Internet Resource Guide for Undergraduate Organic Chemists Cameron Incognito February 8 th, 2013 ENGL 202C
Table of Contents Preface Contents and Scope of this Guide.... 3 Audience and Purpose of this Guide 3 Assumptions of this Guide.. 3 Organization of this Guide.. 4 Tips for Using this Guide 4 Chemical Databases ChemSpider..6 Scifinder Scholar..7 Reaxys..8 SDBS: Spectral Database for Organic Compounds. 9 Scholarly Journals The Journal of Organic Chemistry...11 Organic Letters... 12 Government Resources Catalog of U.S. Government Publications...14 o Interactions of Organic Surfactants with Oxide Nanoparticles Grown in Aqueous Environments.....14 PubChem...15 References....16 1
Guide Preface 2
Contents and Scope of this Guide This guide contains information for undergraduate chemistry students who are studying organic chemistry and are participating in organic chemistry research. This guide contains online resources for four different chemistry websites, two different chemical scholarly journals, and two different government databases. All of these resources contain vital information that is necessary for all stages of undergraduate research including retrosynthetic analysis, spectral analysis and classification, and substance information. These resources contain all of the information necessary for a student to successfully design and carry out organic syntheses. Audience and Purpose of this Guide This guide is intended for sophomores and juniors in chemistry, specifically those who are taking organic chemistry lectures and are participating in organic chemistry laboratories and research. This information may also be pertinent to undergraduates in other disciplines of chemistry, as branches of chemistry often intersect during research. This guide may also be useful for lecturers and professors who are instructing students about how to prepare and participate in organic chemistry research, in particular organic syntheses. This guide is intended to aid students participating in research to find any information that may be important in the designing and implementation of an organic chemistry experiment. This includes any chemical substance properties, any reaction mechanisms, spectral data and constants, and journal articles publishing information about successful reactions and experiments. Assumptions of this Guide This guide assumes that the reader has participated in chemistry for several years and is therefore familiar with the terminology which accompanies it. It also assumes that the reader is focused on organic chemistry and is just recently entering into the field, as the contents of have most likely been mastered for those who have been participating in organic research for an extended period of time. This guide assumes that the reader has access to all discussed websites, databases, and contents therein. Lastly, it is assumed that the reader is proficient in the use and navigation of the internet. 3
Organization of this Guide This guide is organized in a manner that allows the reader to first become introduced to the more commonly used websites and then be introduced into more technical websites. Two highly specific and renowned organic chemistry journals are presented to the reader as well as the more detailed government databases after a foundation has been formed with the first four websites. The government databases are more broad and general containing a vast store of knowledge, however at the cost of being more difficult to navigate. The guide is therefore divided into three individual sections: Chemical Databases, Scholarly Journals, and Government Resources. Tips for Using this Guide Individual tips for each online resource are presented to the reader below each abstract. These tips provide insights into the resource that have been obtained through extensive use of the resource and may not at first be transparent to the user. The tips contain a wide range of information including the most precise ways of completing a database search, how to organize results as to make resources more easily navigable, and the locations of the most pertinent information on each site. It is advised that the reader first use the resources found in the beginning of the guide before advancing to the more complex and highly technical resources found in the Scholarly Journals and Government Resources sections. 4
Chemical Databases 5
ChemSpider Location: http://www.chemspider.com/ Abstract: ChemSpider is one of the largest free online chemical databases containing structure information and properties for over 28 million compounds. These compounds can be searched via simple name-based searches or through several Java structure searches such as JME, Ketcher, Elemental, and JChemPaint. Once on a substance detail page, there is a variety of chemical information ranging from properties and constants to spectra. The page also contains a variety of links to journal articles, patents, and even more specific areas of interest such as use in medicine, pharmacology, and biology. Lastly, each structure detail page will contain links to other large reference databases such as PubChem and PubMed which may contain even more areas of research interest. ChemSpider is one of the most useful online resources available for undergraduate chemists due to its simple interface and searches and the fact that it is free. Tips: Use ChemSpider as a tool for the beginning of research involving reactions and chemical compounds. Use the site's drawing function to determine how to name compounds and also to identify any common names that the compound may be called. This will increase your capacity to search on other larger databases such as SciFinder Scholar and Reaxys. Always check the ChemSpider SyntheticPages tool to determine if there is any pertinent synthetic information about the compound that may not be contained on the substance detail page. For common compounds it is easiest to search using the simple search function and the input of the chemical name. For more complex compounds, in name or structure, it is often easiest to search using the structure elemental search. 6
SciFinder Scholar Location: https://scifinder.cas.org Abstract: SciFinder Scholar is one of the largest collections of online chemistry information ranging from references to substance information to reaction conditions and properties. SciFinder Scholar contains over 36 million articles from 10,000 scientific journals and 63 different patent authorities, all of which can be browsed easily using sub-searches such as topic, author information, and year. Chemical structures are also able to be searched via structure drawing, Marakush formatting, or molecular formulas to obtain chemical properties such as boiling point, density, melting point, and various spectra. These properties, however, are theoretical calculations and are not verified experimentally. The Explore Reactions tab allows users to input hypothetical reactions to navigate through references in order to determine reagents, conditions, and any other pertinent information for a given reaction. SciFinder Scholar is a database which is valuable for undergraduate chemists designing synthetic pathways via retrosynthetic analysis. Tips: When searching for a synthetic route for a desired product, begin by drawing the structure of the desired compound using the Reaction Structure function. After identifying the structure as the product, search using the Substructure function to obtain a list of possible reactions to produce said product. This process can be extrapolated backwards until a simple, cost effective starting material is reached. The simplest way to explore substances is through the Chemical Structure function. It is not even necessary to know the compound name! When viewing reaction results, it is possible to click on the compounds in the reaction detail section. This will link to the substance detail page for that compound and will contain information such as constants, properties, and spectra ( 1 H and 13 C NMR, IR, and UV-Vis). 7
Reaxys Location: https://www.reaxys.com/info/ Abstract: Reaxys is an integrated search tool which combines both reaction and experimentally determined substance data into one database. Reaxys utilizes data, journal articles, and patents accumulated since 1771, making it one of the most thorough resources available to chemists. One of the most impressive features includes the ability to search previous reactions and obtain information about the reaction and the commercial availability of the reagents. This is useful for determining whether a synthetic pathway is cost effective and worthwhile, ultimately preventing potentially poor synthetic decisions. Reaxys provides the chemical structure, experimental facts (properties, preparations, reactions), and also citations for each entry on the site. This accessibility of the substance citations makes navigating journals straightforward and simple. Lastly, Reaxys allows for the compilation of many different reactions into a Synthesis Plan to allow a full synthetic map to be created and stored under the user s account. This retrosynthetic analysis tool is unrivaled in any other chemistry online resource and is beneficial for students who will be creating theses syntheses both inside and outside the classroom. Tips: If working on a synthetic route, create alerts for compounds or reaction steps which are troublesome. This function will provide updated information regarding this alert as it made available. There are a variety of different mediums of notification including text messaging and email. Download the ReactionFlash Application on a smart phone for portable reaction and substance information. Categorize searches and save them in the reports section, which is accessible in the upper right section of the homepage. This will allow for easy access to these searches in the future rather than searching through the entire history section. 8
SDBS: Spectral Database for Organic Compounds Location: http://sdbs.riodb.aist.go.jp/sdbs/cgi-bin/cre_index.cgi Abstract: SDBS is a website which is operated by the National Institute of Advanced Industrial Science and Technology in Japan and contains spectral data for a vast array of organic compounds. Any information regarding spectral data that an undergraduate chemistry student may need can be found on this site. The site potentially contains 6 different spectra for each searched compound including: Mass Spectroscopy, Carbon NMR, Proton NMR, Infrared Spectroscopy, Raman, and ESR. These spectra are all labeled for simple interpretation, in fact the Proton and Carbon NMR spectra are labeled using the structure of the compound to show which peaks correspond to which part of the structure. Each result page also includes several important pieces of information such as the SDBS and CAS numbers, the official compound name, molecular weight, and molecular formula. This information makes searching the web for more information on the compound significantly easier. This site is particularly helpful for a student when trying to categorize a product or an intermediate. This is often encountered when working on an organic synthesis as the compounds created often contain many impurities and are therefore difficult to interpret manually. SDBS allows the chemist to spot the significant and relevant peaks while also identifying the impurities present. Tips: Before a synthesis it is often important to understand what chemicals you may potentially be synthesizing. This can be done by searching the compounds using the simple search option of either the compound name or the molecular formula. The result page then shows the different types of spectra available to the user and the compound name. You can then click on a particular spectra or the SDBS number link to be taken to the specific compound result page containing all of the spectra links. In the undergraduate chemistry laboratory classes it is advised to identify the Proton and Carbon NMR and IR for each compound. If an unknown compound needs to be identified using the given spectra, one can search on the right hand side of the home page using significant peaks on the IR, Carbon and Proton NMR, and other given spectra. This will then link the user to a list of compounds that contain similar spectral peaks. These compounds can then be sorted through to determine which compound is present. 9
Scholarly Journals 10
The Journal of Organic Chemistry Location: http://pubs.acs.org/journal/joceah Abstract: The Journal of Organic Chemistry (JOC) is one of the most prestigious scholarly journals in the field of organic chemistry, being highly ranked in 2011 for both impact factor (4.450) and also number of citations (98,614). Based out of the University of Utah, JOC contains the most impressive journal articles and even full papers relevant to both theoretical and experimental organic chemistry. As of 2011, JOC publishes two unique forms of articles not found in any other journal medium: Brief Communications and JOCSynopses. Brief Communications are results of experiments that are unique and novel giving chemists a glimpse into full articles that will be fully publicized in the future. JOC Synopses are short reviews of current events in the field of organic chemistry and serve a similar function as the Brief Communications articles. All forms of journal material are searchable on the JOC central website using the Browse the Journal tab found at the top of the page. This allows users to search using the author information, an index of journal articles, or even the most read articles. The main page also contains pertinent information organized into tabs including Just Accepted, Articles ASAP, Current Issue, and Most Read. A simple subject search is also available at the upper right hand side of the site in a bright yellow box. The Journal of Organic Chemistry is an essential journal for undergraduate chemistry students to stay current on events and findings in their field. Tips: For any information regarding how to properly search through the article database, click on the Advanced Search tab in the yellow search box found at the upper right hand corner of the site. This will bring up a list of search mediums on the left side and information regarding how to properly site on the right hand side. This includes stemming, phrasing, limiting the search to specific journals, etc. Be wary that this search takes the user to the general ACS Publication Search Menu and it is therefore necessary to limit the search to Journal of Organic Chemistry if desired. It is recommended for undergraduate chemistry students to read about current events in their field frequently. This can be easily done using the Current Issue and Most Read tabs found on the home page of the site. This will allow the user to sift through journal articles to find the most pertinent and informative articles. 11
Organic Letters Location: http://pubs.acs.org/journal/orlef7 Abstract: Organic Letters is a 15 year old American Chemical Society Journal published by the University of Pennsylvania Department of Chemistry. Organic Letters is the highest impact journal (5.862) in organic chemistry and contains information regarding physical and theoretical organic chemistry, natural product isolation and synthesis, synthetic methodology, and medicinal and biological chemistry. Organic Letters is also ranked #3 in overall citations, #3 in immediacy index, and #2 in articles, making it one of the most prestigious journals in all of chemistry, and more specifically, organic chemistry. The journal is navigable in the same ways as was previously discussed in the Journal of Organic Chemistry, as they are both publications of the American Chemical Society and therefore utilize the same database and features. Any organic chemistry student in need of information regarding experimental synthetic pathways and routes should utilize Organic Letters. The journal contains highly detailed methods sections, making it beneficial for use in the laboratory. Tips: For aspiring research students looking to publish an article in Organic Letters, click on the link titled Submission and Review. This will provide information about what is expected of the author and paper being submitted and also the process of submission and approval. There is also a video link on the right hand side of the home page titled Publishing Your Research 101 which provides similar information. There are three different effective search categories, all of which are located in the upper right hand corner of the site. These searches include: Search, Citation, DOI, and Subject Search. Citation is most useful if the user has a citation for a specific article, otherwise the simple Search and Subject Search are most suitable. 12
Government Resources 13
Catalog of U.S. Government Publications Location: http://catalog.gpo.gov/f Abstract: The Catalog of U.S. Government Publications (CGP) is an online search tool which contains historical and current federal publications from the 3 branches of U.S. government. The site provides direct links to over 500,000 online articles dating as far back as 1976, as well as information about nearby Federal depositories which offer print versions of these publications. The publications are all capable of being searched by means of Authoring Agent, Title, Subject, Keywords, and also advanced searches which allow for the user to narrow the search criteria. This source is useful for organic chemistry students searching for government research articles regarding organic chemistry, both historical and current, as the government is highly involved and influential in this field publishing many articles every year. One such article pertaining to organic chemistry and more specifically the interactions of TiO 2 molecules in aqueous solutions can be found using the CGP: Tips: Synowczynski, Jennifer. "Interactions of Organic Surfactants With Oxide Nanoparticles Grown in Aqueous Environments." Army Research Laboratory (2007): n. pag. Catalog of U.S. Government Publications. United States, Feb. 2007. Web. 4 Feb. 2013. <http://permanent.access.gpo.gov/lps117893/lps117893/www.arl.army.mil/arlreports/ 2007/ARL-TR-4047.pdf>. The Help tab at the top of the site, above the CGP title, contains information about how to navigate the website and also what can be found in the database. There are detailed instructions on the proper ways to search the database using Boolean terms and keywords, and also information about interpretation of search results. When searching through the database, compile all useful articles that are found via the Bookshelf function located above the Full View of Record title. In the bookshelf it is possible to view all articles that were placed in it during the current session along with any notes the user to left with the sources. This is a great way to organize articles while completing research. 14
PubChem Location: http://pubchem.ncbi.nlm.nih.gov/ Abstract: PubChem is a government index formed in 2004 containing information regarding small molecules and is a combination of 3 different government databases: PubChem Substance, PubChem Compound, and PubChem Bioassay. PubChem Bioassay contains information regarding biological activity for over 200,000,000 chemical samples which can be found in scholarly journal articles. The database organizes the information by depicting the chemical structures of the molecules being tested, an abstract describing the procedure, and finally results organized into several different data tables. This information is also made available using the BioActivity, SAR, and Structure Clustering tabs in the PubChem Bioassay tool. The PubChem Compound tool contains information regarding chemical depictions (both 2D and 3D structures), identification (synonyms, IUPAC, and SMILES), classification, and chemical and physical properties. The PubChem Substance database contains information regarding the use of the over 100,000,000 substances in pharmacology. For each substance, any biomedical effects that have been observed, safety procedures for handling, environmental precautions, exposure regulations, monitoring and analysis procedures, and also literature links are provided. The PubChem database contains a wealth of information for organic chemists who may be working on biochemical syntheses involving bacteria, possible drugs (for example synthetic penicillin derivatives), or other biomedical applications. Tips: Make sure to search in the appropriate PubChem database (Bioassay, Substance, and Compound) as searching in the wrong tab may make it quite difficult to find the intended information! The advanced search option is often not needed for the purposes of undergraduate research. However if ever needed, it contains the option to sub-search according to Field, Year, Chemical Properties, Stereochemistry, Bioassays, Links, Elements, and Source & Categories. 15
References Reference for Cover image: Penn State, n.d. Web. 3 Feb. 2013. <http://www.personal.psu.edu/amd16/images/ethanol.gif>. Reference for Preface, Chemical Databases, Scholarly Journals, Government Resources image: Wise Geek, n.d. Web. 3 Feb. 2013. <http://images.wisegeek.com/chemistry-beakers.jpg>. Reference for SciFinder Scholar image: Georgia State University, n.d. Web. 3 Feb. 2013. <http://homer.gsu.edu/blogs/library/wpcontent/uploads/2011/06/scifinder3.jpg>. Reference for Reaxys image: Elsevier, n.d. Web. 3 Feb. 2013. <http://asia.elsevier.com/elsevierdnn/portals/0/reaxys_logo_rgb_nt_417.jpg>. Reference for ChemSpider image: Royal Society of Chemistry, n.d. Web. 3 Feb. 2013. <http://blogs.rsc.org/rscpublishing/files/2011/12/chemspider-logo-530x235.jpg>. Reference for the Journal of Organic Chemistry image: Bristol University, n.d. Web. 3 Feb. 2013. <http://synthesisdtc.chm.bris.ac.uk/synthesisdtc/sites/default/files/pictures/journal_orgch em_burns_small.jpg>. Reference for Organic Letters image: American Chemical Society, n.d. Web. 3 Feb. 2013. <http://pubs.acs.org/appl/literatum/publisher/achs/journals/covergifs/orlef7/title.gif>. Reference for Catalog of U.S. Government Publications image: Angelo State University, n.d. Web. 3 Feb. 2013. <http://www.angelo.edu/services/library/images/deplib2.jpg>. Reference for PubChem image: Drugable, n.d. Web. 3 Feb. 2013. <http://drugable.com/static/images/pubchem-logo.png>. 16