Listing (short) 9 Technical Program Listing with abstracts 14

Committee Report Communications & Publications 40 Awards – Calls for nominations 42 Interviews James L. Mullins 45 Michael Gordin 50 Book Reviews: Scientific Writing 57 Product Announcements 58 CINF Officers 66

Cover design by Mark Luchetti

ISSN: 0364‐1910

Chemical Information Bulletin, ©Copyright 2011 by the Division of Chemical Information of the American Chemical Society.

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Letter from the Editor I would simply like to thank all those who made contributions to this issue of the Chemical Information Bulletin. Svetla Baykoucheva provided two thought‐provoking interviews and Bob Buntrock contributed several book reviews. Our new division chair, Greg Banik, shared his thoughts on the year (welcome, Greg!). Also included are highlights from the technical program from our program chair, Rachelle Beinstock, as well as the technical program itself. Be sure to check out the product announcements from our sponsors, as well as the information about submissions for awards. Thanks to Mark Luchetti for the cover page design. Finally, I would also recognize the efforts of our webmaster, Danielle Dennie, who designed the templates for the e‐CIB and flowed all of the content seamlessly into the site (well, at least it looked seamless to me). Dave Martinsen Guest Editor

CINF Sponsors Spring 2011

March 2011

The American Chemical Society Division of Chemical Information (CINF) is very fortunate to receive generous financial support from our sponsors to maintain the high quality of the Division’s programming and to promote communication between members at social functions at the ACS Spring 2011 National Meeting in Anaheim, CA, and to support other divisional activities during the year, including scholarships to graduate students in Chemical Information.

The Division gratefully acknowledges contribution from the following sponsors:

Gold: FIZ CHEMIE Berlin

Silver: Bio‐Rad Laboratories InfoChem RSC Publishing

Bronze: Accelrys ACS Publications CambridgeSoft Thieme Publishers

Opportunities are available to sponsor Division of Chemical Information events, speakers, and material. Our sponsors are acknowledged on the CINF web site, in the Chemical Information Bulletin, on printed meeting materials, and at any events for which we use your contribution.

Please feel free to contact me if you would like more information about supporting CINF.

Graham Douglas Chair, Fundraising Committee Email: [email protected] Tel: 510‐407‐0769

The ACS CINF Division is a non‐profit tax‐exempt organization with taxpayer ID no. 52‐6054220.

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scientific research data by Dr. Sens, curated scientific data resources by Dr. C.R. Groom and Open Data by Peter Murray‐Rust. Leah Solla, Robert McFarland, Norah Xiao have organized "Data Archiving, E‐Science and Primary Data", which features presentations on Librarian 2.0 data management (Blanton‐Kent), PubChem (S. Swamidass), hosting a computing centric resource for chemistry data by Tony Williams and data curation profiles by Jeremy Garritano. Dr. Guenter Grethe has selected and organized review of our student award posters for the CINF Scholarship for Scientific Excellence (sponsored by Accelrys) which will be presented in a poster session on Sunday evening March 27th. We will also have some interesting presentations in our general papers session on Wednesday morning March 30th and a small CINF poster session as part of the Sci Mix session on late Monday evening. The number of papers presented is too numerous to mention each by title and author so I only hoped to give you an overview flavor of the rich variety of topics and material. The Spring 2011 Anaheim meeting is the first which I have organized as CINF program chairperson. I want to thank Dr. Rajarshi Guha, past program chair, for all his advice and assistance. With the capable assistance of all the symposium chairpersons, I think we have put together an interesting program which will cover the diverse interests of the CINF membership. Please come and experience first hand! Rachelle Bienstock Chair, Program Committee


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CINF Committee Meetings and Social Events Spring, 2011 ACS National Meeting, Anaheim, CA (March 27‐31)Saturday, March 26

7:30 AM – 9:00 AM: Long Range Planning and Breakfast Meeting, 201 A, Anaheim Convention Center

9:00 AM – 12:00 PM: Program Committee Meeting, 201 B, Anaheim Convention Center 9:00 AM – 10:30 AM: Membership Committee Meeting, 202 B, Anaheim Convention Center 11:00 AM – 12:00 PM: Finance Committee Meeting, 202 A, Anaheim Convention Center 9:00 AM – 12:00 PM: Communications & Publications Committee, 203 A, Anaheim Convention Center 10:00 AM – 11:00 AM: Fundraising Committee Meeting, 202 A, Anaheim Convention Center 10:30 AM – 12:00 PM: Careers Committee Meeting, 202 B, Anaheim Convention Center 9:00 AM – 12:00 PM: Education Committee Meeting, 203 B, Anaheim Convention Center 9:00 AM – 10:00 AM: Awards Committee Meeting, 202 A, Anaheim Convention Center 12:00 PM – 1:00 PM: CINF Functionary Luncheon, 201 A, Anaheim Convention Center 1:00 PM – 5:30 PM: Executive Committee Meeting, 201 B, Anaheim Convention Center

Sunday, March 27

12:00 PM – 2:00 PM: CINF‐CSA Trust Group Meeting, Orangewood 3, Clarion Hotel Anaheim Resort 6:30 PM – 8:30 PM: CINF Welcoming Reception & Scholarships for Scientific Excellence Posters

Ballroom A, Anaheim Convention Center Reception co‐sponsored by ACS Publications, Bio‐Rad Laboratories, CambridgeSoft, InfoChem & Thieme Chemistry Scholarships for Scientific Excellence sponsored by Accelrys

Monday, March 28

4:20 – 4:30 PM: CINF Open Meeting, Room 204 A, Anaheim Convention Center 4:30 – 5:30 PM: ACS Publications/CAS Open Meeting, Room 204 A, Anaheim Convention Center 5:30 – 8:00 PM: Harry’s Party, 2nd Floor Suite, Sheraton Park Hotel at the Anaheim Resort

Sponsored exclusively by FIZ CHEMIE Berlin * Use ACS Shuttle #2

Tuesday, March 29

12:00 PM – 1:30 PM: CINF Luncheon, Anaheim Marriott, Platinum Room 7 Sponsored exclusively by RSC Publishing

* Ticketed event 6:30 PM – 8:30 PM: CINF Reception, Room 204 B, Anaheim Convention Center

Reception hosted by the ACS Division of Chemical Information *Cash bar

Wednesday, March 30

12:00 PM – 5:00 PM: CINF‐CIC Collaborative Working Group, 204 A, Anaheim Convention Center


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CINF Symposia ACS Chemical Information Division (CINF)

Spring, 2011 ACS National Meeting

Anaheim, CA (March 27‐31) R. Bienstock, Program Chair

S M T W T Session title

A 50 Years of Computers in Organic Chemistry: Symposium in Honor of James B. Hendrickson ‐ Cosponsored by ORGN

P Integration of Combinatorial Chemistry with Cheminformatics: Current Trends and Future Directions in Drug Discovery and Material Science

P 50 Years of Computers in Organic Chemistry: Symposium in Honor of James B. Hendrickson ‐ Cosponsored by ORGN

E CINF Scholarship for Scientific Excellence Financially supported by Accelrys

A Natural Products and Drug Discovery: Chemiformatics and Computational Chemistry

A Open Data Open Data‐, Open Science‐, Open Knowledge‐ Financially supported by Chemical Structure Association Trust

P Natural Products and Drug Discovery: Cheminformatics and Computational Chemistry

P Data Archiving, E‐Science, and Primary Data

E Sci‐Mix

A Internet and Chemistry: Social Networking ‐ Cosponsored by YCC

P Internet and Chemistry: Social Networking ‐ Cosponsored by YCC

A Internet and Chemistry: Social Networking ‐ Cosponsored by YCC

A General Papers

P Internet and Chemistry: Social Networking ‐ Cosponsored by YCC

Legend: A = AM P = PM E = Evening See also: Complete Program


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Technical Program Listing ACS Chemical Information Division (CINF)


Anaheim, CA (March 27‐31) R. Bienstock, Program Chair

SUNDAY MORNING Section A Anaheim Convention Center, 213 C 50 Years of Computers in Organic Chemistry: Symposium in Honor of James B. Hendrickson ‐ Cosponsored by ORGN M. Walker, Organizer, Presiding

9:00 Introductory Remarks. 9:10 1 James Hendrickson: A life‐long quest for systematizing organic synthesis. G. Grethe 10:00 2 Reaction classification, an enduring success story. V. Eigner‐ Pitto, H. Kraut, H. Saller, H. Matuszczyk, P. Loew, G. Grethe 10:30 Intermission. 10:40 3 Back to the future of synthesis planning: How new technology and new resources revitalize the vision of computer aided synthesis design. J. Law, M. Mirzazadeh, A. P. Cook, O. Ravitz, P. A. Johnson, A. Simon

SUNDAY AFTERNOON Section B Anaheim Convention Center, 211 B Integration of Combinatorial Chemistry with Cheminformatics: Current Trends and Future Directions in Drug Discovery and Material Science J. Medina‐Franco, Organizer M. Haranczyk, Organizer, Presiding

1:00 Introductory Remarks. 1:05 4 Experimental design for high throughput materials development. J. N. Cawse 1:30 5 High‐throughput strategies for synthesis and characterization of metal‐ organic frameworks for CO2 capture. K.

Sumida 1:55 6 Combinatorial library design revisited: Finding new uses for old tools. D. K. Agrafiotis, V. S. Lobanov 2:20 7 How to screen 10^14 cores per second. P. S. Shenkin, K. P. Lorton 2:45 Intermission. 3:00 8 Synergies of combinatorial chemistry and fragment‐based drug design for efficient generation of focused virtual libraries. L. Meireles, G. Mustata, I. Bahar 3:25 9 Chemical library design: From diversity, similarity, and multicriterion optimization to a versatile cheminformatics content management system (CCMS). W. Zheng 3:50 10 Six years of collaborative drug discovery in the cloud. B. Bunin, S. Ekins, M. Hohman, K. Gregory, B. Prom, S. Ernst 4:15 11 Managing giant combinatorial chemistry spaces in silico. C. Detering, H. Claussen, M. Lilienthal, C. Lemmen

SUNDAY AFTERNOON Section A Anaheim Convention Center, 213 C 50 Years of Computers in Organic Chemistry: Symposium in Honor of James B. Hendrickson ‐ Cosponsored by ORGN M. Walker, Organizer, Presiding

1:30 12 Toward the ideal synthesis: The role of step economy and function oriented synthesis in first‐in‐class approaches to HIV eradication, overcoming cancer resistance and treating Alzheimer's disease. P. A. Wender 2:20 13 Aiming for the ideal synthesis. P. S.


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Baran 3:10 Final introduction. 3:25 14 Half a century of computers in chemistry. J. B. Hendrickson

SUNDAY EVENING

Section A Anaheim Convention Center, Ballroom A 6:30 PM – 8:30 PM CINF Scholarship for Scientific Excellence Financially supported by Accelrys G. Grethe, Organizer

6:30 ‐ 8:30

15 Exhaustive docking protocol with SAR‐based pose selection. F. Klepsch, G. F. Ecker 16 Comparison of weighted and unweighted consensus approaches in QSAR/QSPR. D. Zhuang, A. Lee, R. Fraczkiewicz, M. Waldman, B. Clark, W. Woltosz 17 When is chemical similarity significant? The statistical distribution of chemical similarity scores and its extreme values. P. Baldi, R. J. Nasr 18 Reaction prediction as ranking molecular orbital interactions. M. A. Kayala, C. A. Azencott, J. H. Chen, P. Baldi 19 Re‐examining the tubulin‐binding conformation of antitumor epothilones using QSAR and crystallographic refinement. S. A. Johnson, A. J. Smith, J. P. Snyder, K. N. Houk 20 Efficient core structure searches using various fingerprinting methodologies: Advantages, particularities and pitfalls. S. M. Furrer, D. J. Wild 21 DockingDB: A cyberinfrastructure for computer‐aided drug design based on ChemDB. P. M. Rigor

MONDAY MORNING Section A Anaheim Convention Center, 207 C Natural Products and Drug Discovery: Chemiformatics and Computational

Chemistry R. Bienstock, Organizer X. Wang, Organizer, Presiding

8:30 Introductory Remarks. 8:35 22 Protein Fold Topology: Will it aid drug discovery or is it the reason natural products have drug properties? R. J. Quinn, E. Kellenberger 9:05 23 Screening of herbs used in traditional Indonesian medicine for inhibitors of aldose reductase. D. Barlow, S. Naeem, P. Hylands 9:35 24 Common cold and flu: Computational strategies for the identification of antiviral leads from nature. J. M. Rollinger, J. Kirchmair, U. Grienke, D. Schuster, K. R. Liedl, M. Schmidtke 10:05 Intermission. 10:20 25 Chemoinformatic analysis of natural products: Towards the discovery of DNA methyltransferase inhibitors of natural origin. J. Medina‐Franco, F. López‐ Vallejo, R. Guha, A. Bender, D. Kuck, F. Lyko 10:50 26 Lessons from covalent inhibitor modeling. O. Eidam, S. Bonazzi, S. Guttinger, J. Wach, I. Zemp, U. Kutay, K. Gademann

MONDAY MORNING Section B Anaheim Convention Center, 202 A Open Data Open Data‐, Open Science‐, Open Knowledge‐ Financially supported by Chemical Structure Association Trust P. Rusch, Organizer I. Sens, Organizer, Presiding

9:00 Introductory Remarks. 9:10 27 Open Data and the Panton Principles. P. Murray‐Rust 9:35 28 Making priors a priority. M. D. Segall, A. Chadwick 10:00 Intermission. 10:10 29 Ensuring sustainability of a comprehensive and highly curated scientific data resource. I. J. Bruno, C. R. Groom


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10:35 30 Visual search in scientific research data. I. Sens, O. Koepler

MONDAY AFTERNOON Section A Anaheim Convention Center, 204 C Natural Products and Drug Discovery: Cheminformatics and Computational Chemistry X. Wang, Organizer R. Bienstock, Presiding

1:30 31 Specific targeting of the G‐quadruplex in the c‐Myc promoter with ellipticine. T. A. Brooks, V. Gokhale, R. Brown, L. H. Hurley 2:00 32 Exploring natural products for drug discovery by mining biomedical information resources. N. Baker, N. Rice, D. Fourches, E. Muratov, A. Tropsha 2:30 33 In silico strategies in natural product research to combat inflammation and lifestyle diseases: Identification of FXR‐inducing triterpenes from Ganoderma lucidum. U. Grienke, J. Mihály‐Bison, D. Schuster, D. Guo, B. R. Binder, G. Wolber, H. Stuppner, J. M. Rollinger 3:00 Intermission. 3:15 34 Discovery of natural product‐derived 5HT‐1A receptor binders by QSAR modeling of known inhibitors, virtual screening and experimental validation. X. S. Wang 3:45 35 Traditional medicine patents lead to enhanced drug discovery derived from natural products. J. Zabilski, R. Schenck

MONDAY AFTERNOON Section B Anaheim Convention Center, 204 A Data Archiving, E‐Science, and Primary Data R. McFarland, N. Xiao, Organizers L. Solla, Organizer, Presiding

1:30 Introductory Remarks. 1:40 36 Librarian2.0: Synthesizing data management and subject expertise. B. Blanton‐Kent, S. Lake, A. Sallans

2:05 37 Anatomy of a PubChem project. S. Swamidass, B. Calhoun, M. Browning 2:30 38 Evolution of the University of Minnesota Libraries' approach to e‐ scholarship. M. Lafferty, L. Johnston 2:55 Intermission. 3:05 39 Hosting a compound centric community resource for chemistry data. A. J. Williams, V. Tkachenko, R. Kidd 3:30 40 Library data services in the social sciences: Lessons for science? K. Peter 3:55 41 Using Data Curation Profiles (DCPs) as a means of raising data management awareness. J. R. Garritano 4:20 CINF Open Meeting 4:30 Open Meeting with the Joint Board‐Council Committees on Publications and Chemical Abstracts Service

MONDAY EVENING Section A Anaheim Convention Center, Hall B Sci‐Mix R. Bienstock, Organizer

8:00 ‐ 10:00 16. See previous listings.

42 Synthesis of 3‐halo‐2‐butanones. J. Porter 43 Visualizing molecule similarity. K. Boda

TUESDAY MORNING Section A Anaheim Convention Center, 204 A Internet and Chemistry: Social Networking ‐ Cosponsored by YCC H. Rzepa, Organizer S. Bachrach, Organizer, Presiding

8:25 Introductory Remarks. 8:30 44 Collaborative agile Internet projects: The Green Chain Reaction. P. Murray‐Rust, S. E. Adams, L. Hawizy, D. M. Jessop 9:10 45 Re‐imagining scientific communication for the 21st century: Is chemistry low hanging fruit or the worst‐case scenario? C. Neylon


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9:50 46 Quixote: An Internet project to build a distributed Open Knowledgebase for quantum chemistry. P. Murray‐Rust, J. Thomas, P. Echenique, J. Estrada, M. D. Hanwell, S. E. Adams, W. Phadungsukanan, L. Westerhoff 10:30 Intermission. 10:40 47 Catching the mobile wave. S. M. Muskal 11:20 48 Chemistry in your pocket: Shrinking cheminformatics applications for mobile devices. A. M. Clark

CINF LUNCHEON Anaheim Marriott, Platinum Room 7 12:00 PM – 1:30 PM (Ticketed Event)

TUESDAY AFTERNOON Section A Anaheim Convention Center, 204 A Internet and Chemistry: Social Networking ‐ Cosponsored by YCC H. Rzepa, Organizer S. Bachrach, Organizer, Presiding

1:30 49 chemicalize.org: Adding chemistry to Web pages and predicted data and links to structures. A. Allardyce, A. Stracz, D. Bonniot, F. Csizmadia 2:10 50 Using Campus Guides for leveraging Web 2.0 technologies and promoting the chemistry and life sciences information resources. S. Baykoucheva 2:50 Intermission. 3:00 51 How the web has weaved a web of interlinked chemistry data. A. J. Williams 3:40 52 What is the Internet doing to chemistry and our brains? S. Heller

WEDNESDAY MORNING Section A Anaheim Convention Center, 204 B Internet and Chemistry: Social Networking ‐ Cosponsored by YCC H. Rzepa, Organizer S. Bachrach, Organizer, Presiding

8:30 53 Bridging the gap: Publishing and consuming the scientific literature in a digital, device‐agnostic world. D. P. Martinsen 9:10 54 Open access in chemistry: Information wants to be free? J. Kuras, B. Vickery, D. Kahn 9:50 Intermission. 10:00 55 OpenTox: An open‐source web‐service platform for toxicity prediction. D. A. Gallagher, B. Hardy, S. Chawla 10:40 56 CAS Registry: Maintaining the gold standard for chemical substance information. R. Schenck, J. Zabilski 11:20 57 Evolution of the science journal and the chemical publication. H. S. Rzepa

WEDNESDAY MORNING Section B Anaheim Convention Center, 201C General Papers R. Bienstock, Organizer, Presiding

9:00 Introductory Remarks. 9:05 58 Collaborative QSAR analysis of Ames mutagenicity. E. Muratov, D. Fourches, A. Artemenko, V. Kuz'min, G. Zhao, A. Golbraikh, P. Polischuk, E. Varlamova, I. Baskin, V. Palyulin, N. Zefirov, L. Jiazhong, P. Gramatica, T. Martin, F. Hormozdiari, P. Dao, C. Sahinalp, A. Cherkasov, T. Oberg, R. Todeschini, V. Poroikov, A. Zaharov, A. Lagunin, D. Filimonov, A. Varnek, D. Horvath, G. Marcou, C. Muller, L. Xi, H. Liu, X. Yao, K. Hansen, T. Schroeter, K. Muller, I. Tetko, I. Sushko, S. Novotarskyi, N. Baker, J. Reed, J. Barnes, A. Tropsha 9:25 59 How (not) to build a toxicity model. A. C. Lee, R. Clark, M. Waldman, J. Chung, R. Fraczkiewicz, W. S. Woltosz 9:45 60 Metabolic site prediction using artificial neural network ensembles. M. Waldman, R. Fraczkiewicz, J. Zhang, R. D. Clark, W. S. Woltosz 10:05 61 Withdrawn. 10:25 Intermission. 10:35 62 Use and results of using an online


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chemistry laboratory package in a large general chemistry course. R. L. Nafshun 10:55 63 Reaction prediction as ranking molecular orbital interactions. M. A. Kayala, C. A. Azencott, J. H. Chen, P. Baldi

WEDNESDAY AFTERNOON Section A Anaheim Convention Center, 204 B Internet and Chemistry: Social Networking ‐ Cosponsored by YCC H. Rzepa, Organizer S. Bachrach, Organizer, Presiding

1:40 64 Automated semantic data embargo and publication by the CLARION project. S. E. Adams, N. Day, J. Downing, B. Brooks, P. Murray‐Rust 2:20 65 Chemical eCommerce. K. Gubernator 3:00 Intermission. 3:10 66 Waiting on the Chemical Internet. S. M. Bachrach 3:50 67 Rapid dissemination of chemical information for people and machines using Open Notebook Science. J. Bradley, A. S. Lang


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CINF Symposia with Abstracts ACS Chemical Information Division (CINF)


Anaheim, CA (March 27‐31) R. Bienstock, Program Chair CINF 1

James Hendrickson: A life‐long quest for systematizing organic synthesis

Guenter Grethe(1), [email protected], 352 Channing Way, Alameda CA 94502‐7409, United States . (1) Self employed, 352 CA 94502‐7409, United States

During his long academic tenure, James Hendrickson was interested in applying logic and systematic characterization of molecules and reactions to organic synthesis. Starting in the early 70's, his work gradually evolved from a mathematical presentation of the structural and functional features of molecules and their reactions to the development of systematic signatures for organic reactions. In this presentation we will discuss the individual steps along the way illustrated by examples. Some recent developments by other groups in the area of reaction classification will be mentioned

CINF 2

Reaction classification, an enduring success story

Valentina Eigner‐Pitto(1), [email protected], Landsberger Str. 408, Munich Bavaria 81241, Germany ; Hans Kraut(1); Heinz Saller(1); Heinz Matuszczyk(1); Peter Loew(1); Guenter Grethe(2). (1) InfoChem GmbH, Munich 81241, Germany (2) None, United States

Beginning in the late 1980s InfoChem started to develop a deep understanding of the storage and handling of chemical structure and reaction information. The first major

project was the development of an electronic version of the printed abstract series “ChemInform” published by FIZ CHEMIE Berlin. Then in 1989 InfoChem acquired an exclusive license to a reaction database (SPRESI) of (initially) 2.3 million records. Since the reaction database management systems (REACCS and ORAC) commercially available at that time could not handle more than 500,000 records, InfoChem was forced to conceive a concept for the selection of meaningful subsets of SPRESI. Based on a high quality reaction center detection module, InfoChem's sophisticated reaction type classification application, “Classify”, remains unique to this day. This concept allowed the generation of widely used reaction type databases such as ChemReact (400,000 reaction types) and ChemSynth (100,000 reaction types). Classify also enables reaction type searching, and clustering of reaction databases, and, in particular, it is the only way of linking different reaction databases. The world's major vendors of chemical information have adopted this technology to enhance the reaction retrieval capabilities of their products. More recent developments at InfoChem have resulted in a processing tool for detecting name reactions in any reaction database, and the retrosynthesis tool ICSYNTH, both of which are based on the company's earlier fundamental work. This talk will briefly present the background and technology of these software modules and their efficient use in the field of modern reaction planning.


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CINF 3

Back to the future of synthesis planning: How new technology and new resources revitalize the vision of computer aided synthesis design

Orr Ravitz(1), [email protected], 135 Queen[apos]s Plate Dr., Unit 520, Toronto Ontario M9W 6V1, Canada ; James Law(1); Mahdi Mirzazadeh(1); Anthony P Cook(2); Peter A Johnson(2); Aniko Simon(1). (1) SimBioSys Inc., Toronto Ontario M9W 6V1, Canada (2) School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom

Sophisticated systems like LHASA and SYNGEN were regarded in the late 1980's as a great promise to the field of organic synthesis. Their intent, as Hendrickson stated, was “not to replace art … but to show where real art lies”. Sparked by the introduction of retrosynthetic analysis, the newborn field of computer aided synthesis design proved that chemical perception and synthetic thinking can be formulated in an algorithmic fashion. However, the vision of routine use of such tools has not materialized, and research in that area came to a lull in the early 1990's. The major obstacle was the difficulty of generating high quality and up‐to‐date databases of synthetic transforms. We show how our retrosynthetic analysis system, ARChem, capitalizes on the advent of comprehensive reaction databases and the dramatic progress in computing capabilities to automatically generate expansive synthetic rule‐sets, which pave the way to representation and application of synthetic strategies.

CINF 4

Experimental design for high throughput materials development

James N Cawse(1), [email protected], 132 Kittredge Rd, Pittsfield MA 01201, United States . (1)

Cawse and Effect LLC, Pittsfield MA 01201, United States

High‐throughput methods of chemical experimentation present a challenge to experimental planning. Experiments run in arrays of dozens to hundreds require rethinking of the classic methods of Design of Experiments. This talk will review the adaptation of classical methods and improvisation of new methods for high throughput systems. These methods are becoming more important as laboratories for chemistry and materials science are being equipped with the robots and high‐speed analytical tools for the acceleration of research. In particular, the use of these methods for effective protection of a chemical patent will be discussed.

CINF 5

High‐throughput strategies for synthesis and characterization of metal‐organic frameworks for CO2 capture

Kenji Sumida(1)(2), [email protected], 214 Lewis Hall, Berkeley CA 94720, United States . (1) Department of Chemistry, University of California, Berkeley, Berkeley CA 94720‐1460, United States (2) Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720‐1460, United States

High‐throughput methodologies are a tremendously versatile platform for the discovery of next‐generation materials (metal‐organic frameworks) for CO2 capture. However, the considerable impact that the reaction conditions employed in the synthetic step can have on the material properties results in a large number of synthetic trials, which result in tremendous quantities of data from powder X‐ray diffraction and gas adsorption experiments. An ideal computational support system in this regard would allow rapid, automated identification of the highest performance materials, and


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provide feedback to the high‐throughput synthetic step, such that the preparation of a material may be more rigorously optimized, and new target materials that might show high CO2 capture performance can be identified. Here, we discuss our overall progress towards this goal, and present a number of examples in which the system has been employed to discover the optimal synthetic conditions for the preparation of new metal‐organic frameworks for CO2 capture.

CINF 6

Combinatorial library design revisited: Finding new uses for old tools

Dimitris K Agrafiotis(1), [email protected], Welsh & McKean Roads, Spring House PA 19477, United States ; Victor S Lobanov(1). (1) Informatics, Johnson & Johnson Pharmaceutical Research & Development, LLC, Spring House PA 19477, United States

In the 15 years since our first publication on diversity analysis and library design, the field of combinatorial chemistry has traversed the entire length of the hype curve, from the initial excitement, to the peak of inflated expectations, to the trough of disillusionment, and finally to the plateau of productivity. Along the way, many of the tools that were originally developed for analyzing massive virtual libraries were either forgotten or adapted to the realities of modern pharmaceutical research. While the need to mine massive combinatorial libraries is no longer there, the tools have found a new life in supporting and automating smaller parallel synthesis efforts in lead generation and lead optimization. In this talk, we review some of these earlier technologies and describe their adaptation and integration in today's discovery workflows.

CINF 7

How to screen 10^14 cores per second

Peter S Shenkin(1), [email protected], 120 W. 45th St. Suite 1700, New York NY 10036, United States ; K Patrick Lorton(1). (1) Schrodinger, New York NY 10036, United States

We describe Schrodinger's attachment‐based core‐hopping method and present results achieved using it. The method starts with a template compound in which core and side‐chains are identified. The core is replaced by new cores from a library while maintaining side‐chain positions as well as possible. No receptor is required, but if a docked pose is available, receptor interactions can be conserved. Several scores are computed. These include a synthesizability score as well as a score reflecting how well side‐chain positions are maintained. A combination of GPU processing, multithreading, and automatic linker addition lead to an overall screening rate in excess of 1.0e14 unique cores per second.

CINF 8

Synergies of combinatorial chemistry and fragment‐based drug design for efficient generation of focused virtual libraries

Lidio Meireles(1), [email protected], 3064 BST3, 3501 Fifth Ave, Pittsburgh PA 15260, United States ; Gabriela Mustata(1); Ivet Bahar(1). (1) Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh PA 15260, United States

While combinatorial chemistry used to emphasize rapid synthesis and screening of large libraries of compounds, the current trend is to synthesize much smaller focused compound libraries. In this talk, we present our recently developed computational strategy that combines combinatorial chemistry and fragment‐based drug design techniques, fragment linking and fragment


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growing, to generate focused virtual libraries more efficiently. Once combinatorial chemistry scaffolds are placed in the binding site, fragments can be grown from and/or linked to the scaffold side chains to maximize favorable interactions with the target protein. Different methods for placing the scaffold on the binding site will be discussed along with rules that are essential for effective filtering. One advantage offered by our strategy is that it can also be universally applied to design compounds that replicate onto combinatorial chemistry scaffolds the essential binding features of proteins, peptides and small molecules. The application of the methodology to designing inhibitors of c‐Myc‐Max protein interaction will be presented.

CINF 9

Chemical library design: From diversity, similarity, and multicriterion optimization to a versatile cheminformatics content management system (CCMS)

Weifan Zheng(1), [email protected], 1801 Fayetteville Street, BRITE Building, Durham North Carolina 27707, United States . (1) Pharmaceutical Sciences, North Carolina Central University, Durham North Carolina 27707, United States

Combinatorial chemistry and high throughput screening research often involve the generation, storage and analysis of large datasets. These data are often complex and heterogeneous in nature. To enable the most efficient design of chemical libraries and biological assays, various computational methods have been developed in the past 15 years. More recent research in chemical genomics and systems chemical biology require the integration of different data sources and computational tools. For example, target family‐ and pathway‐ based library design may require information about biological targets and pathways. These requirements call for an integrated system

that can organize data, models and computational tools in a flexible and extensible fashion. In this talk, I will first briefly review some concepts for library design, and then describe our effort to develop a flexible cheminformatics content management system (with tagging, sharing as well as user uploading of data and tools).

CINF 10

Six years of collaborative drug discovery in the cloud

Barry Bunin(1), [email protected], 1633 Bayshore Highway, Suite 342, Burlingame CA 94010, United States ; Sean Ekins(1); Moses Hohman(1); Kellan Gregory(1); Barry Prom(1); Sylvia Ernst(1). (1) Collaborative Drug Discovery (CDD, Inc.), Burlingame CA 94010, United States

Collaborative Drug Discovery hosts a widely used drug discovery data cloud platform with advanced collaborative capabilities for distributed researchers. The CDD Vault, Collaborate, and Public together host private, collaborative (selectively shared), and public data spanning the competitive, precompetitive, and neglected disease domains including publicly disclosed collaborations with GlaxoSmithKline, Pfizer, and the Bill & Melinda Gates Foundation, as well as with hundreds of academic and biotech startup companies. CDD provides a novel, collaborative approach for integration experimental and computational screening with distributed data collection, storage, visualization and analysis – balancing privacy‐security with encouraging collaborations, when desired. Experiences will be shared with researchers using the “CDD Vault” – a secure, private industrial‐strength database combining traditional drug discovery informatics (registration and SAR) with social networking capabilities. CDD Collaborate enables real‐time collaboration by securely


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exchanging selected confidential data. Traditional drug discovery capabilities include the ability to import/export to Excel™ and sdfiles, Boolean queries for potency, selectively, and therapeutic windows for small molecule enzyme, cell, and animal data, substructure and Tanimoto similarity search, physical chemical property search, as well as IC50 calculation/curve generation, heat‐maps, and Z/Z' statistics for archived data (protocols, molecules, plates, hyperlinked files). CDD Public has unique, constantly growing drug discovery SAR content.

CINF 11

Managing giant combinatorial chemistry spaces in silico

Carsten Detering(1), [email protected], An der Ziegelei 79, 53757 Sankt Augustin Germany, Germany ; Holger Claussen(1); Markus Lilienthal(1); Christian Lemmen(1). (1) BioSolveIT, Sankt Augustin NRW 53757, Germany

We will introduce a method which catches the two aforementioned two birds (chemcial complexity and chemical universe) with one stone: by cleverly searching a fragment space on the fly without the need to enumerate compounds, the computational overhead is kept to a minimum, and thus, search times are low (minutes for 1010 molecules). Secondly, if the fragment space is composed of the inhouse available chemistry, results obtained are much more likely to be synthesizable, as the chemical reaction protocol is automatically delivered together with the hits. We will show a few validation cases from the industry, and look at the properties of one publicly available fragment space which contains 12 billion molecules.

CINF 12

Toward the ideal synthesis: The role of step economy and function oriented synthesis in first‐in‐class approaches to HIV eradication, overcoming cancer resistance and treating Alzheimer's disease

Paul A Wender(1), [email protected], 333 Campus Drive, Mudd Building, Room 121, Stanford CA 94305‐5080, United States . (1) Department of Chemistry, Stanford University, Stanford CA 94305, United States

Jim Hendrickson has had a major impact on how we think about synthesis. He was also an inspiring influence of my early career. Evolving from that time are programs in our group directed at the eradication of HIV (Science 2008,649), overcoming resistant cancer (PNAS 2008 12128, the major cause of chemotherapy failure) and novel strategies for treating Alzheimer's disease (Neurobiology of Disease 2009, 332). A major aspect of these programs is the singular importance of step economy in synthesis and how that can be achieved by computational analysis, new reactions and function oriented synthesis (Accounts 2008 40). In this lecture we will show three case studies of how step economy provides a key to addressing major therapeutic challenges of our time.

CINF 13

Aiming for the ideal synthesis

Philip S Baran(1), [email protected], 10550 North Torrey Pines Road, La Jolla CA 92037, United States . (1) Department of Chemistry, Scripps Research Institute, La Jolla CA 92037, United States

Our laboratory is focused on the practical total synthesis of complex natural products such as alkaloids and terpenes by aiming to achieve the “ideal synthesis”. Hendrickson defined such a synthesis in 1975, stating: ”The ideal synthesis creates a complex molecule . . . . . in a sequence of only construction reactions


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involving no intermediary efunctionalizations, leading directly to the target, not only its skeleton but also its correctly placed functionality.” (JACS 1975, 97, 5784). In order to achieve this level of efficiency one must minimize superfluous refunctionalization steps such as protecting group and non‐strategic redox chemistry. Such considerations require exquisite control of chemoselectivity by the invention of chemistry and logical frameworks to aid in the planning of such routes. This invention‐oriented approach to total synthesis will be illustrated with several case studies from our laboratory.

CINF 14

Half a century of computers in chemistry

James B Hendrickson(1), [email protected], MS 015, 415 South Street, Waltham MA 02453, United States . (1) Department of Chemistry, Brandeis University, Waltham MA 02453, United States

My half‐century of chemistry and computers may be divided into three areas. The first was to calculate the lowest‐energy conformations of the 6‐10‐membered cycloalkane rings, and then their pseudorotation energies, to assist in synthesis planning. The second area was to define a process to seek the optimal plans for efficient synthesis design. We developed a process to find just the few shortest synthesis routes to any input target structure and this has resulted in the SynGen program. This effort led to the third area, the development of a general system to afford a unique, linear string to describe any organic reaction, defined by its input reactant and product structures, irrespective of mechanism or number of operational steps in the reaction. This has afforded a program to assign a unique “signature” for any given reaction and has the important feature of providing searchable indexing for any reaction database.

CINF 15

Exhaustive docking protocol with SAR‐based pose selection

Freya Klepsch(1), [email protected], Althanstrasse 14, Vienna Vienna 1090, Austria ; Gerhard F Ecker(1). (1) Department of Medicinal Chemistry, University of Vienna, Vienna 1090, Austria

The polyspecific nature of the transmembrane drug efflux pump P‐glycoprotein (P‐gp) represents a great impediment for standard docking protocols. Furthermore, a ~6000 Å3 large transmembrane binding cavity, consisting of several binding sites, the high flexibility of P‐gp and the lack of structural information render the correct ranking of docking poses a quite challenging task. Thus, we present a docking protocol that combines exhaustive conformational sampling of propafenone‐type P‐gp inhibitors with common scaffold clustering and SAR‐based pose selection. The resultant binding hypotheses are in agreement with experimental data, which strengthens the validity of this approach. Analogous protocols were performed with other membrane proteins, like the GABAA receptor and the serotonin transporter. We acknowledge financial support provided by the Austrian Science Fund, grant F03502.

CINF 16

Comparison of weighted and unweighted consensus approaches in QSAR/QSPR

Dechuan Zhuang(1), dechuan@simulations‐plus.com, 42505 10th Street West, Lancaster CA 93534, United States ; Adam Lee(1); Robert Fraczkiewicz(1); Marvin Waldman(1); Bob Clark(1); Walt Woltosz(1). (1) Life Science, Simulations Plus, Inc, Lancaster CA 93534, United States

Two flavors of making consensus categorical predictions in QSAR/QSPR, 'unweighted consensus' and the 'weighted consensus'


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approaches, were compared with several datasets using ADMET Predictor(TM). While the unweighted method gives equal weight to every member model, the weighted implicitly assigns different weights to the outcomes of its member models. To find out if there is any benefit of using one approach over the other, we constructed several datasets, which have different structural characteristics (balanced, imbalanced, diverse, non‐diverse, and etc.), and built predictive models from them. The performances of the two approaches on these datasets were compared head‐to‐head using paired t‐test. Our results show that the performances of the two approaches on the selected datasets are statistically equal, and thus in general there is no clear advantage of using one approach over the other. Possible reasons for the observation will be discussed.

CINF 17

When is chemical similarity significant? The statistical distribution of chemical similarity scores and its extreme values

Ramzi J. Nasr(1), [email protected], University of California, Irvine, Irvine CA 92697, United States ; Pierre Baldi(1). (1) Department of Computer Science, University of California, Irvine, Irvine CA 92697, United States

As repositories of chemical molecules continue to expand and become more open, it becomes increasingly important to develop tools to search them efficiently and assess the statistical significance of chemical similarity scores. Here, we develop a framework for modeling, predicting, and approximating the distributions of chemical similarity scores and their extreme values in large databases. From the distributions of the scores and their analytical forms, Z‐scores, E‐values, and p‐values are derived to assess the significance of similarity scores. In addition, the framework also allows one to predict the value of standard chemical retrieval metrics,

such as sensitivity and specificity at fixed thresholds, or receiver operating characteristic (ROC) curves at multiple thresholds, and to detect outliers in the form of atypical molecules. Numerous and diverse experiments that have been performed, in part with large sets of molecules from the ChemDB, show remarkable agreement between theory and empirical results.

CINF 18

Reaction prediction as ranking molecular orbital interactions

Matthew A Kayala(1), [email protected], 243 ICS 2, Irvine CA 92697, United States ; Chloe A Azencott(1); Jonathan H Chen(1); Pierre Baldi(1). (1) Department of Computer Science, University of California, Irvine, Irvine CA 92697, United States

Being able to predict the course of chemical reactions is essential to the practice of chemistry. While computational approaches to this problem have been extensively studied in the past, a fast, accurate, and scalable solution has yet to be described. Here, we propose a novel formulation of reaction prediction as a machine learning ranking problem: given a set of molecules and a description of conditions, learn a ranking over potential filled to unfilled molecular orbital (MO) interactions approximating the corresponding transition state energy ranking. Using an existing rule‐based expert system (ReactionExplorer), we derive restricted chemistry dataset consisting of 1300 full multi‐step reactions with 2200 distinct starting materials and intermediates. This yields 3600 predicted MO interactions and 14 million unpredicted MO interactions. A two‐stage machine learning scheme is used to learn the model. First, we train reactive site predictors using a combination of topological and real‐valued global features to filter out 61% and 44% of non‐predicted filled and unfilled MOs with a 0.0001% error rate.


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Then various ranking models are trained on the MO interactions using features engineered to approximate transition state entropy and enthalpy. Using cross‐validation, current best models recover a perfect‐ranking 61% of the time and recover a within‐4‐ranking 95% of the time.

CINF 19

Re‐examining the tubulin‐binding conformation of antitumor epothilones using QSAR and crystallographic refinement

Scott A Johnson(1), [email protected], 607 Charles E. Young Drive E., Los Angeles CA 90095, United States ; Adam JT Smith(1); James P Snyder(2); Kendall N Houk(1). (1) Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles CA 90095, United States (2) Department of Chemistry, Emory University, Atlanta GA 30322, United States

Several different bioactive conformations of epothilones, potent anti‐tumor compounds, have been reported in the literature. We proposed to provide additional support to one of these conformations using a QSAR‐based approach. By assuming a common pharmacophore for a set of epothilone analogs, we clustered conformations of these analogs using dihedral angles responsible for orienting functional groups with known SAR effects. We identified clusters common among the most active compounds, and developed simple QSAR models that relate the experimental IC50 values to the conformational strain energy. The resulting epothilone conformer that minimizes strain energy in the active epothilone analogs is different from previously proposed conformers. This conformation demonstrates good agreement when refined in the experimental electron crystallographic density for tubulin‐bound epothilone.

CINF 20

Efficient core structure searches using various fingerprinting methodologies: Advantages, particularities and pitfalls

Stefan M Furrer(1)(2), [email protected], 1199 Edison Drive, Cincinnati OH 45215, United States ; David J Wild(2). (1) Science & Technology, Givaudan Flavors Corp, Cincinnati OH 45216, United States (2) School of Informatics and Computing, Indiana University, Cincinnati OH 45216, United States

The complexity of medicinal chemistry patent applications as well as the number of compounds enumerated as examples was increasing spectacularly in recent years. Finding the structures of major interest using traditional methods is often a difficult task. Molecular fingerprinting methods are excellent tools to rapidly organize chemical information. Different fingerprinting methods however represent structural characteristics in different ways. Multiple fingerprinting methodologies were evaluated in their capacity to differentiate and isolate core compounds in chemical patents. It was found that the fingerprint designs as well as medicinal chemistry approaches have significant impact on the overall performance: different tools shed different "lights" over the molecular landscape. Modal fingerprints were investigated to focus on core compounds in patents, through a relative over‐expression of co‐occurring molecular features. Concrete examples will be given based on several major patent cases.

CINF 21

DockingDB: A cyberinfrastructure for computer‐aided drug design based on ChemDB

Paul M Rigor(1), [email protected], 248 ICS2 Bldg, Irvine CA 92697, United States . (1) School of Information and Computer Sciences,


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University of California in Irvine, Irvine CA 92697, United States

Although there are several open‐source and commercially available computational tools for virtual high‐throughput drug screening ‐‐ including DOCK, Autodock and Schroedinger's Maestro; there is still a lack of a more general, tool‐agnostic and scalable framework that is able to leverage the advantages offered by readily available docking and molecular dynamics programs in a high‐performance computing (HPC) environment. We have developed a cyber‐infrastructure built on top of an HPC pipeline and existing proteomics and chemical informatics tools ‐‐ such as ChemDB and SCRATCH ‐‐ to support an iterative computer‐aided drug design methodology. We have applied our approach to two biological problems and describe preliminary results. Moreover, growing extensions to the pipeline and related tools are discussed.

CINF 22

Protein Fold Topology: Will it aid drug discovery or is it the reason natural products have drug properties?

Ronald J Quinn(1), [email protected], Nathan Campus, Brisbane Queensland 4111, Australia ; Esther Kellenberger(2). (1) Eskitis Institute, Griffith University, Brisbane Queensland 4111, Australia (2) Université de Strasbourg, Illkirch F‐67400, France

Natural products are made by nature through interacting with biosynthetic enzymes. Natural products also exert their effect as drugs by interaction with proteins. We have explored the question does the recognition of the natural product by biosynthetic enzymes translate to recognition of the therapeutic target. Molecular modeling of flavonoid biosynthetic enzymes and protein kinases with a series of natural product kinase inhibitors led to the development of the concept of Protein Fold Topology (PFT). PFT

describes cavity recognition points unrelated to protein fold similarity. The topology or spatial properties are preserved even though there is deformation of the protein elements that participate in the protein‐ligand interactions. We observe helices or β‐sheets as equivalent in providing the invariant topology for protein‐ligand interaction and, as such, are seeking to find automated methods to interrogate these interactions.

CINF 23

Screening of herbs used in traditional Indonesian medicine for inhibitors of aldose reductase

Dave Barlow(1), [email protected], Franklin‐Wlikins Building, 150 Stamford Street, London London SE1 9NH, United Kingdom ; Sadaf Naeem(1); Peter Hylands(1). (1) Pharmacy, King[apos]s College London, London London SE1 9NH, United Kingdom

Virtual screening of phytochemical constituents of herbs used in traditional Indonesian medicine has been performed to search for novel leads active against the enzyme aldose reductase (AR). The screening was performed using the docking software, MolDock, and the activities (IC50s) of the docked compounds predicted using an artificial neural network (ANN) trained using the crystallographic data for AR complexes involving inhibitors of known potency. The ANN gave a mean accuracy of ~ 98% for the activities of those compounds involved in the known protein crystal structures. The trained ANN was used to predict the IC50s for all carboxyl containing compounds in the database of Indonesian herbal constituents, and the predicted IC50 values ranged from 17 nM to 118 mM. Selected hits were subsequently tested in vitro against human recombinant AR and while some of these proved to be about as active as predicted, others proved significantly less potent than predicted.


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CINF 24

Common cold and flu: Computational strategies for the identification of antiviral leads from nature

Judith M. Rollinger(1), [email protected], Innrain 52c, Innsbruck Tirol 6020, Austria ; Johannes Kirchmair(2); Ulrike Grienke(1); Daniela Schuster(1); Klaus R. Liedl(2); Michaela Schmidtke(3). (1) Institute of Pharmacy and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria (2) Institute of Theoretical Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria (3) Institute of Virology and Antiviral Therapy, Friedrich Schiller University, Jena 07745, Germany

The search for new drug leads against respiratory viruses remains an area of active investigations. In this regard natural products offer a tremendous potential as source for antivirals. In our lab several virtual screening campaigns on 3D natural product databases such as pharmacophore searches, similarity‐based approaches and docking have proven to be highly efficient for the target‐oriented identification of bioactive candidates. Integration of these heuristic approaches with empirical ones, like ethnopharmacology and in vitro extract screening, are helpful strategies for prioritizing compounds to be isolated from natural sources and pharmacologically tested. Here we demonstrate the application of different in silico techniques for the discovery of new anti‐rhinoviral and anti‐influenza virus natural compounds using well defined molecular targets, such as the hydrophobic pocket in the rhinoviral capsid and the influenza virus neuraminidase.

CINF 25

Chemoinformatic analysis of natural products: Towards the discovery of DNA methyltransferase inhibitors of natural origin

Jose Medina‐Franco(1), [email protected], 11350 SW Village Parkway, Port St. Lucie Florida 34987, United States ; Fabian López‐Vallejo(1); Rajarshi Guha(2); Andreas Bender(3); Dirk Kuck(4); Frank Lyko(4). (1) Torrey Pines Institute for Molecular Studies, Port St. Lucie Florida 34987, United States (2) NIH Chemical Genomics Center, Rockville Maryland 20850, United States (3) Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (4) Division of Epigenetics, Deutsches Krebsforschungszentrum, Heidelberg 69120, Germany

A comparative diversity analysis of natural products, drugs, the Molecular Libraries Small Molecule Repository (MLSMR), and combinatorial libraries is presented in this work. To this end, a multiple criteria strategy was employed including physicochemical properties, scaffolds and different fingerprints as molecular descriptors. The approach enabled a comprehensive analysis of property space coverage, the degree of overlap between collections, scaffold and structural diversity and overall structural novelty. Since several natural products contained in dietary products are implicated in the inhibition of DNA methyltransferases (DNMTs), which are emerging targets for the treatment of cancer, we conducted a docking‐based virtual screening of a natural product database with a homology model of the catalytic domain of DNMT1. Herein we discuss the results of the virtual screening that represents a first step towards the systematic screening of compounds with natural origin targeting DNMTs.


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CINF 26

Lessons from covalent inhibitor modeling

Oliv Eidam(1), [email protected], 1700 4th St, San Francisco CA, United States ; Simone Bonazzi(2); Stephan Guttinger(3); Jean‐Yves Wach(2); Ivo Zemp(3); Ulrike Kutay(3); Karl Gademann(2). (1) Department of Pharmaceutical Chemistry, UCSF, San Francisco CA, United States (2) Chemical Synthesis Laboratory, EPFL, Lausanne VD, Switzerland (3) Institut fur Biochemie, ETHZ, Zurich ZH, Switzerland

Leptomycin B (LMB) has antifungal, antibacterial and anti‐tumor activity and is an important “tool compound” in cell biology. It inhibits the export of certain proteins from the nucleus through specific alkylation of Cys528 of human CRM1. The recently published x‐ray structure of CRM1 motivated us to model LMB to rationalize the activity of recently discovered LMB analogues. A manual modeling approach combined with all‐atom energy minimizations was used. We found that modeling was largely guided by the structural environment, and steric and geometric restraints imposed both from the binding site and the ligand. Mechanistic considerations of covalent inhibitor binding highlight important residues in the binding site, and the internal energy of the ligand may play a crucial role in the binding mode of covalent inhibitors. Perhaps the most important lesson is that manual modeling can generate models useful for the design of future analogues.

CINF 27

Open Data and the Panton Principles

Peter Murray‐Rust(1), [email protected], Lensfield Road, Cambridge Cambridgeshire CB 2 1EW, United Kingdom . (1) Department of Chemistry, University of Cambridge, Cambridge Cambridgeshire CB 2 1EW, United Kingdom

Although an increasing amount of chemical data is becoming visible on the Internet it cannot be re‐used without explicit permission to avoid potentially breaking copyright. The Open Knowledge Foundation and Science Commons have collaborated on a definition of Open Data and produced a set of principles and practices (Panton Principles) to help authors and publishers assert that their published data is truly Open. An example of fully Open Data is shown in Crystaleye http://wwmm.ch.cam.ac.uk/crystaleye with over 200,000 crystallographic datasets from the literature. Several publishers are adopting Panton, and this presentation will show the advantages of doing so

CINF 28

Making priors a priority

Matthew D Segall(1), [email protected], CB25 9TL, Cambridge Cambridgeshire CB25 9TL, United Kingdom ; Andrew Chadwick(2). (1) Optibrium Ltd., Cambridge CB25 9TL, United Kingdom (2) Tessella plc., Burton upon Trent Staffs DE15 0YZ, United Kingdom

When we build a predictive model of a drug property we rigorously assess its predictive accuracy, but we are rarely able to address the most important question, “How useful will the model be in making a decision in a practical context?” To answer this requires an understanding of the prior probability distribution and hence prevalence of negative outcomes due to the property. We will illustrate the importance of the prior to assess the utility of a model to select or eliminate compounds for further investigation. A better understanding of the prior probabilities of adverse events due to key factors will improve our ability to make good decisions in drug discovery, finding higher quality molecules more efficiently. As the data necessary to estimate these priors does not include proprietary compound


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structures, this presents an opportunity for collaboration to improve the basis for good decision‐making for all.

CINF 29

Ensuring sustainability of a comprehensive and highly curated scientific data resource

Colin R Groom(1), [email protected], 12 Union Rd, Cambridge Cambridgshire CB2 1EZ, United Kingdom ; Ian J Bruno(1). (1) CCDC, Cambridge Cambridgshire CB2 1EZ, United Kingdom

The Cambridge Crystallographic Data Centre (CCDC) has been established as the primary repository for the experimentally determined 3D structures of organic and organometallic compounds for over 45 years. Individual data sets are available to the scientific community free of charge through CCDC's structure request service. Additionally structures are made available as part of the Cambridge Structure Database (CSD). Structures in the CSD are expertly curated by editorial staff so as to facilitate reliable and sophisticated retrieval, visualisation and analysis by software that the centre also develops. The CSD and associated software is made available on a subscription basis with significant discounts applied for academic institutions. The income generated from subscriptions has ensured until now the sustainability of a comprehensive and highly curated scientific resource. This presentation will discuss the implications that increasing throughput and scientific complexity have for the way CCDC must operate, opportunities for alternative distribution models that respond to evolving expectations of the scientific community, and the pitfalls we must avoid to ensure sustainability in the years ahead.

CINF 30

Visual search in scientific research data

Irina Sens(1), [email protected]‐hannover.de, Welfengarten 1B, Hannover Lower‐Saxony, Germany ; Oliver Koepler(1). (1) German National Library of Science and Technology, Hannover 30167, Germany

In recent discussions among research institutions and research funding agencies, scientific research data has been identified as of strategic interests. As a consequence there are ongoing efforts to establish an infrastructure to support storage, long‐term preservation, and accessing of scientific research data. Registration of datasets with DOI names makes research data citable and searchable. To date a number of operational Digital Library systems for scientific research data already exist. Datasets often comprise numeric data on continuous or discrete scales and are often associated with textual metadata including data description, author and origin information. While searching in textual metadata is commonly available a content‐based access to the research data is an open challenge. Thereby visualisation and visual analysis of numeric data is common when processing scientific research data. To close this gap in the information retrieval process we report on a concept and first implementations to support visual retrieval and exploration in a specific class of primary research data, namely, time‐oriented data. The concept discusses relevant challenges for a general approach to scientific primary data and we present first implementations on a real‐world dataset.

CINF 31

Specific targeting of the G‐quadruplex in the c‐Myc promoter with ellipticine

Laurence H. Hurley(1)(2)(3), [email protected], 1703 E. Helen St., Tucson Arizona 85721, United States ; Tracy A. Brooks(1)(2)(3); Robert Brown(1);


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Vijay Gokhale(1)(2)(3). (1) College of Pharmacy, University of Arizona, United States (2) Arizona Cancer Center, University of Arizona, United States (3) BIO5 Institute, University of Arizona, United States

Previous studies have shown that the G‐quadruplex in the c‐Myc promoter is the silencer element for transcriptional control. More recent studies have shown the involvement of NM23‐H2 and nucleolin in the activation and silencing of c‐Myc transcription. Using a computational overlay of c‐Myc G‐quadruplex‐binding compounds and virtual screening, we have identified ellipticine as a potential G‐quadruplex‐interactive compound. Then, by taking advantage of a Burkitt's lymphoma cell line in which only the non‐translocated allele is under the direct control of the promoter containing the G‐quadruplex, we were able to show that the c‐Myc‐lowering effect is directly due to interaction with the G‐quadruplex. In follow‐up studies using CADD we designed further ellipticine analogs. These studies provide the best available cellular evidence not only for the presence of G‐quadruplex in the promoter elements of oncogenes such as MYC but also that inhibition of specific transcription can be mediated by small molecules that bind to this promoter element.

CINF 32

Exploring natural products for drug discovery by mining biomedical information resources

Nancy Baker(1), [email protected], Beard Hall, South Columbia Street, CHAPEL HILL NORTH CAROLINA 27599, United States ; Denis Fourches(1), [email protected], Beard Hall, South Columbia Street, CHAPEL HILL NORTH CAROLINA 27599, United States ; Natalie Rice(1); Eugene Muratov(2); Alexander Tropsha(1). (1) Laboratory for Molecular Modeling, UNC Eshelman School of

Pharmacy, University of North Carolina at Chapel Hill, CHAPEL HILL NORTH CAROLINA 27599, United States (2) Laboratory of Theoretical Chemistry, Department of Molecular Structure, Bogatsky Physical‐Chemical Institute NAS of Ukraine, Odessa 65080, Ukraine

Parallel screening of Natural Products (NPs) is a typical approach for identifying drug candidates and their targets. However, biomolecular targets of NPs are often discovered serendipitously. We report on the use of Chemotext, a database of assertions extracted from biomedical literature that link chemicals, targets, and diseases [J Biomed Inform 2010, 43:510‐9] to rationalize the search for NP targets in the context of the Systems Chemical Biology paradigm [Nat Chem Biol 2007, 3:447‐50]. We have identified similar biochemical pathways that NPs are known to interact with in both plants and humans. Through this analysis, we can deduce novel compound‐target‐disease associations as well as novel molecular targets for NP‐derived compounds. Using Chemotext, we have collected and integrated cross‐species NP‐target associations. We present the case studies of Diabetes mellitus for predicting new compound‐target interactions and Tacrolimus‐Binding Proteins for detecting similar biochemical pathways in both plants and animals/humans.

CINF 33

In silico strategies in natural product research to combat inflammation and lifestyle diseases: Identification of FXR‐inducing triterpenes from Ganoderma lucidum

Judith M. Rollinger(1), [email protected], Innrain 52c, Innsbruck Tirol 6020, Austria ; Ulrike Grienke(1); Judit Mihály‐Bison(2); Daniela Schuster(1); De‐An Guo(3); Bernd R. Binder(2); Gerhard Wolber(1); Hermann Stuppner(1). (1)


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Institute of Pharmacy and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria (2) Center of Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna 1090, Austria (3) Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China

Farnesoid X receptor (FXR) is a ligand‐activated transcription factor. The available structural information and the importance of FXR to control endogenous pathways related to inflammation and lifestyle diseases, like metabolic syndrome, dyslipidemia, atherosclerosis and type 2 diabetes renders FXR an attractive target for computational approaches. Virtual screenings of our in‐house Chinese Herbal Medicine database with structure‐based pharmacophore models revealed mainly triterpenes of the famous TCM fungus Ganoderma lucidum Karst. as putative FXR ligands. Ganoderma fruit body extracts verified the predicted FXR‐inducing effect in a reporter gene assay which prompted us to determine its bioactive constituents. Five out of 25 secondary metabolites from G. lucidum, i.e. ergosterol peroxide, lucidumol A, ganoderic acid TR, ganodermanontriol, and ganoderiol F, dose‐dependently induced FXR in the low micromolar range. To rationalize the binding interactions, additional molecular docking studies were performed, which allowed establishing a first structure activity relationship of the investigated triterpenes.

CINF 34

Discovery of natural product‐derived 5HT‐1A receptor binders by QSAR modeling of known inhibitors, virtual screening and experimental validation

Xiang S. Wang(1), [email protected], Laboratory of Cheminfomatics and Drug Design, 2300 4th St. NW, Washington DC

20059, United States . (1) Department of Pharmaceutical Sciences, Howard University, Washington DC 20059, United States

The 5‐Hydroxytryptamine receptor subtype 1A (5‐HT1A) has been an attractive target to treat mood disorders such as anxiety and depression. In this study we have developed combinatorial Quantitative Structure‐Activity Relationship (QSAR) models for 105 5‐HT1A binders and 61 non‐binders retrieved from the Psychactive Drug Screening Program (PDSP) Ki database. Three advanced methods, k‐Nearest Neighbor (kNN), Random Forest (RF) and Support Vector Machine (SVM), were employed for model building. The robust QSAR models of 5‐HT1A binders were then used to mine major natural product libraries such as the TimTec Natural Product Library (NPL) and Natural Derivatives Library (NDL). Multiple potential hits were identified and are currently examined by the PDSP for experimental validation. The success ratios, chemical diversities and structural novelties of the natural product libraries for the purpose of virtual screening were further explored in comparison with other types of screening libraries, i.e. drug‐like libraries, targeted libraries and diversity libraries.

CINF 35

Traditional medicine patents lead to enhanced drug discovery derived from natural products

John Zabilski(1), [email protected], PO Box 3012, Columbus OH 43125, United States ; Roger Schenck(1), [email protected], PO Box 3012, Columbus OH 43202, United States . (1) Content Planning, CAS, Columbus OH 43202, United States

Since ancient times natural products have provided relief from numerous aliments. Hippocrates, the father of modern medicine, noted that powder derived from the bark of the willow tree helped heal pain and headaches. In the 1800's, chemists isolated


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the beneficial substance as salicylic acid and refined it by buffering sodium salicylate with acetyl chloride to create acetylsalicylic acid or aspirin. In more recent years, Traditional Medicine patents have increasingly delved into rich vein of natural products for potential drug discovery. The CAS databases have mined this wealth by adding more than 50,000 new traditional patent records from several countries. This presentation will illustrate the vast content available and methods to easily explore it by using SciFinder or STN.

CINF 36

Librarian2.0: Synthesizing data management and subject expertise

Beth Blanton‐Kent(1), [email protected], P.O. Box 400124, Charlottesville VA 22904, United States ; Sherry Lake(1); Andrew Sallans(1). (1) University of Virginia Library, Charlottesville VA 22903, United States

The University of Virginia Library is working to support new data management requirements in science and engineering by developing a model that first draws upon close collaboration between data experts and subject librarians, and culminates in policy and infrastructure recommendations to the University's Office of the Vice President for Research (VPR) and the Office of the Vice President/Chief Information Officer (VP/CIO). This model begins with a data interview to assess the researcher's data management practices and needs and to establish a baseline awareness of current practice. After collecting this information, the results are furnished to the institutional repository team and NSF Data Management Plan working group to inform their processes. In aggregate form, this information is provided to the VPR and VP/CIO as policy and infrastructure recommendations. Ultimately, the entire process cycles back to the researcher. This presentation will offer a case study following

a chemist/chemical engineer through this process.

CINF 37

Anatomy of a PubChem project

S. Joshua Swamidass(1), [email protected], 606 S. Euclid, Box 8118, St Louis MO 63110, United States ; Bradley Calhoun(1); Michael Browning(1). (1) Department of Pathology and Immunology, Washington University in St Louis, St Louis MO 63110, United States

More raw data from high‐throughput screens is made available to the public every day, often through repositories like PubChem. This data, however, is often unorganized and incompletely annotated. Of particular interest, often several screens are components of a larger project. Each screen is a step in the project's workflow, its anatomy. Knowledge of the project's workflow includes non‐obvious but valuable information. For instance, the scaffolds the project team chose to pursue and how exactly compounds were chosen for follow testing. Although, these details are not well annotated in PubChem projects, it is possible to infer them from the raw screening data using a collection of statistical techniques. Moreover, inferred workflows can be used to automatically discover additional active molecules, inform useful views of screening data, and identify methodological errors.

CINF 38

Evolution of the University of Minnesota Libraries' approach to e‐scholarship

Meghan Lafferty(1), [email protected], 108 Walter Library, 117 Pleasant St SE, Minneapolis MN 55455, United States ; Lisa Johnston(1). (1) Science and Engineering Library, University of Minnesota, Minneapolis MN 55455, United States

Libraries have struggled with how best to respond to the challenges of e‐science since


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the middle of the last decade. The University of Minnesota Libraries' approach to e‐science and other cyberinfrastructure issues has changed multiple times since our initial response in 2006; it has primarily taken the form of groups rather than a dedicated position. We have more recently expanded our focus beyond e‐science to e‐scholarship in order to include areas such as the digital humanities. The talk will address the evolution of group structures and their primary emphases over the past 5 years, the rationales for different changes, and potential future directions.

CINF 39

Hosting a compound centric community resource for chemistry data

Antony J Williams(1), [email protected], 904 Tamaras Circle, Wake Forest NC 27587, United States ; Valery Tkachenko(1); Richard Kidd(2). (1) ChemSpider, Royal Society of Chemistry, Wake Forest NC 27587, United States (2) Informatics, Royal Society of Chemistry, Cambridge, United Kingdom

Laboratories around the world continue to generate immense amounts of data that are non‐proprietary and of value to the community. If available these data could dramatically reduce costs by minimizing rework and ultimately facilitating faster research. High quality reference data collections of chemical compound dictionaries, properties and spectra have been generated over many decades. With the advent of social networking tools and platforms such as Wikipedia, the community has an opportunity to contribute. The ChemSpider platform hosted by the Royal Society of Chemistry is a compound centric database with associated data. Already populated with almost 25 million unique compounds the community can deposit and host their own data, and curate and annotate existing data including those generated in

Open Notebook Science Efforts. This presentation will provide an overview of progress to date and outline the vision of this community platform for chemistry and ensuring the longevity of chemistry reference data.

CINF 40

Library data services in the social sciences: Lessons for science?

Katharin Peter(1), [email protected], VKC Library, B40a USC, Los Angeles CA 90089, United States . (1) University of Southern California Libraries, University of Southern California, Los Angeles CA 90089, United States

Social science data have a rich history within universities: aggregate statistical publications, such as Statistical Abstract of the United States, and even more detailed U.S. decennial census results, have long held a place within academic depository library collections. Following the development of Machine Readable Data Files, social science data archives were established within several universities across the United States—notably, the Inter‐university Consortium for Political and Social Research and Roper Center for Public Opinion Research. Although differences between social science and science data are not insignificant (for example, average file size), as data librarians we face the similar obstacles to: outreach, access, archiving and management and, in general, effectively creating a place within libraries for data and data services. This presentation will outline current library services and service models for social science data in hopes of launching a dialog and skill‐share between social science and sciences data professionals.

CINF 41

Using Data Curation Profiles (DCPs) as a means of raising data management awareness


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Jeremy R Garritano(1), [email protected], 504 West State St., West Lafayette IN 47907, United States . (1) Purdue University, West Lafayette IN 47907, United States

While one can discuss data management plans in a general sense, there is no single solution for managing the diverse data generated by various disciplines and projects. Therefore one possible solution is to determine best practices for individual data management plans guided by a more general Data Curation Profile (DCP). The DCPs were created at Purdue University and the University of Illinois Urbana‐Champaign through a grant from the Institute of Museum and Library Services. Using a DCP, librarians and/or researchers explore various data management issues. Once a profile has been completed, not only will the librarian have a richer understanding of the kind and quantity of data that might have to be curated and archived, but the researcher will have a better understanding of their data preferences related to sharing and intellectual property, regardless of where the data ultimately resides. Current applications of the DCP at Purdue will be discussed.

CINF 42

Synthesis of 3‐halo‐2‐butanones

Joseph Porter(1), [email protected], 300 North Broadway, Lexington KY 40508, United States . (1) Transylvania University, United States

This study is attempting to find out the effect of adding a halide group to a ketone. The main molecules I worked with were 3‐halo‐2‐butanones. I used ether as a solvent and performed Grignard reactions under nitrogen adding ethynyl Grignards as the nucleophiles. I was measuring diastereomeric ratios using GC‐MS, H1 and C13 NMR, and GC. Unexpectedly, results showed that ratios were similar to those found using LiAlH4 as the nucleophile. Future experiments will be

working with larger nucleophiles as well as using larger ketones.

CINF 43

Visualizing molecule similarity

Krisztina Boda(1), [email protected], 9 Bisbee Court, Santa Fe New Mexico 87508, United States . (1) OpenEye Scientific Software, Santa Fe New Mexico 87508, United States

Similarity searching based on fingerprint similarity is one of the most common approach for virtual screening. The main advantages of the method that it provides a rapid calculation of similarity scores to identify molecules that are similar to the reference structure. However, most fingerprint methods does not provide any insight into molecule similarity beyond a single numerical score. The poster will represent a method where molecular graphs are highlighted using a color gradient scheme that emphasizes shared fragments encoded into fingerprints. This representation not only makes molecular similarity immediately apparent but also reveals information about the underlying fingerprint method. The method is utilized to analyze the hit‐lists using different fingerprint methods on datasets of previously published benchmarks. The 2D graphics are generated using OpenEye's Ogham package that provides a framework to construct molecular diagrams. The poster will also represent various Ogham functionalities that allow the customization of molecule depiction.

CINF 44

Collaborative agile Internet projects: The Green Chain Reaction

Peter Murray‐Rust(1), [email protected], Lensfield Road, Cambridge Cambridgeshire, United Kingdom ; Samuel E Adams(1); Lezan Hawizy(1); David M Jessop(1). (1) Department of Chemistry, University of Cambridge,


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Cambridge Cambridgeshire CB 2 1EW, United Kingdom

An Open Science project was designed, implemented and completed within a month to investigate whether chemical reactions were using "greener" solvents than formerly. 10 volunteers wrote or implemented code to extract recipes from European patents. The recipes were analysed by OSCAR and chemical Natural Language processing using medium‐depth parsing to extract solvents, with high precision. The volunteers crawled the patent website, analysed over 100,000 recipes and posted the results to a communal, Open server, using the Lensfield "make/build" philosophy. The solvent information was then aggregated and presented for the years 2000 to 2010. There is no obvious trend showing that "green" solvents are becoming commoner.

CINF 45

Re‐imagining scientific communication for the 21st century: Is chemistry low hanging fruit or the worst‐case scenario?

Cameron Neylon(1), [email protected], Rutherford Appleton Laboratory, HSIC, Didcot NON‐US OX11 0QX, United Kingdom . (1) ISIS Neutron Source, Science and Technology Facilities Council, Didcot NON‐US OX11 0QX, United Kingdom

We are told that “the web changes everything” but scientific communication still owes more to the 17th century than to the 20th. The central problem with current practice is the view of “the paper” as a monolithic object, and the only form of communication that is rewarded. We need to both technically enable the publication of many different research objects and to create tools to aggregate these together into large narrative works that retain the structure and meaning of internal links. Along with this we need both technical and social infrastructure to help us filter and discover this large range

of items. I will argue that chemistry, and in particular synthetic organic chemistry, is a special case with its own particular difficulties, but that the inherent structure and regularity of synthetic research makes it a good target for testing and demonstrating new approaches to scholarly communication.

CINF 46

Quixote: An Internet project to build a distributed Open Knowledgebase for quantum chemistry

Jens Thomas(1), [email protected], Daresbury Laboratory, Daresbury Science and Innovation Campus, Warrington Cheshire WA4 4AD, United Kingdom ; Peter Murray‐Rust(2); Pablo Echenique(3); Jorge Estrada(3); Marcus D Hanwell(4); Samuel E Adams(2); Weerapong Phadungsukanan(5); Lance Westerhoff(6). (1) Computational Science and Engineering Department, Science and Technology Facilities Council, Daresbury Laboratory, Daresbury Cheshire WA4 4AD, United Kingdom (2) Department of Chemistry, University of Cambridge, Cambridge Cambridgeshire CB 2 1EW, United Kingdom (3) Instituto de Química Física [quot]Rocasolano[quot], CSIC, Madrid E‐28006 Madrid, Spain (4) Department of Scientific Visualization, Kitware, Inc, Clifton Park NY NY 12065, United Kingdom (5) Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge Cambridgeshire CB2 3RA, United Kingdom (6) QuantumBio Inc., State College PA PA 16803‐6602, United States

Quixote is a distributed semantic knowledgebase for quantum chemistry deliberately prototyped within a month by distributed volunteers. It uses a wide range of existing Open Source tools such as from the Blue Obelisk collection and uses them to translate conventional QC files (log, punch, archive, input) into semantic form. The semantics are controlled by per‐program


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dictionaries which are created by program experts. The process is controlled by and rests heavily on modern Internet approaches such as Etherpad, Skype, Wiki, REST, HTTP, RDF and SPARQL. Parsing is through ANTLR and recursive descent. Semantics are provided by namespaced dictionaries, elements and attributes allowing lossless transmission of information. The system is completely Open/free and allows anyone to clone and run a node, on a peer‐to‐peer system with as much or little security as desired.

CINF 47

Catching the mobile wave

Steven M Muskal(1), smuskal@eidogen‐sertanty.com, 3460 Marron Road, Oceanside CA 92056, United States . (1) Eidogen‐Sertanty, Oceanside CA 92056, United States

With the explosive growth of mobile computing environments, including the iPhone, Android‐based devices, the iPad, and its fast‐followers, it has become important for scientific software companies to enable technology and content access on these ubiquitous devices. Coupled with cloud computing environments (e.g. Amazon's EC2 and RDS environments), these platforms represent the new frontier for scientific computing. We will describe both technical and business challenges and lessons learned as we developed our mobile apps ‐ iKinase, iKinasePro, iProtein, and MobileReagents.

CINF 48

Chemistry in your pocket: Shrinking cheminformatics applications for mobile devices

Alex M Clark(1), [email protected], 1900 St. Jacques West #302, Montreal Quebec H3J2S1, Canada . (1) Molecular Materials Informatics, Montreal Quebec H3J2S1, Canada

Internet resources are now a routine part of the workflow of a research chemist, and in

recent years many of these services have been made accessible from ultra‐portable devices such as smartphones and tablet computers. Efforts have been hampered by the need to draw chemical structures to access certain functionality, e.g. searching databases by structure. To a large extent mobile devices have been limited to use for content consumption. Implementing a chemical structure sketching interface on a tiny device is difficult, because the traditional paradigm requires an accurate pointing device, such as a mouse. A finger on a touchscreen is simply too clumsy for standard structure drawing techniques, and many devices lack a pointing device entirely. This presentation will describe a new approach to drawing 2D chemical structures, which reevaluates the traditional drawing techniques in order to make them work well with input‐constrained devices. This is accomplished by using a high degree of automation and inference, which is provided by newly developed algorithms. The end result is a mobile application which can be used to create publication quality 2D sketches with a small number of steps, which is convenient to use on a variety of current smartphones and tablets, including BlackBerry, iPhone and iPad devices. Also discussed will be some of the internet‐based applications which are possible now that a viable structure editor is available. With this hurdle removed, a large number of desktop‐based cheminformatics applications can be migrated to smaller devices by splitting the interface between a mobile client and web‐based services. Mobile devices can now be used for creating, managing, viewing and sharing chemical information.

CINF 49

chemicalize.org: Adding chemistry to Web pages and predicted data and links to structures


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Alex Allardyce(1), [email protected], Maramaros Koz 3/a, Budapest Pest, Hungary ; Andras Stracz(1); Daniel Bonniot(1); Ferenc Csizmadia(1). (1) ChemAxon, Budapest H1037, Hungary

chemicalize.org is a new free online service developed by ChemAxon which adds chemistry to Web pages as well as data and Web pages to structures. The primary use is to parse chemical names from Web page text and serve an annotated Web page version which includes structure images hyper‐linked from the chemical name source. By storing structures and Web page URL's we can search the database to find those Web pages containing any given structure query. For each structure users can also generate structure based prediction results within a user customizable report, predictions include logP, pKa, logD etc. Current developments center around user profiles, 'tracking' structures in newly chemicalized pages and presenting chemicalize.org user activity to give a snapshot of current Web pages and structures that are interesting chemists online. This presentation will outline the aims of the development, describe the service, current developments and overview use and user feedback.

CINF 50

Using Campus Guides for leveraging Web 2.0 technologies and promoting the chemistry and life sciences information resources

Svetla Baykoucheva(1), [email protected], White Memorial Chemistry Library, College Park MD 20742, United States . (1) White Memorial Chemistry Library, University of Maryland, College Park MD 20742, United States

The introduction of Campus Guides and a “lighter” version of this program, Lib Guides, in the last few years has created many exciting opportunities for science librarians to promote the chemistry and life sciences

information resources in a new way using multimedia and social networking tools. The flexibility and the wide range of solutions these programs provide have tempted librarians to use them in many innovative ways, which has not been possible to do in static web pages controlled by rigid rules and other external factors. This presentation will show how users have responded to the new dynamic information environment created with Campus Guides and what the statistical data show about their preferences toward particular information resources in chemistry and the life sciences.

CINF 51

How the web has weaved a web of interlinked chemistry data

Antony J Williams(1), [email protected], 904 Tamaras Circle, Wake Forest NC 27587, United States . (1) ChemSpider, Royal Society of Chemistry, Wake Forest NC 27587, United States

The internet has provided access to unprecedented quantities of data. In the domain of chemistry specifically over the past decade the web has become populated with tens of millions of chemical structures and related properties of assays together with tens of thousands of spectra and syntheses. The data have, to a large extent, remained disparate and disconnected. In recent years with the wave of Web 2.0 participation, any chemist can contribute to both the sharing and validation of chemistry‐related data whether it be via Wikipedia, the online encyclopedia, or one of the multiple public compound databases. This presentation will offer a perspective of what is available today, our experiences of building a public compound database to link together the internet, and a suggested path forward for enabling even greater integration and connectivity for chemistry data for the


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masses to both use and participate in developing.

CINF 52

What is the Internet doing to chemistry and our brains?

Stephen Heller(1), [email protected], 100 Bureau Drive, Bldg 221, Gaithersburg Maryland 20899, United States . (1) NIST, Gaithersburg Maryland 20899, United States

The Internet, like any technology, has good, bad, and ugly sides to it. This lecture will attempt to talk about these aspects with examples in chemistry that should both enlighen and disturb.

CINF 53

Bridging the gap: Publishing and consuming the scientific literature in a digital, device‐agnostic world

David P Martinsen(1), [email protected], 1155 16th ST NW, Washington DC 20036, United States . (1) American Chemical Society, Washington DC 20036, United States

Scientific publishing has seen a steady transition from the primarily paper‐based model of the pre‐2000 era to the digital world of the late 1990s and now the first decade of the 21st century. While usage analysis, as well as end‐user studies, indicate that paper, or at least PDF files printed out on paper, are still the preferred way for most scientists to interact with the scholarly literature, there is a growing percentage of scientists who are asking for more. New data formats, new devices, and new applications present a challenge for publishers as well as authors and readers. Publishers try to keep up with the demands of authors and readers who want to push the technology, while at the same time addressing the more modest concerns of the majority of scientists who just want to get the article text and not be bothered with bells and whistles. While some call for a revolution in publishing, the reality is

a much slower evolution. Publishers, authors, editors, reviewers, and readers all make inputs into the ecosystem, and each responds, sometimes in unexpected ways, to the changes that are made. As the journal of the future and the article of the future, emerge from the old models, it is useful to consider the impact of those changes.

CINF 54

Open access in chemistry: Information wants to be free?

Jan Kuras(1), [email protected], 236 Gray[apos]s Inn Road, London WC1X 8HB, United Kingdom ; Bryan Vickery(1); Deborah Kahn(1). (1) Chemistry Central, London, United Kingdom

The open access (OA) publishing movement was motivated by a desire to increase visibility and dissemination of scientific information. Electronic publishing and the advent of the Internet helped establish and accelerate the growth of OA in the early 2000s. Acceptance and uptake was significant amongst e.g. the high‐energy physics and biomedical research communities as demonstrated by the success of initiatives such as ArXiv, BioMed Central, and the Public Library of Science. In chemistry, the growth of OA has been more conservative. This presentation will review the development of OA in chemistry, examine the current situation with reference to recent studies, and look forward to future directions in particular with the emergence of other open data initiatives and Web technologies.

CINF 55

OpenTox: An open‐source web‐service platform for toxicity prediction

David A Gallagher(1), [email protected], 13690 SW Otter Lane, Beaverton Oregon, United States ; Barry Hardy(2); Sunil Chawla(3). (1) CAChe Research


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LLC, Beaverton Oregon, United States (2) Douglas Connect, Zeiningen, Switzerland (3) Seascape Learning LLC, Cuppertino California, United States

The new European Union (EU) REACH chemical legislation will require 3.9 million additional test animals, if no alternative methods for toxicity prediction are accepted. However, the number of test animals could be significantly reduced by utilizing existing experimental data in conjunction with (Quantitative) Structure Activity Relationship ((Q)SAR) models. To address the challenge, the European Commission has funded the OpenTox (www.OpenTox.org) project to develop an open source web‐service‐based framework, that provides unified access to experimental toxicity data, in Silico models (including (Q)SAR), and validation/reporting procedures. Now, in the final year of the initial three‐year project, the current state of architecture, Open API, algorithms, ontologies, and approach to web services will be presented. Our experiences on current collaborative approaches aiming to combine OpenTox with other systems such as CERF, Bioclipse, CDK, and SYNERGY to create “super‐interoperable K‐infrastructure” will be discussed both in terms of conceptual promise and implementation reality.

CINF 56

CAS Registry: Maintaining the gold standard for chemical substance information

Roger Schenck(1), [email protected], 2540 Olentangy River Road, Columbus OHIO 43202‐1505, United States ; John Zabilski(1). (1) Department of Content Planning, Chemical Abstracts Service, Columbus OHIO 43202‐1505, United States

CAS has traditionally built its databases from the journal and patent literature. With the advent of the Internet, CAS now has another major source of chemical substance information. This presentation will discuss

these internet resources and how CAS evaluates them for inclusion in CAS REGISTRY, while maintaining its quality standards. Since 1965, the scientific experts at CAS have identified more than 56 million organic and inorganic substances. This presentation will examine the sources of this growth and illustrate what CAS is doing to keep pace with this explosion in small molecule chemistry.

CINF 57

Evolution of the science journal and the chemical publication

Henry S Rzepa(1), [email protected], Exhibition Road Campus, London London SW7 2AY, United Kingdom . (1) Department of Chemistry, Imperial college London, London Sw7 2AY, United Kingdom

The concept of a modern scientific journal becomes 346 old in 2011 (DOI: 10.1098/rstl.1665.0001), although only since 1994 has the journal article been embedded in the Internet and Web era (DOI: 10.1039/C39940001907). Although the structure of the article itself morphed little during the first part of the Internet age, there are now signs that many aspects of its creation and dissemination are starting to evolve more rapidly. Here, several potential future enhancements are reviewed, including the role of the scientific blog in augmenting the effectiveness of the peer‐review processes, the role of data‐integrity within the article, integration of Web‐enhanced and other data‐rich and functional objects, the role of open digital repositories, article semantification, and delivery and re‐functionalisation of the re‐invented article via new generations of mobile personal devices.

CINF 58

Collaborative QSAR analysis of Ames mutagenicity

Eugene Muratov(1)(2), [email protected], Beard Hall, CB7568, Chapel Hill NC 27599,


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United States ; Denis Fourches(1); Anatoly Artemenko(2); Victor Kuz[apos]min(2); Guiyu Zhao(1); Alexander Golbraikh(1); Pavel Polischuk(2); Ekaterina Varlamova(2); Igor Baskin(3); Vladimir Palyulin(3); Nikolai Zefirov(3); Li Jiazhong(4); Paola Gramatica(4); Todd Martin(5); Farhad Hormozdiari(6); Phuong Dao(6); Cenk Sahinalp(6); Artem Cherkasov(7); Tomas Oberg(8); Roberto Todeschini(9); Vladimir Poroikov(10); Alexey Zaharov(10); Alexey Lagunin(10); Dmitriy Filimonov(10); Alexandre Varnek(11); Dragos Horvath(11); Gilles Marcou(11); Cristophe Muller(11); Lili Xi(12); Huanxiang Liu(12); Xiaojun Yao(12); Katja Hansen(13); Timon Schroeter(13); Klaus‐Robert Muller(13); Igor[apos] Tetko(14); Iurii Sushko(14); Sergii Novotarskyi(14); Nancy Baker(1); Jane Reed(15); Julia Barnes(15); Alexander Tropsha(1). (1) University of North Carolina, Chapel Hill NC, United States (2) A.V. Bogatsky Physical‐Chemical Institute NAS of Ukraine, Chapel Hill NC, United States (3) Moscow State University, Moscow, Russian Federation (4) University of Insubria, Varese, Italy (5) US Environmental Protection Agency, Cincinnati OH, United States (6) Simon Fraser University, Burnaby, Canada (7) University of British Columbia, Vancouver, Canada (8) University of Kalmar, Kalmar, Sweden (9) University of Milano‐Bicocca, Milan, Italy (10) Institute of Biomedical Chemistry RAS, Moscow, Russian Federation (11) University of Strasbourg, Strasbourg, France (12) Lanzhou University, Lanzhou, China (13) Technical University of Berlin, Berlin, Germany (14) Institute for Bioinformatics, Nuremberg, Germany (15) BioWisdom Ltd, Cambridge, United Kingdom

We report the results of a collaborative QSAR modeling project between 15 teams to develop predictive computational QSAR models of in vitro Ames mutagenicity induced by organic compounds. The Ames dataset consisted of 6542 compounds (after curation). In total, 32 predictive classification

QSAR models were developed using different combinations of chemical descriptors and machine learning approaches, representing the most extensive combinatorial QSAR modeling study ever done in the cheminformatics field in public domain. The resulting consensus model had the highest external predictive power nearly reaching the experimental reproducibility of 85% for the Ames test. In addition, we found published evidence indicating that 31 of 130 outliers (29 mutagens and 2 non‐mutagens) were erroneously annotated in the original dataset. This work presents a model of collaboration that integrates the expertise of participating laboratories to establish the best practices and most reliable solutions for difficult problems in chemical and computational toxicology.

CINF 59

How (not) to build a toxicity model

Adam C Lee(1), adam@simulations‐plus.com, 42505 10th Street West, Lancaster 1 93534, United States ; Robert Fraczkiewicz(1); Robert Clark(1); Walter S Woltosz(1); Marvin Waldman(1); John Chung(1). (1) Department of Life Sciences, Simulations Plus, Inc., Lancaster CA 93534, United States

When a seemingly well‐curated chemical data set hits the press, a modelers' first impulse is to apply their preferred QSAR method to the data in hopes of building a model that exhibits superior statistics to other published models. Occasionally, the results appear too good to be true. Are these models useful? This work details a procedure for building a useful and well‐validated model, using respiratory sensitization data. We highlight the do's and don'ts of data selection, pre‐ and post‐ data curation, QSAR methodologies, and validation strategies implemented from 1984 to present. The examples demonstrate how to identify a narrow sampling of chemical space by examining good‐looking


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models, applying a model to (believable) real‐world data in order to determine its usefulness both inside and outside the model's applicability domain, and techniques that modelers (should) use to validate as well as assess the robustness of a model.

CINF 60

Metabolic site prediction using artificial neural network ensembles

Marvin Waldman(1), marv@simulations‐plus.com, 42505 10th Street West, Lancaster CA 93534, United States ; Robert Fraczkiewicz(1); Jinhua Zhang(1); Robert D. Clark(1); Walter S. Woltosz(1). (1) Simulations Plus, Inc., Lancaster CA 93534, United States

Hepatic first‐pass metabolism of drugs and prodrugs plays a key role in oral bioavailability, and the cytochrome P450 enzymes are responsible for metabolism of most drugs. Knowledge of likely sites of metabolic attack in a drug molecule can aid in designing out unwanted metabolic liabilities early on in the drug discovery process as well as in the design of prodrugs where metabolic transformation is desired. Using datasets constructed from literature compilations and commercially available databases, we have constructed models based on artificial neural network ensembles that predict one or more likely sites of metabolism for a given molecule for several CYP isoforms including 2C9, 2D6, and 3A4. The models employ atomic descriptors describing charge, reactivity, steric accessibility, and other properties of the candidate atom and its local environment. Model performance will be shown based on various statistical criteria as well as specific examples demonstrating scope and limitations.

CINF 61

WITHDRAWN

CINF 62

Use and results of using an online chemistry laboratory package in a large general chemistry course

Richard L Nafshun(1), [email protected], 139 Gilbert Hall, Corvallis Oregon 97331, United States . (1) Department of Chemistry, Oregon State University, Corvallis Oregon 97331, United States

In addition to traditional on‐campus general chemistry courses, The Department of Chemistry at Oregon State University has been offering an online general chemistry sequence since 2003. We have struggled to identify a method of facilitating an appropriate distance laboratory program. We have investigated a "kitchen" chemistry kit and various online virtual toolboxes. We are currently using a virtual laboratory package (www.onlinechemlabs.com) which presents the user with a split screen: one side contains chemistry laboratory tools and the other is text. The tools include standard experimental equipment such as an analytical balance, flasks, pipettes, and reagents, as well as more complex analytical instruments or reaction equipment such as an absorbance spectrophotometer, calorimeter, NMR, and a combustion chamber. The logical progress (or flow) of these tools in experiments is analogous to that in classroom labs. The tools incorporate both random and systematic error, providing data simulations where detailed error analyses can be performed that are analogous to that in classroom laboratory experiments. Each of these features allows for a significant enhancement in instructional capabilities, and could integrate very well with the instructional modalities of models and argumentation that have been recently developed and outlined in more detail below. Results of the use of the online chemistry laboratory package in three different modes


38

(fully online/hybrid/supplemental) and methods of use will be discussed.

CINF 63

Reaction prediction as ranking molecular orbital interactions

Matthew A Kayala(1), [email protected], 243 ICS 2, Irvine CA 92697, United States ; Chloe A Azencott(1); Jonathan H Chen(1); Pierre Baldi(1). (1) Department of Computer Science, University of California, Irvine, Irvine CA 92697, United States

Being able to predict the course of chemical reactions is essential to the practice of chemistry. While computational approaches to this problem have been extensively studied in the past, a fast, accurate, and scalable solution has yet to be described. Here, we propose a novel formulation of reaction prediction as a machine learning ranking problem: given a set of molecules and a description of conditions, learn a ranking over potential filled to unfilled molecular orbital (MO) interactions approximating the corresponding transition state energy ranking. Using an existing rule‐based expert system (ReactionExplorer), we derive restricted chemistry dataset consisting of 1300 full multi‐step reactions with 2200 distinct starting materials and intermediates. This yields 3600 predicted MO interactions and 14 million unpredicted MO interactions. A two‐stage machine learning scheme is used to learn the model. First, we train reactive site predictors using a combination of topological and real‐valued global features to filter out 61% and 44% of non‐predicted filled and unfilled MOs with a 0.0001% error rate. Then various ranking models are trained on the MO interactions using features engineered to approximate transition state entropy and enthalpy. Using cross‐validation, current best models recover a perfect‐ranking 61% of the time and recover a within‐4‐ranking 95% of the time.

CINF 64

Automated semantic data embargo and publication by the CLARION project

Samuel E Adams(1), [email protected], Department of Chemistry, Lensfield Road, Cambridge Cambridgeshire CB2 1EW, United Kingdom ; Nick Day(1); Jim Downing(1); Peter Murray‐Rust(1); Brian Brooks(1). (1) Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge Cambridgeshire CB2 1EW, United Kingdom

The CLARION project has created the infrastructure to enable research chemists to make selected data available as Open Data, shared over the Semantic Web, without requiring technical expertise themselves. Data is automatically collated from central services, such as the Departmental Crystallographic Service, and chemists' Electronic Lab Notebooks. An Embargo Manager application presents research groups with a view of the data they own, and allows them to set embargo conditions and add additional metadata. Once the embargo period expires data is automatically semantified and deposited as Open Data in a public Chem# repository.

CINF 65

Chemical eCommerce

Klaus Gubernator(1), [email protected], 380 Stevens Avenue #311, Solana Beach CA 92075, United States . (1) eMolecules, Inc., Solana Beach CA 92075, United States

Chemist are late adopters of the internet. The main obstacle is that search engines and eCommerce systems are text‐based and as such inherently inadequate to handle chemical structures. Also, chemical nomenclature and names are poorly standardized and inconsistently used by both suppliers and buyers of chemicals. Therefore, only the combination of a chemical search


39

engine and a chemical eCommerce system can address the needs of the market. Such a system has to handle millions of chemical structures, return results in seconds, and provide tools to handle lists of thousands of molecules. In addition, user expectations are created by their experiences with Amazon and eBay: Prices and availability should be on line. The purchasing process is expected to be predictable: you get what you order on time. Implementing and operating a chemical eCommerce system therefore requires a paradigm shift in the quality of the entire purchasing process.

CINF 66

Waiting on the Chemical Internet

Steven M. Bachrach(1), [email protected], 1 trinity place, San Antonio TX 78212, United States . (1) Department of Chemistry, Trinity University, San Antonio TX 78212, United States

The chemical internet dates back roughly to 1994. Over that time the impact of the Internet and the web on society in general has been overwhleming. Business have come and gone, communication has evolved from web sites to blogs to tweets. But for chemists, the impact has been of much less significance. The talk will present some of the causes of the slow uptake of the Internet by chemists and what potentially the future might hold for us.

CINF 67

Rapid dissemination of chemical information for people and machines using Open Notebook Science

Jean‐Claude Bradley(1), [email protected], [email protected], 32nd and Chestnut streets, Philadelphia PA 19104, United States ; Andrew SID Lang(2). (1) Department of Chemistry, Drexel University, Philadelphia PA 19104, United States (2) Department of Mathematics, Oral Roberts University, Tulsa OK 74171, United States

This presentation will cover methods and tools used to collect, record and disseminate chemical information using Open Notebook Science, the practice of making a laboratory notebook and all associated raw data available publicly in as close to real time as possible. Both solubility measurements and organic chemistry reactions are handled in this way. The recording of laboratory data is handled primarily using free and hosted services such as Wikispaces and Google Spreadsheets. The information is made discoverable using redundant communication channels, including Google, Google Scholar, Wikipedia and other vehicles. The abstraction of key elements from the solubility measurements and the chemical reactions allows for the use of live machine‐readable feeds and web services. The implications for the future of the automation of the scientific process based on Open Data and Open Services will be discussed.


40

Committee Report CINF Communications & Publications Committee

Transfer from the CINF Yahoo! Group to the ACS Network

The decision to close the CINF Yahoo! Group and transfer all CINF Division business to the ACS Network has been implemented. The CINF Yahoo! Group still exists but access is limited to the former group moderators and the group will not be closed until we can decide how to preserve the email archive.

The CINF Division group on the ACS Network has now grown to 127 members and CINF members have begun to use the group in a serious manner after some initial reluctance due to unfamiliarity with the new network. The discussion on the new CINF website has generated almost 900 views and a large number of postings. This group is open to all ACS Network members. There are also closed groups for the CINF Executive and also for this committee where private business can be conducted.

Switchover to the new CINF website

In January, Danielle Dennie, the new CINF webmaster reported as follows:

“Ideally, I would have liked to survey or talk with members of CINF to ask you how you use the site and what you would like to see in a new site. This would have meant that I would have kept the old site while gathering data that could be used to create the new site. Unfortunately, because of my limited knowledge of the software that was used to create the old site, I could not make any edits to it. Which means that if there were any updates to be made to the old site before a new site could be built, I would not have been able to make them.

“Therefore, I quickly designed a new template that I could work with. To make it easy for myself, and for users of the site, I kept the same logical organization that was on the old site. This means that the menu on the left hand side is practically (with minor exceptions) the same as the old menu, as well as the organization of the secondary pages.

“That being said, I was not able to transfer over all content. Specifically, there are 3 sections that I could not transfer:

“Because the old site used a database to generate past meetings information, I have not, for the moment transferred over the tremendous amount of content that was in that section of the site. Therefore, I simply link to it from the new site. (http://acscinf.org/meetings/past.php).

“I did not transfer over volume 62 of the e‐CIB newsletter (http://acscinf.org/publications/bulletin.php). However, for the upcoming e‐CIB, I will create a new template. Perhaps once a new template is agreed upon, I will be able to transfer over volume 62.

“The CINF electronic newsletter has not, as yet, been transferred to the new template (again, because of the tremendous amount of content). A link was made to the individual newsletters on the old site. (http://acscinf.org/publications/enews.php).

“Furthermore, there are a couple of links in the left hand menu that I did not add to the new site. If


41

these are needed, please let me know and I will add them:

Surveys Metrics Disclaimers “Otherwise, I went through every section of the old site, and recoded each page that I came across to fit the new template. If there were files on the old site that were orphan pages (i.e. not linked to from any other page), these files were unfortunately probably not transferred over. I hope I did not miss anything too important. If you notice anything glaring, please let me know.

“Overall, there are still some little tweaks that I need to bring to the site, but the bulk of the work is completed. I look forward to working with everyone to make the site as user‐friendly as possible. If you have any questions or concerns, please don’t hesitate to contact me.” The new website has been well received by CINF members but we still have some way to go to achieving our vision of a website to which it will be easier for CINF members to post content themselves. eCIB editorship for 2011 At the end of 2010, Svetla Baykoucheva retired as eCIB editor but will continue to contribute actively to future editions. In Spring 2011, David Martinsen has agreed to be guest editor and will try to experiment with new workflows based on using the ACS Network. Svetlana Korolev will edit the Summer and Winter edittions which follow and report on National ACS meetings and the Fall edition will be edited by Judith Currano.

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46

SB: Last year you organized a conference on e‐Science. What were the topics discussed at this conference? Could you point to some future conference on e‐Science? JM: Purdue was host to the 31st Annual Conference of IATUL (International Association of Scientific and Technological University Libraries); the theme of the program was: “The Evolving World of e‐Science: Impact and Implications for Science and Technology Libraries.” The intent of the conference was to start with the broadest concept—what is e‐science/computational science, what is the role of data in computational science and how are scientists coping (or not) with managing data? The keynote speaker was Dr. Dan Kleppner of MIT who co‐chaired a task force for the National Academies on issues related to data. In addition, Dr. Arden Bement, who had stepped down as director of the NSF a few weeks before the conference, spoke about the interest the funding agencies have in ensuring that data generated through sponsored research would be available generally to researchers. Dr. Bement assumed the position of executive director of the Global Policy Research Institute at Purdue earlier that month, so his interest was twofold: the management of data and the need to create a global policy on data management to facilitate research. Most of the program was focused on how data can be managed and what the role can or should be for librarians; so it wasn’t just a theoretical discussion, as it provided an opportunity for librarians to gain knowledge of the processes that could assist them in developing e‐science programs in their institutions. Rather than having me provide a complete summary of the program, it would be easy for readers who are interested in the topics to go to the website: http://blogs.lib.purdue.edu/iatul2010/program/. There are many organizations that have a focus on e‐science/data management within the international library community, especially the Digital Curation Centre (DCC) in the United Kingdom: http://www.dcc.ac.uk/events. In the United States, the Distributed Data Curation Center (D2C2) at Purdue is a research center focused on exploring and researching ways in which data can be accessed and archived. Further description can be gained at the link: http://d2c2.lib.purdue.edu/index.php. The Coalition for Networked Information (CNI) at its twice annual briefing sessions often has papers focused on e‐science and data management. Also, on the CNI website (http://www.cni.org/regconfs/) there is a list of upcoming conferences and workshops that include ones on e‐science/data management Finally, the Association of Research Libraries (ARL) and the Digital Library Federation (DLF) are in the early stages of developing an e‐science institute planned for fall, 2011. Initially the Institute will be open to sponsoring libraries (ARL/DLF members), but the intent is that it will be repeated for the broader community in 2012. SB: How do you see the role that librarians could play in this new area? What kind of expertise will be required from them? JM: Working in the area of data management draws upon the principles of library and archival sciences. Our ability to see structure to overlay on a mass of disparate “parts,” as well as the ability to identify taxonomies to create a defined language for accessing and retrieving data is what is needed from us. The challenge will be for librarians to understand that we have collections that we cannot see and may not actually understand the importance of, but that we will have a responsibility to steward and preserve for researchers now and in the future. Archival science is


47

important since there are requirements and expectations from investigators that there will be limited access to data that will require that an embargo be in place. Just as people can give their personal papers to archives with an expectation that access will be limited to specific researchers or closed for a period of time, researchers may similarly want to protect their intellectual property by creating an embargo. For librarians this would normally be unacceptable, while for archivists this is standard procedure. I also think it helps us to think about our present print archives as being raw bits of data, until a researcher (typically a humanist or social scientist) "mines" them to answer a research question, which is similar to scientists or engineers consulting digital data in their research. SB: Will e‐Science change the way academic libraries function? Will it change the infrastructure and the services libraries provide? JM: Many of our librarians (even those working in scientific and engineering disciplines) often have humanities or social sciences backgrounds. However, the trepidation that many librarians may have about sitting down with researchers and discussing their data management needs shouldn’t be a controlling factor. Once a librarian has the experience of talking with researchers about their research and the challenges they have with managing data, it becomes clear that the most important factor is not our subject expertise (although some subject understanding is needed) but rather the librarian’s knowledge of metadata and taxonomies. In the old days we would have said that this is “cataloging and classification,” but today, to convey that we have morphed into a new role, it is best to use the more technical terminologies since it may help identify our “new” role as a cutting edge initiative and not be encumbered with past misperceptions. In fact, a few times I have seen researchers frustrated by librarians with significant subject expertise, who more or less intrude their subject knowledge into what the investigator is researching, while what investigators want is the library/archival science contribution to their team. We need to remember that and be proud of the special expertise that we as librarians bring to the research team. The impact for libraries in the broadest sense is the recognition that we have an important role to ensure the archiving and preservation of important data sets that initially may not be apparent to the researchers or us. We need to be able to think of treating these data sets as important collections, which is not that dissimilar to how we have stewarded our print book and serial collections or our archives. Responsibility for digital data brings new challenges and cost models—ones that we will need to work through with our university administrations and develop further collaboration with our colleagues in research administration and information technology. SB: What kind of problems do you see for librarians to be able to get involved in e‐Science? Will faculty be willing to share raw data with outsiders and how could this potentially affect intellectual property rights? JM: I have touched on some of the problems for librarians to become involved with e‐Science; so I will focus on the second part of your question. And the simple answer, from my perspective, is, "it depends." The one thing we have learned from the work we have done so far with disciplinary faculty and their research is that no two disciplines have identical policies or principles guiding them about sharing data. When we at Purdue embarked on this work six years ago, we thought it was going to be simple to help researchers manage and share their data. However, that naïve assumption was soon disproved. Some disciplines share data through a central database available


48

to all, while others keep their data "close to the vest" while the research is being undertaken and are willing to share it only when it is needed to document findings in a published research article. The mandate by the NSF and the likelihood this will be adopted by other funding agencies will trump, possibly, the traditions of data sharing (or not) within a field. It will take some time before it becomes an accepted, required step of the process. The NSF mandate is a start, but ultimately it will gain acceptance when researchers themselves begin to see benefits of sharing data beyond what they have done in the past. SB: How will e‐Science affect the way research is performed and reported? What will be the consequences for the science and technology publishing field? JM: Some of the effects have been discussed above; so I won’t go back over them here. But I will amplify some of the potential impact that may come from the availability of data and the requirements necessary to provide that access. During the past several years, the publishing industry has begun to assign digital object identifiers (DOIs) through the service provided by CrossRef. This has been very successful as it assigns a persistent identifier that will tag this article for retrieval, now and far into the future. The DOI serves somewhat like a barcode or ISBN, a unique tag that provides access to this article. So, with this ability to identify the article, there comes the concurrent need or desire to link relevant data to it. That initiative has been taken on by libraries around the world, through the development of the international organization called DataCite (http://datacite.org/). Its charge is to create a registry available to researchers throughout the world to permanently tag a data set, and provide enough description to allow for access and retrieval, if desired by a researcher. In the United States, the coordination and assignment of DOIs through DataCite is being undertaken by the California Digital Library (CDL), Purdue University Libraries and the Office of Science and Technology (OSTI) of the Department of Energy (DOE). Creating DataCite and the assignment of DOIs is a major undertaking, not unlike what took place forty years ago with ISBN—the difference being that ISBN was collaboration between publishers and national libraries, which had the reach and the clout to make it a standard in a short time and which were dealing with a finished product (a book). For DataCite, it is a few international libraries banding together to try to get this elephant headed in the right direction. At this time, the DOI assignment to a data set is not mandatory. There is a possibility, however, with OSTI recently joining DataCite, that the DOI assignment will become a requirement by funding agencies. SB: I have done many interviews for the Chemical Information Bulletin, but this is the first time I am interviewing a dean of libraries. And I would like to ask you a question that all academic librarians are asking: how do you see the academic libraries and the work librarians are doing change in the next few years? As dean of libraries in such prominent institution as Purdue, what changes are underway in your own libraries? JM: There is a shift from the trend that was happening ten years ago, which was the reduction of the number of librarians and other professionals and the increase in the number of clerical and student staff. In the "post print" world, the effort necessary to acquire, check‐in, catalog, bind, and manage print collections has significantly been reduced. However, the work that needs to be done in collaboration with the faculty in the classroom and lab has increased.

At Purdueof the prothat comnot only eLibraries science pinitiativesintegratethe operaLibraries.the work becomingneed to mmanagemreferenceoperationprofessioand able instructiocommunicomplace

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51

Svetla Baykoucheva: The United Nations has designated 2011 as the International Year of Chemistry, and I am very pleased to be able to interview someone who has performed such extensive research in the field of history of chemistry. Your book on Dmitrii Mendeleev1 shows deep understanding not only of chemistry, but also of the socio‐political environment in Russia at the time. How does the cultural milieu of an epoch, a country, a region, or an organization influence the developments in science and the public attitude about it? Michael Gordin: This is a great question, and in many ways it is the central concern of the history of science, and clearly there is no straightforward answer to it. There are many factors that influence the development of science at any particular time and place: the experimental equipment and resources available to the scientist, his or her level of education and preparation, access to communication from other scientists, and the general state of science at the time, to name just a few. Some of these factors are pretty tightly bound with intellectual matters, and some of them are more broadly social or cultural, and I think it would be an error to rule out any particular factor by fiat. In some cases, such as Mendeleev's, the need to reform the pedagogy of chemistry for students in St. Petersburg proved crucial to his creating a framework for organizing the elements which eventually grew into the periodic system we know today. The concerns were both social and political (how do you educate a large number of students who have inadequate preparation) and intellectual (the rapidly expanding knowledge of the properties of elements, especially their atomic weights, in the 1860s). That’s not to say we wouldn’t have a periodic table without educational reform in Russia — far from it, as we know by the existence of multiple competing systems. Rather, I mean to say that the form we received has a great deal to do with the specifics of that time and place; the content is a more nuanced philosophical matter. The purpose of the history of science is to elucidate all these various factors and point to their relative weights in specific episodes. SB: Two of your books (Five Days in August: How World War II Became a Nuclear War2 and Red Cloud at Dawn: Truman, Stalin, and the End of the Atomic Monopoly3) were devoted to nuclear proliferation in the context of the Cold War. How do these topics relate to the history of chemistry? MG: My colleagues often ask me the same thing. Nuclear weapons in the early Cold War, after all, are indeed a long way from Mendeleev and Imperial St. Petersburg. Certainly as topics they are pretty different, but as ways of investigating the past they are not that far apart. One of the great challenges in writing the history of science is avoiding what we call "Whiggish" interpretations of history; that is, writing a history of the past which leads inevitably to the present, placing the end of the story right there in the beginning. This kind of presentist version of history is very tempting in the history of science, because science’s achievements are so obvious, and seem so inalterable. The important point, from the historical point of view, is that they were not obvious to the scientists engaged in making the discoveries. They were beset by uncertainties, alternatives, doubts, and vigorous arguments. It is the historian's task to capture those uncertainties and show the past as it unfolded, not tell a just‐so story for the present. Well, after publishing the Mendeleev book, I found myself grabbed by a set of questions concerning the early nuclear arms race, and wanted to see if the same approach would yield results there, even if these weren’t, strictly speaking, classic "history of science" questions. For example, in Five Days in August, I focused on how American military officials, politicians, and scientists thought about the atomic bomb in the period before surrender of the Japanese government in August 1945, and especially in the five days between the bombing of Nagasaki and that surrender. At that time, no one could say that the bomb "ended the war,"


52

because the war was not yet over; so how did they think about it? Was it a revolutionary weapon or not? And in Red Cloud at Dawn, I concentrated on the period between the end of World War II and the detonation of the first Soviet atomic device in August 1949, in order to explore how people on both the American and Soviet sides evaluated the arms race before, strictly speaking, any such race existed. The approach is heavily indebted to the history of chemistry, even if the topics aren’t. To be honest, I’m looking forward to returning to more chemical questions now that I have spent all this time with nuclear weapons. SB: You are the co‐editor of a monograph, Intelligentsia Science: The Russian Century, 1860‐1960, for which you also wrote an essay on the Heidelberg Circle — a group of Russian chemists who specialized in Germany and who later founded the Russian Chemical Society. Who were these people and what impact did they have on the development of chemistry both in and outside Russia? What motivated them to choose chemistry as a career? What was the role of learned societies at that time? MG: Russia entered the decade of the 1860s facing a series of severe challenges. In 1856 it had lost the Crimean War, a defeat which was interpreted by the elite and the intelligentsia as a sign that Russia was "backward" in significant ways with respect to the Western powers. They began to promote a series of military and fiscal reforms in an effort to modernize the state, the most famous of which was the abolition of serfdom in February, 1861. But the problem of technical modernization also occupied these decision makers, and they initiated a program to sponsor talented young scientists (and other scholars, like lawyers and physicians) to study abroad, absorb the very latest word in their specialties, and then return to Russia to help rebuild a self‐sustaining community at home. And, to a great degree, it worked. Many of the leading lights of Russian chemistry, to pick the example I know best, and those behind the formation of the Russian Chemical Society in 1868, were part of this temporary emigration: Dmitrii Mendeleev, Aleksandr Borodin, Vladimir Markovnikov, and others. Each was drawn to chemistry for different personal reasons, but the choice was in a sense no surprise: chemistry was the most dynamic and exciting science at mid‐century, and it was the science most well established in both St. Petersburg and Kazan, which trained these individuals to a level where they could take advantage of their sojourn abroad. As for learned societies, we see a proliferation of chemical societies all across Europe during this time period, and they served a crucial role in creating a national community of scholars who could communicate with each other, establish journals, and lobby their states and national industries for greater support of chemistry. As a step in the professionalization of chemistry, these societies were vital. SB: In a chapter published in the same book, you characterized the Russian national style of scientific discourse as "theoretical, bold, impulsive, and stridently argumentative. It was the style of D. I. Mendeleev and V. V. Markovnikov. It was also the style of Emil Erlenmeyer." Are there national differences in the way scientists perform research and discuss scientific ideas and experimental results? MG: Yes and no. At almost any point in the past two centuries (although, interestingly, not so much before then), you can find cases of scientists claiming that their work bears some specific "national style" in a laudatory sense, or that the manner of research of their competitors from another national context bears a deleterious national style. We can easily jot down a number of these crude


53

stereotypes: Russians are impulsive and bold; Germans are nit‐picking and meticulous; the French are abstract and conceptual; the Americans are pragmatic and application‐oriented. I do not endorse any of these points of view as being accurate descriptions of how people really were or are. Instead, in the article you mentioned I point to how certain Russians chose to brand themselves as being bold and speculative; the irony being that the person they were patterning themselves on most was Erlenmeyer, a German. These assertions of "national styles" have been over the years very important aspects of how scientists have understood their own activity, and as such they are significant for the historian to analyze. Some of them — such as the high level of mathematics found in certain chemical communities — can be traced to national educational systems and thus are more likely to bear a relationship to deeper processes, but many of the others are rhetoric. But, at the risk of belaboring a point: just because something is rhetoric doesn't mean it is historically insignificant. SB: Which events and discoveries in the history of chemistry have happened unexpectedly and have become turning points for the development of science? MG: This is a great question, and one that opens up a number of very interesting issues about how science has evolved over time. No one would doubt that unexpected events happen in the laboratory all the time — Becquerel leaving his uranium salts on top of some film in a drawer, for example. But it is pretty rare for something completely unexpected to happen, since the chemist has a certain collection of equipment and reagents available and is usually trying to accomplish something particular in the laboratory that day. As anyone who has spent any time in a laboratory knows, you don't always get what you expected, but that doesn't mean that the choices you have made have no impact on the set of unexpected outcomes that result. And if something completely unexpected were to happen, one which would have no framework in the concepts available to chemists at the time, then it would surely meet with a lot of resistance, as one finds with the way established chemists objected to the discovery of noble gases. (Mendeleev initially thought argon had to be N3, since the notion of an element that was chemically inert made no sense to him.) Generally, when an unexpected finding comes along in the historical record, closer investigation reveals that a certain group of chemists made a concerted effort to claim that it was a revolution in the science, and argued for thinking about this "unexpected" discovery as a confirmation of their prior theoretical arguments. This interplay between the serendipity of discovery and the hopefulness of theoretical speculation is one of the wellsprings of scientific creativity. SB: You have taught a course on pseudoscience. What did you cover in that course? MG: I find the topic of pseudoscience fascinating, and when I’ve taught this course I’ve covered a large variety of topics of things that have been variously classified (not without controversy) as pseudosciences: astrology, alchemy, phrenology, mesmerism, spiritualism, creationism, cold fusion, Lysenkoism, eugenics, and others. In the course, we emphasized what we can learn about how science works from these rejected domains of knowledge. After all, no one calls themselves a "pseudoscientist"—every single person so designated thinks that they are engaged in real scientific work. They don’t have to be right about that, but there is a lot of interest in trying to understand them in their own terms.


54

SB: Although scientific fraud is much less seen in chemistry than in the life sciences, cases like the one of Hendrick Schön, from Bell Labs, shook the chemical community several years ago. Schön had published numerous articles before it was discovered that he had submitted the same data repeatedly. Many of his papers had to be retracted, including ones that were published in reputable journals such as Science and Nature. How can scientific fraud be prevented or, once it has happened, punished? Do you consider peer review capable of filtering bad science? MG: With regard to Schön, there is an important distinction to be made. On the one hand, we have the category of "pseudoscience," which can be roughly defined as something that is not science but tries very hard to look like science and adopt its methods and approaches. That is not quite the same thing as "fraud," which connotes a level of insincerity that one doesn’t find, for example, among seventeenth‐century alchemists. (There is a third category, the hoax, which is something else again.) Now, as to what can be done about any of these things, I do not have any particular insights. Wherever you find science, you will find something that scientists label pseudoscience; the two always come together. Fraud, if one subscribes to a particular model of psychology, is a matter of incentives, and it is possible that with intensified safeguards, one can reduce its occurrence. But we almost certainly can’t eliminate it altogether. Peer review, as you mention, is often put forward as a solution to this problem, and it is likely better than having no safeguard at all — at least this guarantees that a few scientists read over the piece before it is published — but the evidence of recent years has shown that it is far from foolproof in catching fraud. But, as in the case of Schön, eventually the misdeeds come to light. Time seems to be our best tool in this matter. SB: There are some historians who are very passionate about "The Kekulé Riddle".7 To chemists, the notion that it was Archibald Scott Couper and not Kekulé who found out that carbon is tetravalent and that it was Johann Josef Loschmidt, who drew the benzene ring for the first time, is quite surprising. What do you think of the claims that Kekulé has received credit for concepts in structural organic chemistry that had actually already been developed by others—such as Couper, Loschmidt, Ladenburg, Frankland and Butlerov? And does it matter, from a science historian point of view, who was the first to make the discovery? MG: Being first in making a discovery certainly matters to the scientist! And, in that sense, it does matter for historians of science, since the passions and debates of the scientists are one of the most important things we investigate. Personally, I have spent a lot of time researching the priority dispute over the periodic system between Mendeleev and Julius Lothar Meyer. I am not interested in deciding who was "right" — I don't think historians are in the business of awarding prizes or credit — but the fact that this fight took place, and the kinds of arguments Mendeleev and Meyer used to argue for who was first, makes for a fascinating story to uncover. For better or worse, our system of assigning credit in the sciences centers on priority, and the historian is obligated to explore why that particular system emerged, and what its consequences have been. With respect to Couper, Butlerov, Kekulé, and others — I’m afraid I am a spectator in that historiography and am not going to weigh in on one side or the other, but I can tell you my own particular approach to this kind of question. The fact remains that Kekulé was awarded the credit by his peers. I am personally more interested in why they thought he should receive the credit, rather than in adjudicating whether they were correct or incorrect in doing so.


55

SB: How are the current conditions in academia (I have in mind such things as wider collaborations, struggling for grants, requirements for tenure that include publishing in high‐impact journals, pre‐prints, open‐access, etc.) changing the way research is performed, reported and credited? MG: It's generally a bad idea for a historian to speculate on the future, but there is no question that there have been significant transformations in the way of doing science both inside and outside academia that are bound to have important implications for how various disciplines develop in the future. One obvious factor has to do with funding. On the one hand, science is continually becoming more expensive, and there are more scientists competing for a fixed (or in some cases shrinking) pool of funds. On the other hand, the linkages between academia and industry are becoming tighter now than they have typically been (at least in the American context, with which I am most directly familiar), and this is shaping questions that are asked within universities as well as those asked in industrial laboratories. Conditions of publication are also changing in interesting ways. The problem of "information overload" has been with us as long as we have had journals (which is over three hundred years), and probably even longer than that. There is simply so much information for researchers to keep abreast of, so many venues where it appears, and not enough time in the world to track it. Managing this volume of information is a tremendous challenge, and the Internet has both provided tools for addressing this issue and in other ways also compounded the problem. We are seeing strains in the peer review system — exemplified in the use of the pre‐print server among physicists, as well as other experiments in open‐access — and also mounting costs for libraries. Without sufficient funding for research and access to information, science will suffer, or at the very least be forced to adapt. But I am not a pessimist on these questions. One of the most inspiring things about the history of science is how flexible scientists have been in adjusting to different conditions, and I am confident that while science will look different in thirty years than it did thirty years ago, the developments are going to be quite exciting. SB: What projects have you been working on recently? What are you going to work on in the near future? MG: I'm now beginning a large research project that connects with your query about the changes in chemistry in recent years. One of the most significant transformations in science over the last two hundred years has been the replacement of a polyglot community with an increasingly monoglot one. To take the example of chemistry, which is the focus of my research, in 1850 a chemist would be expected to be able to read, and to a lesser degree speak, German, English, and French. Today, almost no PhD program in chemistry requires any foreign‐language competence at all, as the global production in chemistry becomes increasingly Anglophone. This is an extremely important development, and I believe there has not been enough attention to it aside from a dedicated group of sociological linguists based mostly in Germany. I am planning to write a history that spans from the decline of Latin as a language of scientific communication in the early eighteenth century, through the rise of national languages (including Russian), experiments with artificial languages like Esperanto, the fate of German (almost certainly the most important language in chemistry in the early twentieth century), and the current ascendancy of English. Before embarking on that, however, I am finishing another project related to my interests in pseudoscience as a way of exploring the history of science, with a book on the debates over the theories of Immanuel Velikovsky in Cold War America.


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SB: Thank you for promoting the history of chemistry to a broad audience and for agreeing to discuss these interesting topics. References

1. Gordin, M. D., A Well‐ordered Thing: Dmitrii Mendeleev And The Shadow Of The Periodic Table. Basic Books: 2004; p 384.

2. Gordin, M. D., Five Days in August: How World War II Became a Nuclear War. Princeton University Press: 2007; p 226.

3. Gordin, M. D., Red Cloud at Dawn: Truman, Stalin, and the End of the Atomic Monopoly. Farrar, Straus and Giroux: 2009; p 416.

4. Intelligentsia Science: The Russian Century, 1860‐1960. Gordin, M.; Hall, K.; Kojevnikov, A., Eds. University of Chicago Press Journals: 2008; p 316.

5. Utopia/Dystopia: Conditions of Historical Possibility. Princeton University Press: 2010; p 264. 6. Velikovsky, I., Worlds in Collision. Paradigma Ltd: 2009; p 436. 7. John H. Wotiz, E., The Kekulé riddle: a challenge for chemists and psychologists. Cache River Press:

Clearwater, FL, 1993; p 329.


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Book Reviews: Scientific Writing Robert E. Buntrock [email protected] For this issue, several books on scientific writing will be covered either with brief reviews or by citation. Writing is not only fundamental to dissemination of information but it is a viable alternative career path for chemists and other scientists. The first is on scientific communication, for both written and oral presentations, Harmon, Joseph E.; Gross, Alan G. The Craft of Scientific Communication; University of Chicago Press: Chicago, 2010. $55. (Hardcover) 240 p. ISBN: 978‐0‐226‐31661‐1; $20 (Paper) ISBN: 978‐022‐31662‐8; $7 rent, $20 (Electronic), 978‐022‐631663‐5. Although little information is given on writing for chemistry, a good text and reference for writing and presenting science to both scientific and public audiences. Crafting of a scientific article is described followed by four examples. Research proposals and communications to a lay audience are described next followed by a discussion of style based on how good scientists actually write. Not all sentences need to be short in active mode nor do long sentences need be split (no mention of the "Fog Index", recommended by some technical editors for "executive summaries"). Method descriptions are similar to Julia Childs’ recipes. Exercises, with answers follow each chapter. Another deficiency is the lack of mention of poor, cluttered, low contrast power point slides. (Preciously reviewed by J. Kovac, J. Chem. Educ., 87(11), 1139‐1140, 2010, doi: 10.1021/ed100882.) The second review covers communication of scientific information to the public, Introducing Scientific Communication: A Practical Guide; Brake, Mark L., Weitkamp, Emma, Eds.; Palgrave Macmillan: New York, 2010. $33.95. (Hardcover) 177 pp., ISBN 978‐02305373864. Excellent text or reference for scientific journalism, for presentation of science to policy makers and the general public. Scientific journalism is a viable but underutilized alternative career path for chemists and scientists for which a few universities are developing courses. (Previously reviewed by R. Buntrock, J. Chem. Educ., 87(11), 1138‐1139, 2010, doi:10.1021/ed100855.) Also reviewed in that issue of J. Chem. Educ. (by L. Montes, J. Chem. Educ.,87(11), 1138, 2010, doi:10.1021/ed100864) is The Oxford Book of Modern Scientific Writing, by Richard Dawkins. Shown and discussed are more than 80 examples of writing by prominent scientists including some Nobel Prize winners. For chemists, the benchmark reference remains The ACS Style Guide: Effective Communication of Scientific Information, 3rd edition, by A. M. Coghill and L. R. Garson. (Previously reviewed by R. Buntrock, J. Chem. Inf. Model., 47(2), 703‐704, 2007, doi: 10.1021/ci600536.) As before, we’re always open to suggestions for books to review as well as volunteer reviewers. With the demise of book reviews in JCIM, it’s up to us to "carry the torch" for book reviews on chemical information and related topics.


58

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64

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Product Announcements RSC Publishing Platform reaches the one million milestone

The one millionth publication to appear on the RSC Publishing Platform went online recently in a landmark achievement for the learned society. The seven figure milestone was reached as the RSC's exceptional range of peer‐reviewed journals, magazines, books, databases and publishing services to the chemical science community more than doubled in output in the last three years. Royal Society of Chemistry editorial director James Milne said: "This marks a significant landmark for the RSC Publishing Platform. Delivering the millionth record, a paper published in the journal Nanoscale, demonstrates not only the significance of the RSC in terms of disseminating high‐quality research content worldwide but also with many millions of article downloads each year, the value researchers place on being able to access this content through our new publishing platform." In the last four years RSC Publishing has gone from being the fifth largest publisher in chemistry to challenging Wiley in third place. Read more about this growth at: http://www.rsc.org/AboutUs/News/PressReleases/2011/Million.asp View the one millionth publication, "Controlled assembly of plasmonic colloidal nanoparticle clusters", at: http://pubs.rsc.org/en/Content/ArticleLanding/2011/NR/C0NR00804D


65

Product Announcements InfoChem Launches Chemisches Zentralblatt Structure Database

At the end of 2010, InfoChem GmbH launched the structure searchable version of Chemisches Zentralblatt, a powerful new way of gaining information from an essential resource for chemists, researchers and intellectual property professionals. Chemisches Zentralblatt is the first and oldest abstracts journal published in chemistry, covering the literature from 1830 to 1969 and describing the "birth" of chemistry as a science. Over the period of 140 years, Chemisches Zentralblatt has published 900,000 pages, containing two million abstracts. InfoChem was able to identify one million unique names and 500,000 unique structures in these documents. Now, the structure searchable database provides non‐German speaking users with the opportunity to query this valuable source in the language of chemistry. Using modern scanning technology, FIZ CHEMIE has digitized the entire content of Chemisches Zentralblatt. Then InfoChem produced the structure searchable database by applying specialized software tools for OCR, chemical named entity extraction and name to structure conversion. InfoChem used its exceptional skills and experience in German naming conventions to achieve optimal conversion results. Chemisches Zentralblatt is available as a web‐based application or as an in‐house database. Scientists can search structures, substructures and full‐text. Then from the hit list, users can link directly to the original page in Chemisches Zentralblatt containing the information. Applications may include preparative chemistry and prior art searches. About InfoChem GmbH Founded in 1989 and based in Munich (Germany), InfoChem has over 20 years' experience in the development and integration of sophisticated software tools for the storage and handling of structure and reaction information. For more information, please visit our website. InfoChem is pleased to announce that we now have a representative in the UK. Dr Stephanie North has over 25 years’ experience in chemical information within the pharmaceutical industry and is delighted to be working with the InfoChem team. Contact address: PO Box 240, Royston, Hertfordshire SG8 1DA, UK; e‐mail:[email protected].


66

CINF Officers 2011

Executive Committee

Member Function Tenure Contact

Gregory M.

Banik

Chair 2011 Bio‐Rad Laboratories, Inc., Informatics Division

Two Penn Center Plaza, Suite 800, 1500 John F. Kennedy

Blvd.

Philadelphia, PA 19102

267‐322‐6952 (voice)

267‐322‐6953 (fax)

Carmen Nitsche Past Chair 2011 Accelrys, Inc.,

254 Rockhill Drive,

San Antonio, TX 78209

210‐820‐3459 (voice)

210‐820‐3459 (fax)

510‐589‐3555 (cell)

Rajarshi Guha Chair‐

Elect

2011 NIH Chemical Genomics Center,

9800 Medical Center Drive,

Rockville, MD 20852

814‐404‐5449 (voice)

812‐856‐3825 (fax)

Leah R. Solla Secretary 2009‐

2010

Cornell University, Clark Library

283 Clark Hall,

Ithaca, NY 14853‐2501

607‐255‐1361 (voice)

607‐255‐5288 (fax)

607‐229‐0287 (cell)

Meghan Lafferty Treasurer 2011‐

2012

University of Minnesota, Science & Engineering Library

108 Walter Library

117 Pleasant Street SE

Minneapolis, MN 55455

612‐624‐9399 (voice)

612‐625‐5583 (fax)


67

Bonnie Lawlor Councilor 2010 ‐

2012

National Federation of Advanced Information

Services (NFAIS),

276 Upper Gulph Road,

Radnor, PA 19087‐2400

215‐893‐1561 (voice)

215‐893‐1564 (fax)

Andrea Twiss‐

Brooks

Councilor 2009 ‐

2011

University of Chicago,

4824 S. Dorchester Avenue, Apt. 2,

Chicago, IL 60615‐2034

773‐702‐8777 (voice)

773‐702‐3317 (fax)

Guenter Grethe Alternate

Councilor

2010 ‐

2012

352 Channing Way,

Alameda, CA 94502‐7409

510‐865‐5152 (voice)

510‐865‐5152 (fax)

510‐333‐7526 (cell)

Charles F. Huber Alternate

Councilor

2009 ‐

2011

University of California, Santa Barbara, Davidson

Library

Santa Barbara, CA 93106‐9010

805‐893‐2762 (voice)

805‐893‐8620 (fax)

Dr. Rachelle

Bienstock

Program Chair 2011‐

2012

Senior Research Scientist

National Institute of Environmental Health

Sciences

PO Box 12233 MD F0‐011

Research Triangle Park, NC 27709

919‐541‐3397 (voice)

Jan Carver Membership

Chair

2009‐

2011

University of Kentucky, Chemistry Physics Library

150 Chem Phys Bldg,

Lexington, KY 40506‐0001

859‐257‐4074 (voice)

859‐323‐4988 (fax)


68

CINF Officers 2011 Committee Chairs

Chair Committee Tenure Contact

Jody Kempf Audit 2009‐2011

University of Minnesota, Science and Engineering Library 108 Walter Library, 117 Pleasant St. SE Minneapolis, MN 55455 612‐624‐9399 (voice) 612‐625‐5583 (fax)

Phil J. McHale Awards 2009‐2011

CambridgeSoft Corporation, 375 Hedge Road, Menlo Park, CA 94025‐1713 650‐235‐6169 (voice) 650‐362‐2104 (fax)

Patricia Meindl Careers 2009‐2011

University of Toronto, A. D. Allen Chemistry Library 80 St George Street, Rm 480, Toronto, ON M5S 3H6, Canada 416‐978‐3587 (voice) 416‐946‐8059 (fax)

Susanne Redalje

Constitution, Bylaws, and Procedures

2007‐ University of Washington, Chemistry Library BOX 351700, Seattle, WA 98195 206‐543‐2070 (voice)

Meghan Lafferty

Finance 2011‐2012

University of Minnesota, Science & Engineering Library 108 Walter Library 117 Pleasant Street SE Minneapolis, MN 55455 612‐624‐9399 (voice) 612‐625‐5583 (fax)

Graham C. Douglas

Fundraising 2011 Scientific Information Consulting Belmont, CA 510‐407‐0769 (voice)

Jan Carver Membership 2009‐2011

University of Kentucky, Chemistry Physics Library 150 Chem Phys Bldg, Lexington, KY 40506‐0001 859‐257‐4074 (voice) 859‐323‐4988 (fax)


69

Carmen Nitsche Nominating 2011 Accelrys, Inc.,254 Rockhill Drive, San Antonio, TX 78209 210‐820‐3459 (voice) 210‐820‐3459 (fax) 510‐589‐3555 (cell)

Dr. Rachelle Bienstock

Program 2011‐2012

Senior Research Scientist National Institute of Environmental Health Sciences PO Box 12233 MD F0‐011 Research Triangle Park, NC 27709 919‐541‐3397 (voice)

William G. Town Communications and Publications

2009 ‐2011

Kilmorie Consulting, 24A Elsinore Rd., London, SE23 2SL, England +44 20 8699 9764 (voice)


70

CINF Officers 2011 Divisional Representatives and Liaisons

Representative Division Tenure Contact

Susan K. Cardinal

SLA DCHE 2006‐ University of Rochester, Carlson Library Box 270236, Rochester, NY 14627 585‐275‐9007 (voice) 585‐273‐4656 (fax)

Guenter Grethe ACS Multidisciplinary Program Planning Group

2007‐ 352 Channing Way, Alameda, CA 94502‐7409 510‐865‐5152 (voice) 510‐865‐5152 (fax) 510‐333‐7526 (cell)

Guenter Grethe Biotechnology Secretariat 2002‐ 352 Channing Way, Alameda, CA 94502‐7409 510‐865‐5152 (voice) 510‐865‐5152 (fax) 510‐333‐7526 (cell)

Erja Kajosalo ASIS&T STI 2006‐ Massachusetts Institute of Technology, MIT Libraries 14S‐134 77 Massachusetts Ave., Cambridge, MA 02139‐4307 Seattle, WA 98195 617‐253‐9795 (voice) 617‐253‐6365 (fax) 781‐223‐3869 (cell))

Peter F. Rusch ACS Committee on Nomenclature, Terminology, and Symbols

2006‐ Rusch Consulting Group, 162 Holland Court, Mountain View, CA 94040‐3864 650‐961‐8120 (voice) 650‐961‐8120 (fax)

Mitchell C. Brownk

ACRL STS 2009 University of California at Irvine,Irvine, CA 92697‐8200 949‐824‐9732 (voice) 949‐824‐3114 (fax)


71

Other Functionaries

Member Function Tenure Contact

Bonnie Lawlor Archivist/Historian 2006‐ National Federation of Advanced Information Services (NFAIS), 276 Upper Gulph Road, Radnor, PA 19087‐2400 215‐893‐1561 (voice) 215‐893‐1564 (fax)

Danielle Dennie

Webmaster 2011‐2013

Concordia University, Vanier Library Building7141 Sherbrooke St. W., Montréal (QC), H4B 1R6, Canada 514.848.2424 x 5237 (voice)

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