Abstracts 242

CINF Symposia

ACS Chemical Information Division (CINF)
Fall, 2011 ACS National Meeting
Denver, CO (August 28 - September 1)

R. Bienstock, Program Chair

 

SUNDAY MORNING

Section A
Colorado Convention Center
room 110

Chemical Environmental Specific Databases and Searching Information Related to the Air, Water, and our Environment
A. Twiss-Brooks, Organizer, Presiding
9:00   Introductory Remarks.
9:05 1 Can a compact means of representing the ionic equilibria of multi-acid/base aqueous solute molecules be devised?
R. Don Wauchope, don_wauchope@citcom.net. Agricultural Research Service, US Department of Agriculture, United States
A number of important databases exist created to tabulate the chemical and physical properties of compounds of environmental interest. Many such compounds are Brönsted acids or bases and some contain multiple acid-base sites. If such sites are "weak", i.e. their degree of ionization varies within the range of pH found in environmental waters, this profoundly effects and complicates the molecule's behavior in all environmental compartments. The representation of such acid-base properties in these databases is poor because (a) no conventions for representation are well established (b) for more complex molecules representation requires a disproportionate amount of space in the database. An approach to a compact representation for such molecules will be proposed.
9:35 2 USGS National Geochemical Database: Recovering, repackaging, and repurposing 50+ years of historical data
Steven M Smith, smsmith@usgs.gov; David B Smith. Mineral and Environmental Resources Science Center, U.S. Geological Survey, Denver Colorado 80225, United States
The U.S. Geological Survey's (USGS) National Geochemical Database (NGDB) contains inorganic analyses for approximately 1.4 million samples of rocks, sediments, soils, plants, water, minerals, and other materials collected since the early 1960s. Additionally, the NGDB project has recovered and compiled data from the U.S. Department of Energy's National Uranium Resource Evaluation (NURE) Hydrogeochemical and Stream Sediment Reconnaissance (HSSR) Program conducted during the late 1970s and early 1980s. The NURE HSSR databases contain analyses from about 398,000 sediment/soil and 335,000 groundwater/surface-water samples. All data are being repackaged into searchable and downloadable datasets on the USGS Mineral Resources On-Line Spatial Data website (http://mrdata.usgs.gov). Although samples were collected to support geologic research and mineral exploration, the historical geochemical data and archived samples are increasingly being repurposed to identify hazards to the environment, to human and animal health, and to provide benchmarks for detecting temporal changes in the chemical environment.
10:05 3 Quality of water resources from the U.S. Geological Syrvey: An introduction
Shu Guo, guo1s@cmich.edu. Reference Department, Central Michigan University, Mt. Pleasant Michigan 48859, United States
The U.S. Geological Survey (USGS) collects and analyzes chemical, physical, and biological properties of water resources from sites across the Nation. The rich collection of data, assessments, publications, reports and maps on quality of water resources is a non-replaceable information resource for chemical environmental research. USGS provides specific data on: water quality (real-time, daily and statistics); contamination and pollution (trace elements, medication, pesticides, nutrients, petroleum, viruses); contaminants in groundwater, aquifers, surface and other water resources. USGS's National Water-Quality Assessment (NAWQA) program provides datasets and reports on: water-quality status and trends for surface and ground water; National-Synthesis assessments; contaminants in lake sediments, public and domestic wells etc. The NAWQA Mapper allow users to view chemical concentrations found in streams, lakes, wells and other water resources in the US, which are generated directly from the 17 million water quality results stored in NAWQA Data Warehouse. Techniques methods and modeling are also provided.
10:35   Intermission.
10:50 4 Public access to toxic release data: Exploring TRI and RTKnet.org
Barbara Losoff, Barbara.Losoff@colorado.edu. Science Library, University of Colorado Boulder, Boulder CO 80309, United States
In response to one of the world's worst industrial accidents, the 1984 Bhopal tragedy, the United States Congress established the Toxic Release Inventory (TRI) in 1986. The TRI, under the jurisdiction of the Environmental Protection Agency (EPA), provides access to toxic release data for entire country. The TRI site is publicly available providing users the ability to investigate toxic release data in their communities. TRI data is also mined by other organizations. One such site is the Right-to-Know Network (RTKnet.org) which strives to empower citizens in the government decision-making process. This talk will compare TRI and RTKnet.og as tools for presenting environmental data to the non-practitioner including: ease of navigation, facility in both understanding and using the data, and level of site support.
11:20 5 CHEMLIST: Chronicling the course of regulated chemistry
Roger J Schenck, rschenck@cas.org. Department of Content Planning, Chemical Abstracts Service, Columbus Ohio 43202, United States
CAS has long been associated with collecting and making publicly available the data about substances in commerce. With the inception of the US Toxic Substances Control Act in 1976 to the present, CAS scientists have been closely associated with the registration of substances in commerce and regulations about their use, transport, and environmental fate. Updated weekly, the CHEMLIST regulated chemicals database is a single place to locate regulatory requirements, inventory status, summaries of regulatory information, and other compliance requirements. In addition to describing the inventories and listings available in CHEMLIST, this presentation will cover the challenges in uniquely representing the wide range of substances typically found in national inventories. From polymers and polymer blends to materials and complex biological entities, CAS techniques for representing these commercial substances in the CAS REGISTRY database will be described.

 

SUNDAY AFTERNOON

Section A
Colorado Convention Center
room 110

Non-Traditional Careers What Else Can I Do With a Chemistry Degree?
P. Meindl, Organizer, Presiding
1:30   Introductory Remarks.
1:40 6 Aligning scientific expertise and passion through a career path in the chemical sciences
Antony John Williams, williamsa@rsc.org. ChemSpider, Royal Society of Chemistry, Wake Forest NC 27587, United States
Antony Williams is the Vice President of Strategic Development for ChemSpider at the Royal Society of Chemistry. ChemSpider is one of the world's primary online resources serving the chemistry community. Antony has a PhD in Chemistry specializing in NMR spectroscopy and has worked in a government laboratory, in academia, for a Fortune 500 company (Eastman Kodak), for a small start-up organization and has started two of his own companies prior to joining the Royal Society of Chemistry. During his career path he has experienced multiple work cultures. Antony will provide a short overview of his career path and discuss the various decisions that helped motivate his change in career from professional spectroscopist to website host and innovator to working for one of the world's foremost scientific societies.
2:00   Intermission.
2:15   Videos.
2:45   Panel Discussion.

 

SUNDAY EVENING

Section A

CINF Scholarship for Scientific Excellence
G. Grethe, Organizer
6:30 - 8:30
  7 Development of an open source ELN
Felix Rudolphi, rudolphi@mpi-muelheim.mpg.de; Lukas J. Goossen. Department of Chemistry, TU Kaiserslautern, Kaiserslautern 67663, Germany; IT department, MPI für Kohlenforschung, Kaiserslautern 67663, Germany
The use of Electronic Laboratory Notebooks (ELN) has many advantages over traditional documentation of experiments. We have developed open enventory, a web-based open source ELN with integrated inventory database that facilitates planning and documentation of chemical reactions, as well as further analysis of the collected data. When planning a reaction, the inventory database provides information on availability of chemicals, physical and safety data. Tools to create and analyze series of reactions have proven to be useful in high throughput applications. Analytical data with preview images is attached to the reaction, providing a complete overview over all relevant information. Researchers can search the reaction database by keywords, numeric parameters, chemical substructures or combinations of criteria. They can access their own data, open data created by colleagues and data of former group members, making the ELN a valuable tool for collaboration and knowledge exchange.
  8 Introduction of InChI to researchers in the Department of Chemistry at Louisiana State University
Karen L. Salazar, ksalaz2@lsu.edu; William W. Armstrong. School of Library and Information Science, Louisiana State University, Baton Rouge Louisiana 70803, United States; Department of LSU Libraries, Louisiana State University, Baton Rouge Louisiana 70803, United States
As chemical information has transitioned from print to electronic format, a universal, non-proprietary method of identifying chemical compounds has been needed in order to take full advantage of new communication and search technologies offered via electronic databases and the web. To this end, InChI was developed by IUPAC, in collaboration with NIST, for identifying well-defined chemical substances. The resulting identification scheme converts chemical structures into machine-readable strings that allow data mining of the web and linking of relevant chemical information. In order to be effective, this new electronic identification system must be understood and used by researchers, educators, and publishers on a large scale. The authors will introduce InChI to researchers in the Department of Chemistry at Louisiana State University through a systematic approach that can be implemented at other similar institutions. This presentation will document our progress.
  9 Stochastic search for the structures of small germanium clusters and their anions: Enhanced stability by spherical aromaticity of the Ge10 and Ge122-systems
Truong Ba Tai, truong.batai@chem.kuleuven.be. Department of Chemistry, Katholieke Universiteit Leuven, Leuven 3000, Belgium
Investigations on germanium clusters in the neutral, anionic and dianion states Genx (n = 2 – 12, x = 0, -1, -2) are performed using quantum chemical calculations with the B3LYP functional and coupled-cluster CCSD(T) methods. An improved stochastic method is implemented for searching the low-lying isomers of clusters. Comparison of our results with previous reports on germanium clusters shows the efficiency of the search method. The Ge8 system is presented in detail. The anionic clusters Gen-/2- are studied theoretically and systematically for the first time, and their energetics are in good agreement with available experiments. The clusters Ge10, Ge102- and Ge122-are, in their ground state, characterized by large HOMO-LUMO gaps, high vertical and adiabatic detachment energies and substantial average binding energies. The enhanced stability of these magic clusters can consistently be rationalized using the jellium electron shell model and the spherical aromatic character.
  10 SMARTNames: A new framework to organize chemical structural information based on chemically relevant functional groups
Barun Bhhatarai, bbhhatarai@med.miami.edu; Stephan Schurer. Center for computational science, University of Miami, Miami Fl 33136, United States
We developed a new framework to describe chemical information based on chemical functional groups (CFGs). For the first time we rigorously associate common CFG names with chemical structural representations. CFGs were defined using the SMARTS query language and extensively validated. Names, structures, and relationships among CFGs were modeled in an ontology leveraging the web ontology language (OWL 2.0). CFGs were organized into four hierarchies: (i) major chemical bonds, (ii) common functional groups, (iii) chemical reactivity, and (iv) undesired properties. Each class is further sub-classified based on atom and bond level descriptions into a formal subsumption hierarchy. This ontological description of CFGs allows the definition of novel CFG classes by combining existing CFGs. Further, CFGs can be part of multiple hierarchies depending on the intended use of the framework. The SMARTNames framework was used to analyze several database providing new insights that are founded in the chemically meaningful definitions of CGFs.
  11 Molecular docking and 3D-QSAR studies for design and development of selective aspartate semialdehyde dehydrogenase inhibitors
Amarjit Luniwal, aamarji@rockets.utoledo.edu; Alexander Pavlovsky; Paul W. Erhardt; Ronald Viola. Department of Chemistry, University of Toledo, Toledo Ohio 43606, United States; Center for Drug Design and Development, University of Toledo, Toledo Ohio 43606, United States
Development of microbial resistance against many antibiotics is a major emerging challenge to human health. Targeting of key enzymes that play an important role in the biosynthesis of essential amino acids can be a effective way to counter antimicrobial drug resistance. We have focused on the discovery and development of selective inhibitors against aspartate semialdehyde dehydrogenase (ASADH). This enzyme constitutes an early branch point in a microbial biosynthetic pathway for both essential amino acids and quruorum sensing molecules. We have carried out a series of docking and 3D-QSAR studies to design and develop new classes of selective inhibitors against ASADH. Our promising preliminary results will be described in the presentation. This work is supported by a grant from the NIH (AI077720).

 

MONDAY MORNING

Section A
Colorado Convention Center
room 110

Chemistry in Mobile Spaces Chemical Apps for Mobile Devices
D. Martinsen, M. Braendle, Organizers, Presiding
9:00   Introductory Remarks.
9:05

12

Chemistry in the hand: The delivery of structure databases and spectroscopy gaming on mobile devices
Antony J Williams, williamsa@rsc.org; Sergey Shevelev; Andrew S.I.D Lang; Jean-Claude Bradley; Kevin Theisen. ChemSpider, Royal Society of Chemistry, Wake Forest NC 27587, United States; Department of Computer Science and Mathematics, Oral Roberts University, Tulsa Oklahoma 74171, United States; Department of Chemistry, Drexel University, Philadelphia PA 19104, United States; iChemLabs, Piscataway NJ 08854, United States
The proliferation of mobile devices in the form of smartphones and tablet devices has put into our hands computational power and capability previously limited to desktop until recently. Couple this with the connectivity of these devices to the internet and the trend of increased capability and accessibility in smaller devices continues. This presentation will provide an overview of our efforts to provide access on mobile devices to a large chemistry database, ChemSpider, containing over 25 million unique chemical compounds and associated data including patents, publications, properties and analytical data. We will also discuss how, by providing programming interfaces and Open Data, it has been possible to produce a Spectral Game (www.spectralgame.com) for scientists and students to practice their spectral interpretation skills. We will discuss some of the technology hurdles associated with delivering such capabilities to the various mobile platforms and how modern technologies can significantly enhance the user experience.
9:35 13 SciFinder mobile: Innovation for today's chemical researchers
Kurt W Zielenbach, kwzielenbach@cas.org; Jeffrey M Wilson; Joseph F Sjostrom. CAS, Columbus Oh 43202, United States
SciFinder is widely accepted as the leading research tool for chemists and related scientists, and now SciFinder Mobile is available for research anytime, anywhere. SciFinder's popularity is due not only to its search, retrieval and analysis tools expressly designed by CAS chemists for chemical research, but to the fact that it provides the most direct access to CAS' databases, including the CAS Registry. The world's largest and highest quality collection of information on small molecules, the Registry has been called the "gold standard' for chemical research. Since launching CAS Online in 1980, CAS has been committed to taking advantage of evolving technologies to meet chemists' research needs. CAS pioneered mobile access to substance information six years ago, with the first ever mobile transmission of structure information to the BlackBerry. In 2011, CAS launched SciFinder Mobile, the latest iteration of its mobile technology. SciFinder Mobile is optimized for a range of mobile standards and equipment. It enables scientists to use some of SciFinder's most popular features including researching subject areas, looking up information on chemical substances, and reviewing results of alerts from anywhere. This presentation will detail the operating features of SciFinder Mobile and demonstrate how convenient access to chemical information helps researchers' productivity.
10:05 14 Useful and fun chemistry on the go
David A. Evans, coralie.fridez@reedelsevier.ch; Pieder Caduff. Chemistry & Life Sciences, Elsevier Properties SA, Neuchatel NE 2000, Switzerland
Mobile apps present a new opportunity for delivering chemical information while on the move. We will discuss the development of mobile chemistry applications. Working with the 2010 Reaxys PhD Prize Finalists and with Prof. Carreira's group at ETH Zürich we identified and refined ideas for today's mobile chemistry world that serve specific scientific needs and novel experiences for targeted communities. Applications were developed in an iterative, collaborative and agile process with a continuous, strong involvement from the target user population. We will outline all phases from idea generation to product delivery highlighting the key factors that make the mobile environment unique for product development as well as the successes and challenges encountered in bringing chemistry to this medium.
10:35   Break.
10:45

15

Nature of publishing anytime, anyplace, anywhere
Jason Wilde, J.Wilde@nature.com. Nature Publishing Group, London N19XW, United Kingdom
With the proliferation of mobile devices scientists have the ability to access information anytime, anyplace and anywhere they have a connection to the internet. This provides many challenges to publishers who, invariably, are used to providing information in a rather static format i.e. print, HTML etc... Nature Publishing Group has spent the last 24 months (the iPhone application launched February 2010 and the iPad application was released January 2011) experimenting with the delivery of scientific content on mobile platforms for both Nature publications, Scientific American and as eBooks. This talk will focus on the lessons learned - technical, editorial and marketing - in developing these applications and a vision for future developments.
11:15 16 Current and emerging mobile technologies at ACS publications
Dan O'Brien, dobrien@acs.org; Yinghao Ma. Information Technology - Production Systems, American Chemical Society, Columbus OH 43210, United States; Information Technology - Publications Delivery Systems, American Chemical Society, Washington DC 20036, United States
The Publications Division of the American Chemical Society is taking steps into the mobile space. This talk will explore what we have done recently with the ACS Mobile app for Apple and Android devices, plus look forward a bit to other mobile technologies that are under consideration by ACS Publications. In our review of the ACS Mobile app, we will cover some of the product and design decisions that were made along the way as well as some of the challenges and success we experienced. Design considerations range from the construction of the mobile app itself, through the back-end services that support the app, and finally to the content and data that feed the app. Next, we will look at some mobile technologies under evaluation by ACS Publications. The EPUB format is one of these technologies, and has seen recent improvements that may allow it to better handle the rich scientific content produced by ACS Publications. We will briefly delve into some of the production and delivery considerations involved with potentially producing and supporting these mobile technologies.

 

MONDAY AFTERNOON

Section A
Colorado Convention Center
room 110

Chemistry in Mobile Spaces
D. Martinsen, M. Braendle, Organizers, Presiding
1:30   Introductory Remarks.
1:35 17 Post-textbook era: What it means for the chemistry classroom
Theodore Gray, theodore@wolfram.com. Wolfram Research and Touchpress, Champaign IL 61820, United States
The textbook is broken, both in content and business model. Students don't want to read something that looks like it's been put through a blender (a result of the need to revise it every year to avoid used book sales), and they certainly don't want to pay $200 for it. Fortunately the high price of textbooks makes replacing them with electronic readers like the iPad an attractive proposition both educationally and financially. Touch Press is working closely with educators and hardware companies to explore and define the future of educational materials.
2:05 18 Riding the mobile wave
Steven M Muskal, smuskal@eidogen-sertanty.com. Eidogen-Sertanty, Inc., Oceanside CA 92056, United States
We now live in the post-PC era. The growth of mobile computing devices from smart-phones to tablets has been simply explosive - updating the older vision of a "computer on every desktop" to a "connected touch screen device in every pocket." Indeed, mobile devices have enabled 24x7x365 connectivity and thus access into workflows previously constrained to the office. Coupled with cloud computing environments (e.g. Amazon's EC2 and RDS environments), mobile platforms represent very important growth areas in scientific computing and communication. We will describe both technical and business challenges as well as lessons learned over the last two years after having developed and deployed several mobile apps including iKinase, iKinasePro, iProtein, MobileReagents, and Reaction101.
2:35 19 ChemWriter: Enabling cross-platform mobile chemistry applications through Web standards
Richard L. Apodaca, rapodaca@metamolecular.com. Metamolecular, LLC, La Jolla CA 92037, United States
The tablet computer market, created by Apple, now shows increasing signs of competition from devices running Android and Windows operating systems. While this shift offers choices for buyers, it presents a dilemma for product and service providers. HTML5 and the remarkable array of new Web technologies around it offer a solution that can work both today and tomorrow. Recently, we introduced ChemWriter, the chemical structure editor designed to run on all common Web browsers, ranging from Microsoft's legacy Internet Explorer releases to the most recently-introduced tablet devices - including iPad. Our decision to implement ChemWriter with standard browser technologies was influenced by growing fragmentation in the tablet computer market. This presentation will describe the kinds of mobile chemistry applications ChemWriter can enable. In this context, we'll discuss the advantages of HTML5 mobile applications compared to platform-specific alternatives for scholarly publishing, electronic lab notebooks, and laboratory information management systems.
3:05 20 Computer Vision based chemical information extraction from digital images and streaming videos
Muthukumarasamy Karthikeyan, m.karthikeyan@ncl.res.in. Digital Information Res Centre (Chemoinformatics Division) & Centre of Excellence in Scientific Computing, National Chemical Laboratory (CSIR), Pune Maharastra 411 008, India
Chemical structures are the perfect examples to test the power of robotic vision to recognize and translate them into truly three dimensional chemical structures. Here we present a open-source based computer program to use digital video devices to capture and analyze rapidly hand drawn or computer generated molecular structures from plain papers. The computer program is capable of extracting molecular images from live streaming digital video signals and pre-recorded chemistry oriented educational videos. The images captured from these sources are further transformed into vector graphics for edge detection, node detection, Optical Character Recognition (OCR) and interpret them into bonds, atoms in molecular context. The molecular information generated is further transformed into re-usable data formats (MOL, SMILES, InCHI, SDF) for modeling and simulation studies. The connection table and atomic co-ordinates (2D) generated through this automatic process can be further used for generation of IUPAC names of the molecules and also for searching the chemical data from public and commercial chemical databases. Applying this software the digital webcams, camcorders can be used for recognition of molecular structure from hand-drawn or computer generated chemical images. The method and algorithms can be further used to harvest chemical structures from other digital documents or images such as PDF, JPEG formats. Effective implementation of this program can be further used for automatic translation of chemical images into common names or IUPAC names for chemical education and research.The performance and efficiency of this workflow can be extended to mobile devices (smart phones) with wi-fi and camera capabilities.
3:35   Break.
4:25   CINF Open Meeting and the Open Meeting of the Joint Board-Council Committees on ACS Publications and CAS.

 

TUESDAY MORNING

Section A
Colorado Convention Center
room 110

Herman Skolnik Award Symposium Information Services in Chemical Sciences: Perspectives
A. Lawson, Organizer, Presiding
8:30   Introductory Remarks.
8:35 21 The Information Century and the Learned Society
Robert J. Massie, rmassie@cas.org; CAS, Columbus Ohio 43202, United States
Learned Societies such as the ACS developed, of course, in the era of print and paper. So, naturally, did the various structures and organizing principles of those societies. Consequently, the meetings, major publications (both primary and secondary), bulletins, reports, magazines, seminars -- in fact every aspect of the life of the Society developed during, and were influenced by, the relatively stable and known world of print communications. That world began slowly to change in the 1970's and 1980's, with change truly exploding in the last fifteen years. What might be the full, long-term implications for learned Societies now that they truly inhabit the digital age? It has been said that, “If it can be digitized, it will be,” with reference to everything from traditional forms of information to personal health information or information in the home never before captured, transmitted and analyzed. Closer to our home, with chemical information now completely electronic and rapidly evolving, what will the impact be on the Societies that have, in the past, organized themselves around the publication of that information in print? This presentation will reflect on the implications and changes already seen and that may be contemplated in the coming years from this ongoing digitization of chemical information.
9:15 22 Beyond the journal: Innovation in 21st century publishing
Martin Tanke, m.tanke@elsevier.com; Rafael Sidi; David A. Evans; Philippe Terheggen. Elsevier, New York NY 10010, United States
Publishing is a balance between the needs of authors and those of the reader. This paper explores how the enormous changes in information technologies are having a profound impact on the way scientific research is disseminated, explored and understood. Today's publishing processes are enriching and enabling content in order to provide researchers and research institutions with far greater insights into the scientific literature. This is a new paradigm for the discovery, use, and sharing of research information to accelerate science and deliver better outcomes.
9:55   Intermission.
10:10 23 ChemSpider: Does community engagement work to build a quality online resource for chemists?
Antony J Williams, williamsa@rsc.org; Valery Tkachenko. ChemSpider, Royal Society of Chemistry, Wake Forest NC 27587, United States
With an intention to provide a high quality free internet resource of chemistry related data for the community, ChemSpider has aggregated almost 25 million compounds linked out to over 400 data sources and provided a platform for the community to both deposit and curate data. This experiment in crowdsourcing for chemistry has now been running for over three years. This presentation will review a number of aspects of the project including (a) the level of community participation in depositing and curating data; (b) the nature of data and content supplied by the community; (c) how ChemSpider is used by the community; (d) using game-based systems to assist in data curation; (e) algorithmic-based approaches to data validation and filtering; and (f) sharing data curation efforts with other online databases.
10:50 24 Riding the wave: TIB`s strategy in the context of non-textual materials
Uwe Rosemann, uwe.rosemann@tib.uni-hannover.de; Irina Sens, irina.sens@tib.uni-hannover.de. German National Library of Science and Technology (TIB), Hannover, Germany
The European High Level Expert Group on Scientific data (2010) has formulated the challenges for a scientific infrastructure to be reached by 2030: “Our vision is a scientific e-infrastructure that supports seamless access, use, re-use, and trust of data. In a sense, the physical and technical infrastructure becomes invisible and the data themselves become the infrastructure – a valuable asset, on which science, technology, the economy and society can advance”. Here, “data” is not restricted to primary data but also includes all non-textual material (graphs, spectra, videos, 3D-objects etc.). The German National Library of Science and Technology (TIB) must now rise to these challenges: developing solutions together with the chemical community to make such data available, citable, sharable and usable, including visual search tools and enhanced content-based retrieval. With solutions such as DataCite and modular development for extraction, indexing and visual searching of new chemical metadata, TIB will ride this wave.

 

TUESDAY AFTERNOON

Section A
Colorado Convention Center
room 110

Herman Skolnik Award Symposium Information Services in Chemical Sciences: Perspectives
A. Lawson, Organizer, Presiding
1:30   Introductory Remarks.
1:35

25

Discovering drugs: Generating pharmacologically relevant leads that target disease
Robert C Glen, rcg28@cam.ac.uk. Department of Chemistry, University Of Cambridge, Cambridge Cambridgeshire CB21EW, United Kingdom
Much of early drug discovery depended on leads from natural sources e.g. willow bark yielded aspirin, which led to numerous non-steroidal anti-inflammatory drugs. However, when presented with a newfound biological target, with no small molecule leads, where do we start? How do we probe the target without suitable pharmaceutically active molecules? One approach is to model the receptor and associated endogenous ligands to understand the criteria for binding (and mechanism of action) combined with compound selection to optimize chemical structures for ADME and the avoidance of toxicity. Using this approach, we are currently investigating a GPCR (Apelin) which is a potent vasoconstrictor and using rational design approaches we have discovered novel agonists, antagonists and small molecule leads. We have combined this approach with access to ethically sourced human tissue, an approach which eliminates many of the problems associated with animal testing and which also allows investigation of not only healthy, but diseased tissue. Drugs can then be targeted at the diseased state, which is more relevant in a clinical setting.
2:15 26 From data to knowledge capture and retrieval in Medicinal Chemistry – if we only knew what we already know
Torsten Hoffmann, torsten.hoffmann@roche.com. Department of Discovery Chemistry, F. Hoffmann-La Roche, Basel BS 4070, Switzerland
Medicinal Chemistry is a complex and central science in Pharmaceutical R&D. The successful design and synthesis of drug candidate molecules requires a firm knowledge and understanding of various interfacing disciplines, such as, for example, pharmacokinetics, physicochemical properties, pharmacology, toxicology, as well as modeling and simulation. Medicinal chemists are constantly challenged with an overwhelming amount of data from both, in-house research as well as literature. Improved software tools are needed, to rapidly access and visualize such data, to retrieve information that can be put into context of chemical structure and ultimately turned into sub-structure based knowledge of molecular function in Medicinal Chemistry. This talk will outline some basic thoughts about the requirements of such advanced software tools and will also offer suggestions for a step change of how sub-structure based knowledge might be used to enable Medicinal Chemists for further improved design of drug candidate molecules.
2:55   Intermission.
3:10 27 Enriched research documents at the cutting edge: When research papers no longer make sense on paper
Rudy Potenzone, rudy@sciencepoint.net; Lee Dirks. SciencePoint Solutions, Redmond WA 98052, United States; Research, Microsoft, Redmond WA 98052, United States
Research papers have long enjoyed the ability to exist not only on paper but in enriched electronic form. The ability to embed figures helped, but incorporating chemical structures that included full bonding and structural information brought significant utility to the electronic form over the printed page. Now we are at the edge of a major revolution of recording not only more elaborate versions of results of research, but capturing the very METHODS used, full data and workflows and documenting completely reproducible results. The implications are wide from helping to improve the quality of science, the intellectual transfer of the core discoveries, and preserving the knowledge learned. Several different electronic prototypes will be discussed and their potential impact on the future of science reviewed.
3:50 28 Reading the e-leaves
Wendy A Warr, wendy@warr.com. Wendy Warr & Associates, Holmes Chapel Cheshire CW4 7HZ, United Kingdom
Award symposia frequently celebrate the achievements of the past. In contrast this symposium looks to the future, with an underlying theme of change. The publishing industry is at a crossroads: the concepts of “journal” and “database” are changing and the journal article is now at the center, integrated with, for example, the literature in SciVerse ScienceDirect and chemistry in Reaxys. The Web and the open access movement, plus the growth in social networking, have made possible innovative new models such as that of ChemSpider, complementary, but not yet alternative, to the “gold standard” of the CAS databases and SciFinder. Change has also impacted libraries and their role in the long term preservation of the scientific record and securing access to data. Chemistry, the central science, reaches out into biology, with an impact on the use of chemical structures in drug discovery. The final talks in the symposium examine future horizons. The present one will draw together some underlying threads from earlier talks and make some personal observations about vision, and Professor Lawson's own contributions.
4:20 29 Challenges and opportunities in preserving the scientific record: Reaxys and beyond
Alexander J Lawson, alexander.lawson@reedelsevier.ch. Elsevier Properties SA, Neuchâtel 2000, Switzerland
The need for accurate, concise and relevant information has always been of fundamental importance to researchers in industry and academe since the earliest days of scientific method. In view of the accelerating growth in the amount of accumulated recorded data, this basic requirement has always been in conflict with the time constraints that limit scientists in finding the detail most relevant to their immediate needs. The present paper will discuss the evolution of responses to this dilemma, not only from the standpoint of suppliers of chemical information, but also from the user community itself.
4:50   Concluding Remarks.

 

WEDNESDAY MORNING

Section A
Colorado Convention Center
room 110

General Papers
R. Bienstock, Organizer, Presiding
8:30   Introductory Remarks.
8:35 30 MarVis: An intuitive patent Markush structure visualization tool for medicinal chemists
Wei Deng, david_w.deng@roche.com; Steven J. Berthel; W. Venus So. Pharma Research and Early Development, Roche, Nutley NJ 07110, United States
Reviewing chemical patents is essential for drug discovery project decision making, but can be time-consuming and tedious. A cheminformatics application, called MarVis (Markush Visualization), has been developed for patent Markush structure visualization and analysis. MarVis can show a graphical table of all possible R-groups described in a patent. If a query substructure matches an R-group, MarVis will expand the Markush structure displaying the query substructure. There is also a unique interactive interface that allows chemists to explore Markush structures and zoom in the chemical space of a patent to find a subset of interest. It is especially helpful in cases where the patent Markush structure is very complex with heavily nested R groups. MarVis can significantly reduce time for manual step of patent analysis from days to minutes. The graphical R-group table also facilitates a more efficient subsequent patent analysis. (A manuscript of this work has been accepted by Journal of Chemical Information and Modeling, and published online http://pubs.acs.org/doi/full/10.1021/ci100261u)
8:55 31 Modeling activity landscapes using multiple representations: Consensus models
Jose L Medina-Franco, jmedina@tpims.org; Austin B Yongye; Kendall Byler; Radleigh Santos; Karina Martinez-Mayorga; Gerald M Maggiora. Torrey Pines Institute for Molecular Studies, Port St Lucie Florida 34987, United States; Department of Pharmacology & Toxicology, University of Arizona, Tucson Arizona 85721, United States; Translational Genomics Research Institute, Tucson Arizona 85721, United States
Activity landscape modeling is a powerful approach to characterizing structure-activity relationships (SAR) including the characterization of activity cliffs.1 For an N-dimensional activity landscape, (N-1)-dimensions comprise the chemical space, while the Nth dimension is composed of the activity space. Since chemical space is largely influenced by molecular representation, using multiple representations has been proposed for SAR modeling.2 Herein, we present an example of consensus modeling of activity landscape using 54 compounds with available activities towards three biological targets.3 2D and 3D representations are employed to represent chemical space. The effects of 3D conformation on activity landscape are also explored. In addition physico-chemical properties representing drug-likeness are utilized. The overall results highlight the benefits of using multiple representations in characterizing SAR. [1] Maggiora, G. M., J. Chem. Inf. Model. 2006, 46, 1535. [2] Medina-Franco, J. L. et al. J. Chem. Inf. Model. 2009, 49, 477. [3] Yongye, A. B. et al. J. Chem. Inf. Model. 2011 (submitted).
9:15 32 Unique cycle families: A set of unique and chemically meaningful rings
Adrian Kolodzik, kolodzik@zbh.uni-hamburg.de; Sascha Urbaczek; Matthias Rarey. Center for Bioinformatics, University of Hamburg, Hamburg Hamburg 20146, Germany
The perception of unique and chemically meaningful rings is fundamental for many chemoinformatic applications like molecular descriptor calculation, substructure (SMARTS) matching, and the generation of 2D and 3D coordinates. This problem is frequently addressed by calculating a Smallest-Set-of-Smallest-Rings (SSSR) cycle base. Unfortunately, SSSRs are not unique resulting in atom order dependent calculations. Relevant Cycles (RC) as described by Vismara are an alternative to SSSRs but exponential in number for complex ringsystems. We introduce Unique Cycle Families (UCFs) as an extension of RCs. UCFs represent an intuitive and chemically meaningful description of the rings in a molecular graph. They are unique and only polynomial in number. Therefore, UCFs are a valuable alternative to the commonly used concepts of the SSSR and RCs. We provide an efficient implementation for the calculation of UCFs and we demonstrate their applicability for real time applications, by showing computing time benchmarks for the PubChem Database.
9:35 33 Improved conformational search using a cooperative swarm of simulation replicas
Neil J Bruce, neil.bruce@postgrad.manchester.ac.uk; Richard A Bryce. School of Pharmacy and Pharm Sci, University of Manchester, Manchester Lancs M13 9PT, United Kingdom
The ability to predict molecular conformation is central to structure-based drug design. A range of effective techniques exist for the conformational analysis of small molecules (up to ~500 g/mol). However, for medium-sized to large molecules, there remains a need for robust approaches to accurate prediction of conformation. While molecular dynamics simulations provide some ability to explore and predict the conformation of molecules of this size, the rugged nature of the molecular free energy surface means that only local minima are often identified. A number of MD-based techniques exist that seek to facilitate conformational analysis, smoothing the free energy surface while maintaining its representative features. One such approach, inspired by the artificial intelligence method of particle swarm optimisation, is SWARM-MD (1). This method attempts to smooth the surface of the system through the use of a swarm of multiple interacting simulation replicas that are driven towards the average conformation of the swarm members. We have recently implemented a version of SWARM-MD in the AMBER molecular dynamics package and for the first time applied this approach to prediction of native states of peptides (2), including Trp-cage miniprotein in aqueous solvent. In each case, the cooperation between swarm replicas was found to improve convergence of the simulations towards the native conformation. Future prospects for this approach will be discussed. References: (1) Huber, T., van Gunsteren, W. F. SWARM-MD: Searching Conformational Space by Cooperative Molecular Dynamics, J. Phys. Chem. A, (1998), 102, 5937-5943. (2) Bruce, N. J., Bryce, R. A. Ab Initio Protein Folding Using a Cooperative Swarm of Molecular Dynamics Trajectories, J. Chem. Theory Comput., (2010), 6, 1925-1930.
9:55 34 System chemical biology studies of endocrine disruptors
Tudor I. Oprea, toprea@salud.unm.edu; Olivier Taboureau. Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby DK-2800, Denmark; Division of Biocomputing, Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Lyngby DK-2800, Denmark
Endocrine disrupting chemicals (EDCs) alter hormonal balance and other physiological systems through inappropriate developmental or adult exposure, perturbing the reproductive function of further generations. While disruption of key receptors (e.g., estrogen, androgen, and thyroid) at the ligand binding domain (LBD) has been associated with EDCs, a significant number of EDCs do not appear to influence the LBDs of these receptors. Therefore, we evaluated the potential biological effects of EDCs in humans with the aim to rationalize the etiology of certain disorders associated with the reproductive function. We compiled 675 (known or suspected) EDCs and examined chemical-protein associations via ChemProt [http://www.cbs.dtu.dk/services/ChemProt/]. Over 1000 proteins susceptible to perturbation by one or more EDCs were subject to a protein-protein interaction network evaluation. Synergistic EDC effects resulting in the perturbation of different proteins associated to particular diseases (e.g., cryptorchidism) were evaluated.
10:15   Break.
10:25 35 Large-scale data analysis of bioactivity information in PubChem using 2D and 3D chemical similarity
Evan Bolton, bolton@ncbi.nlm.nih.gov. NCBI, Bethesda MD, United States
With over 120 million biological assay outcomes from 1.6 million small molecules tested against 3,500 protein targets, PubChem is a massive resource for the bioactivities of substances. Ways to enable effective navigation of these results need to be devised. A proven method is to relate substances by their chemical similarity. Efforts to systematically analyze this data can help one identify chemical similarity motifs and bioactivity patterns across assays and protein targets. Discussed here are efforts to devise the means to navigate biological activity as a function of 2-D and 3-D similarity. While a continual work in progress, these efforts may help researchers rapidly locate bioactivity profiles of interest or help identify cross-target indications.
10:45 36 Structure representations in public chemistry databases: The challenges of validating the chemical structures for 200 top-selling drugs
Antony J Williams, williamsa@rsc.org; David Sharpe; Alex Tropsha; Eugene Muratov; Denis Fourches; Jordi Mestres; Ricard Garcia-Serna; Andrey Yerin; Chris Southan. ChemSpider, Royal Society of Chemistry, Wake Forest NC 27587, United States; ChemSpider, Royal Society of Chemistry, Cambridge Cambridgeshire CB4 0WF, United Kingdom; Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill, Chapel Hill NC 27599, United States; Chemogenomics Laboratory, Parc de Recerca Biomèdica, Barcelona Catalonia 08003, Spain; Chemotargets SL, Barcelona Catalonia 080003, Spain; ACD Limited, Moscow 117513, Russian Federation; ChrisDS Consulting, Goteborg 42166, Sweden
Internet-based public domain databases containing chemical compounds have grown in number, capability and content in recent years. There are now many databases containing millions of chemical compounds associated with different types of data including chemical names, properties, analytical data, and with associated mapping to proteins, assay data, clinical information and so on. These disparate data sources suffer from one common issue – quality of data. This presentation will provide an overview of our efforts to source the appropriate structural representations for 200 top-selling drugs from public domain sources. This intra- and inter-laboratory comparison of approaches, processes and necessary agreements exposed the challenges associated with aggregating structure-based data. The project also provided data regarding the distribution of quality issues associated with many of the community's popular databases.
11:05 37 Merging small molecule compound libraries of Bayer HealthCare AG and Schering AG
Jens F Schamberger, jens.schamberger@bayer.com; Michael Grimm; Alexander Hillisch; Andreas Steinmeyer. Computational Chemistry, Bayer HealthCare AG, Berlin, Germany; Computational Chemistry, Bayer HealthCare AG, Wuppertal NRW D42113, Germany; Medicinal Chemistry, Bayer HealthCare AG, Germany
High throughput screening of in-house libraries is the method of choice for lead identification at Bayer HealthCare AG. Quality and diversity of the compound library is essential for successful generation of leads for drug discovery projects in all relevant indications.The recent merger of Bayer HealthCare AG and Schering AG led to the merging of the pharmaceutical corporate compound collections of both companies. One of the largest compound libraries in pharmaceutical industry was built. Characteristics of a state-of-the-art multi-million screening library are reported by describing the individual compound collections as well as the newly combined collection. in terms of structural identity, similarities and physico-chemical properties.
11:25 38 Functional classification of drugs based on their multiphenotype interaction network
Adam C Palmer, acpalmer@gmail.com; Fred M Harbinski; Florian Nigsch; Christopher J Wilson; Jeremy L Jenkins; Roy Kishony; Joseph Lehár. Department of Systems Biology, Harvard Medical School, Boston Massachusetts 02115, United States; Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge Massachusetts 02139, United States; School of Engineering and Applied Sciences, Harvard University, Boston Massachusetts 02115, United States; Oncology Translational Research, Novartis Institutes for BioMedical Research, Cambridge Massachusetts 02139, United States
High throughput cellular assays often yield many positive hits, but the classification of these compounds by mechanism of action remains challenging. Measuring the interaction network of synergy and antagonism among pairwise combinations of compounds can allow their functional classification. However, it is unclear how to implement this conceptual approach in the case of high content screening, where many different phenotypes are measured, making a simple definition of synergy and antagonism elusive. Here, we provide a new framework for analyzing drug interaction networks in multi-dimensional phenotypic space. Defining a 'phenotypic signature' for each drug in this space enables synergistic or antagonistic interactions to be understood as directed interactions whereby each drug modulates the effective concentration of the other. We apply this approach to a high content screen of 29 bioactive compounds (406 pairs) spanning 15,000 combined concentrations. The analysis demonstrates the classification of these compounds by their known mechanisms of action.
11:45 39 Flavor landscape: Towards a systematic characterization of a comprehensive flavor database
Karina Martinez-Mayorga, kmartinez@tpims.org; Terry L. Peppard; Austin B. Yongye; Gerald M. Maggiora; Jose L. Medina-Franco. Torrey Pines Institute for Molecular Studies, Port St Lucie FL 34987, United States; Robertet Flavors, Inc., Piscataway NJ 08854, United States; College of Pharmacy, University of Arizona, Tucson AZ 85718, United States; Translational Genomics Research Institute, Tucson AZ 85718, United States
Flavor perception challenges our ability to both predict and design new flavor entities. Previously, we analyzed the pattern of flavor descriptions utilized in the commercially available Leffingwell & Associates Flavor-Base Pro© 2010 database, referenced to the ASTM sensory lexicon. In this work, we use a systematic approach to navigate through the structure-property relationships of this comprehensive flavor database and propose the concept of 'flavor landscapes'. The approach is derived as a natural extension of the emerging concept of 'activity landscapes' used in drug discovery. As such, we introduce structure-flavor similarity (SFS) maps and structure-structure similarity (SSS) maps. The SSS maps are derived from the fact that there are two types of molecular similarity, one based on the flavor characteristics of the molecules being compared, and the “standard” one based on molecular fingerprints. These tools can be used by expert and non-expert flavor chemists alike.

 

WEDNESDAY AFTERNOON

Section A
Colorado Convention Center
room 110

General Papers
R. Bienstock, Organizer, Presiding
1:30   Introductory Remarks.
1:35 40 RInChIs and reactions
Jonathan M Goodman, jmg11@cam.ac.uk. Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
InChIs encode molecular structures. How can we best use InChIs to develop a description of chemical reactions? A draft protocol is available and is being tested: http://www-rinchi.ch.cam.ac.uk/ The information, challenges, opportunities and future directions that will arise from these tests before the end of August 2011 will be outlined.
1:55 41 CAS learning solutions: Responding to customer needs worldwide
Jayne Knoop, jknoop@cas.org. Department of Learning and Support Solutions, CAS, Columbus OH 43202, United States
CAS information resources are widely seen as “best in class,” with the CAS Registry recognized as the gold standard for substance collections. CAS' global input centers speed the world's publicly disclosed chemical information into CAS' comprehensive databases, which are customized for rapid and convenient retrieval and analysis through SciFinder and STN. CAS has recently developed a suite of online training resources that we hope will match our services in quality and leadership. The new CAS Learning Solutions resource center is the most extensive of its kind in the chemical information sector, with more information and more interactive features to suit the evolving web generation's learning styles, as well as the preferences of seasoned searchers. This presentation will explore the rationale and key elements of CAS Learning Solutions.
2:15 42 NIST-journals cooperation: Implementation of new tools for editors, reviewers and authors
Joseph W. Magee, joe.magee@nist.gov. Thermodynamics Research Center, National Institute of Standards and Technology, Boulder Colorado 80305-3337, United States
New tools have been recently implemented in support of the ongoing NIST-Journals cooperation. These tools offer enhanced benefits to Editors, reviewers and authors of manuscripts that are submitted to the Journal of Chemical and Engineering Data, Fluid Phase Equilibria, The Journal of Chemical Thermodynamics, International Journal of Thermophysics, and Thermochimica Acta. When an author has submitted a new manuscript to these journals, it will be reviewed by NIST in two stages. The first stage provides to Editors a NIST Literature Report and the second stage provides a NIST Data Report. These two reports are generated on demand by new tools that NIST recently incorporated into ThermoData Engine (TDE) software. The literature report assists Editors and reviewers with their assessment of the manuscript's scientific contribution, the degree of overlap with published data, and the need for comparison with those published data. The second stage of NIST review occurs just after peer review is completed and prior to an Editors' final decision. The data report provides provides a complete assessment of data quality, their underlying uncertainties, their sample descriptions, and their descriptions of experimental methods. Specialized consistency tests, based on requirements of the Gibbs-Duhem equation, are run on vapor-liquid equilibrium (VLE) data, and the final results are summarized with an overall VLE data quality factor. This information is compiled into a data report that is submitted to the Editor. Details of the implementation of these new tools at NIST will be described with examples that illustrate the functionality of the tools. These tools have been part of operations for the five journals for less than one year. A review of the successes and challenges in using the new tools will be presented, together with planned developments.
2:35   Break.
2:45 43 What has your chemistry librarian been doing? A new science librarian's work report and current trends in chemistry/science librarianship
Shu Guo, guo1s@cmich.edu. Reference Department, Central Michigan University, Mt. Pleasant Michigan 48859, United States
Chemistry is a unique science discipline which requires special searching techniques to locate its enormous and fast growing collection of information. Chemistry/Science Librarian plays a critical and indispensable role to bridge existing and potential library resources and information users together in helping our patrons to obtain better results. For the past decade, Case Western Reserve University (CWRU) has not had a librarian with science degree and/or education background to cover Chemistry and other science subjects. As the new science librarian, in the past two years I have made great progresses in the areas of collection development, library instruction, reference services, outreach activities and technology education involved in searching chemistry related information. I will present my working experiences at CWRU library mainly in the subject of Chemistry and also summarize the current trends in Chemistry/Science librarianship in academic libraries servicing in the corresponding areas mentioned above.
3:05 44 Development and assessment of online SciFinder tutorials toward the promotion of scientific literacy in undergraduates
Danielle L Jacobs, djacobs@rider.edu; Patricia H Dawson; Sharon Q Yang. Department of Chemistry, Biochemistry & Physics, Rider University, Lawrenceville NJ 08648, United States; Moore Library, Rider University, Lawrenceville NJ 08648, United States
As recommended by the ACS Committee on Professional Training, students should exhibit proficiency in scientific literacy before entering into a professional atmosphere. In Fall 2008, Organic Chemistry I students at Rider University were required to write a report regarding a relevant societal issue rooted in chemistry. While students reported increased engagement in the material, communication and literacy skills were poor. To address this fundamental deficiency, a collaboration with Rider Libraries evolved, resulting in a semester-long literature project for Organic Chemistry II. The research process is facilitated by online Adobe® Flash® tutorials for SciFinder®, specifically designed to be relevant to Rider's undergraduate population. Herein is reported the ongoing tutorial development process, as well as the results of a two-year comprehensive assessment of their impact on students' scientific literacy. These measurements are crucial in continuing to identify the needs of Chemistry undergraduates, as dictated by the needs of their future employers.
3:25 45 Check us out: Librarians as departmental PR agents
Donna Wrublewski, dtwrublewski@ufl.edu; Michelle Leonard, mleonard@uflib.ufl.edu, P.O. Box 117011, Gainesville Florida 32611, United States. Marston Science Library, University of Florida, Gainesville Florida 32611, United States
In these days of competition and rankings, every department is vying for the best graduate students. The Chemistry department at the University of Florida has been taking steps to increase its web presence and advertise the research of its graduate department. This talk will discuss the role of the science librarian as advisor to this process, including compiling publication lists, negotiating publication restrictions to provide access to published research, and streamlining the collection and dissemination of department achievements. At UF, a local implementation of the VIVO Network, which enables the discovery of research and scholarship across disciplines, is being implemented to achieve these goals. The Marston Science Library has been heavily involved in promoting VIVO across its departments, focusing on how it can be used to expand collaborative opportunities and advertise professional expertise. Some observations on the effectiveness of this strategy will be discussed
3:45 46 Elements of research misconduct
Michelle Leonard, mleonard@uflib.ufl.edu; Donna Wrublewski, dtwrublewski@ufl.edu. Marston Science Library, University of Florida, Gainesville Florida 32611, United States
What do scientists, educators, librarians, and game designers all have in common? In the fall of 2010, this team at the University of Florida was awarded a grant from the the NSF to support Gaming Against Plagiarism (GAP). The purpose is to develop a self-directed, interactive, online game to educate STEM graduate students to recognize and avoid plagiarism, including falsification and fabrication of data. GAP's intellectual merit lies in its goal of training these students in U.S. institutions to function effectively and ethically as authors within multinational research teams. This talk will discuss the four phases of the game: preliminary content development, design and development, usability, and evaluation. The team conducted a survey to elucidate students' perceptions of plagiarism and research misconduct. The overall results, including Chemistry-specific concerns, will be discussed. This grant project highlights the role that subject librarians can “play” in plagiarism and research misconduct awareness campus-wide.

 

Section B
Colorado Convention Center
room 112

CINFlash
R. Guha, Organizer, Presiding
1:30   Discussion.

 

7
Newspaper websites and web design