Chemical Information Retrieval FAQ

2009 FAQ

2010 FAQ


1. Explain the "America Invents Act" passed in September 2011 and what effect it might have on the way chemists record their experiments.

(hint from the New York Times Sept 23, 2011 )

The Leahy-Smith America Invents Act is a bicameral piece of legislation that focuses on the reformation of the patent system in the U.S. The act changes the U.S. patent system, and the legal rights under a patent, from a 'first to invent' to a 'first to file' basis. This means that simultaneous or first discovery does not grant an individual the right to a patent on a specific innovation, rather, the first person to complete a patent application is considered the inventor. The act is designed to help the patent office reduce the number of pending applications and backlogged patents. The act provided the patent office with a large funding increase for new computer systems as well.

With the passage of the act, it is likely that chemists competing in high financially driven fields such as pharmaceuticals will be far more conservative with their experimental details. In all likelihood, smaller companies or less funded works will see a dramatic decline in progress. Companies with the power to push through applications and rally legal support are more than likely to increase the number of patents they hold. In the long run, it could hurt or help the scientific community. It is my belief that the act will help drive progress, but the sharing of information will take much longer and be less thorough.

References:
http://www.inventorsdigest.com/archives/7262
http://www.uspto.gov/aia_implementation/bills-112hr1249enr.pdf
http://judiciary.house.gov/issues/issues_patentreformact2011.html
http://topics.nytimes.com/top/news/science/topics/inventions_and_patents/index.html

(CRAIG GUNNETT)
[Full Marks JCB]

2. Describe 10 strategies for obtaining melting points

1. Type 'melting point of __(insert compound here)' into google search bar
Screen_shot_2011-11-13_at_10.54.10_AM.png
This works well for common compounds like Benzene; however, this method can present problems for isomers, pharmaceuticals (whether a compound is a salt or a free base), and for names like benzene that could accumulate hits for chlorobenzene, nitrobenzene, etc.

In the latter case, the CAS number and the compound name can be placed in separate quotations in the google search bar

2. Determine the melting point experimentally using a melting point apparatus or a differential scanning calorimeter (DSC), which is also used to determine glass transition and crystallization temperatures

For a description of good practice to take a melting point, follow this link to an informative 'after school special' on taking melting points (start at 10:47)

Tips for taking a melting point:
1. Heat rapidly until about 15C before the expected melting point
2. Heat the sample a few degrees per minute (~1-3C) until you reach the onset of melting
3. Record the temperature range of melting from onset to completion

3. Obtain experimenta data from peer reviewed scientific journals; SciFinder can be used to find melting points

Here are step by step instructions on how to obtain a melting point using SciFinder:
1. Login and click 'Explore substances'
2. Click on the tab 'substance identifier' and input an IUPAC name, common name, or CAS number (cannot use SMILES or InChI in SciFinder); click 'search'

3. Click on 'substance detail' and slide to the very bottom of the page for experimental melting points

4. Reaxys can be used to expedite strategy 3
In Reaxys, melting points can be obtained providing a structure or some identifier of that compound (name, InChI, CAS, or SMILES) and by selecting 'melting point' under substance data->physical data; Reaxys can be found at the following link
Reaxys

The image below shows the experimental melting points of Benzene using Reaxys
Screen_shot_2011-11-18_at_1.32.14_PM.png
5. Scroll through the list of compounds in the open melting point data explorer (to expedite this process, type the first letter of the compound's name when the list opens); melting point values from different sources should appear automatically below the search bar
open melting point data explorer
Screen_shot_2011-11-13_at_11.17.19_AM.png

6. A substructure search, in the open melting point data explorer) can be run using SMARTS language with the option of filtering the results by melting point range; additionally information on SMARTS language can be found at the following link
SMARTS

7. Type the systematic name, synonym, trade name, registry number, SMILES, or InChI of a compound in the ChemSpider search bar
Screen_shot_2011-11-14_at_11.26.59_PM.png
Melting point data can be found under the properties tab in one of two sections: experimental data or predicted - EPISuite

In experimental data, melting points are usually found with links leading to MSDS sheets
In predicted - EPISuite, melting points (up to two predicted and one experimental) are found under the heading 'Boiling Pt, Melting Pt, Vapor Pressure Estimations (MPBPWIN v1.42):'

-or-

Draw the structure, load a chemical or image file, or convert one of the six identifiers listed in strategy number 6 to the structure of a compound in the ChemSpider 'structure search' bar

To upload an image file, 'click to edit structure' and select the 'load structure tab.' Then click 'choose file' to browse your computer for a chemical or image file of the following formats:

Chemical files include - MOL, SDF, CDX, SKC, etc

8. In the ChemInfo Validation spreadsheet, type the name of the compound and use the 'getMP' function
Screen_shot_2011-11-18_at_11.58.02_AM.png
If you want a very crude approximation, you can use the 'getPredictedMP' function; it would be beneficial to know what compounds were used to develop this model in order to tell whether it's applicable for the compound of interest (here is a link to this model)

To access the spreadsheets from 2009, 2010, and 2011 follow these links:
2009/2010
2011

There is also a web-based interfaced which can be accessed by following this link ChemInfo Validation; simply scroll down the list of common names and the select melting point (if it appears in the list)

9. Obtain MSDS's from physical collections kept by the University; at Drexel, these are kept in yellow bins in the hallways of every floor of Disque

To search MSDS sheets online, follow this link MSDS Index

10. Search through the index of reference books for melting points and scan those pages for the compound; listed below are some common chemistry reference books

- CRC Handbook of Chemistry and Physics (Drexel students have access to an e-book version; to access it, follow this link CRC Handbook)
- Merck (Drexel students also have access to this; to access it, follow this link Merck Index)
- Chemistry textbooks

(Robert Wexler)
[Full Marks JCB]

3. Describe 10 strategies for obtaining boiling points

(detailed images are in my log page http://cheminfo2011.wikispaces.com/Yiwei+Wang+log )

1.CRC handbook of Chemistry and Physics http://www.hbcpnetbase.com/
Log on to the CRC handbook website, there is a “text search” on the upper right position of the website. Enter “the compound name bp” There will be an interactive table under the physical constant of organic compounds or inorganic compounds based on the compound you’re choosing.
2.Reaxys https://www.reaxys.com
Log on to the Reaxys website, and draw the structure (or enter SMILES, InChI or name) of your compound under “Substances and Properties” bar and click search button. Then boiling point could be found in physical data—boiling point with several reference papers indicating several boiling point value.
3.Wikipedia http://en.wikipedia.org
Search t “your compound name” on Wikipedia website and get to the compound Wikipedia page, boiling points could be found on the right under the properties.
4.Wolframalpha http://www.wolframalpha.com
Directly search your compound name on the website and boiling point is under the “basic properties”
5.Sigma-Aldrich http://www.sigmaaldrich.com/
Search the compound name or CAS number on the Sigma-Aldrich website and then select the product of your choice like anhydrous or not. Then on the compound page, there will be a properties sheet on the left of the page and boiling point could be found in the “bp” row.
6.NIST http://webbook.nist.gov/chemistry/
Log on to the website and search with compound name or CAS number, and in your compound’s page, boiling point could be found in the “phase change data” showed in Tboil.
7.Google https://www.google.com/
Google could give us some compounds’ boiling point with different sources. Just input “ boiling point of (your compound CAS number)” .
8.Chemspider http://www.chemspider.com/
Search your compound name in the chemspider search bar and it will show boiling points with different sources and predicted boiling point is also showed in the same page.
9.MSDS http://msds.chem.ox.ac.uk/
Go to the Oxford MSDS website and click the “CAS number”, than click the “A list of CAS numbers for selected chemicals” and select your compound’s CAS number’s initial figure. Find your compound in the next page and click on that, then this compound’s MSDS data is showed on the screen.
10.Chemical Validation data http://showme.physics.drexel.edu/onsc/cir/
People on cheminfo class for the last a few years have done an incredible job on the chemical properties validation including boiling point. So we might be able to found the boiling point of your compound by this chemical validation explorer. Go to that website and scroll down the tab and try to found the boiling point.
(completed Yiwei Wang)
[Full Marks JCB]

4. Describe 10 strategies for obtaining aqueous solubility data

1.Google https://www.google.com/
Type the “ aqueous solubility of a certain compound’s CAS number” in the Google search bar.

google.JPG



2.Wikipedia http://en.wikipedia.org
Type the certain compound name on right upper search bar and get to the compound Wikipedia page, aqueous solubility data could be found on the right under the properties.
wiki.JPG


3. Reaxys https://www.reaxys.com


Choose the Query tab and then select the Substances and Properties tab. Draw the structure of the certain compound or use Generate structure from name, and then click search button. Then aqueous solubility data could be found in Available data column--Physical data--Solubility data.

Reaxys.JPG

4.Sigma-Aldrich http://www.sigmaaldrich.com/
Search the certain compound name on the search bar and then select the product. The solubility data appears in the Properties column.
sigma.JPG

5.Chemspider http://www.chemspider.com/
Type the certain compound name in the search bar and it will show aqueous solubility data in the Properties column.
chemspider.JPG

6.CRC handbook of Chemistry and Physics http://www.hbcpnetbase.com/
On the right upper of the website there is a “text search” bar. Enter “the certain compound name solubility”. Choose the “Physical Constants of Organic/Inorganic Compounds” item.

CRC.JPG

7.Chemical Validation data http://showme.physics.drexel.edu/onsc/cir/
Students collected the various properties of chemical compound in the last few years. You could find the certain compound in the Common Name scroll and then find aqueous solubility data there.

8.MSDS http://msds.chem.ox.ac.uk/
Select the “CAS number” tab, then click the “A list of CAS numbers for selected chemicals” and select the certain compound’s CAS number’s initial digital. Find the compound in that page and the aqueous solubility data showed below the Physical data.
MSDS.JPG

9Textbook (For example, Lange's Handbook of Chemistry Lange's Handbook)
Search through the index of reference books for aqueous solubility data and scan those pages for the compound.

10 Determine the aqueous solubility data from experiments by different methods.
http://www.sciencebuddies.org/science-fair-projects/project_ideas/Chem_p050.shtml
For example
experiment.JPG
(completed Yingji Feng)
[Full Marks JCB]

5. Describe the procedure to submit a new compound to ChemSpider.


In order to submit a new compound to ChemSpider, you need first to be a registered user and login. Click on "My ChemSpider" and select "Deposit Structures" and click on "Input Structure" and then go through the following steps:
1: Draw the structure in one the online app on ChemSpider or in a desktop software and upload it to ChemSpider
2: Annotate the deposition with text(general information about the chemical entity) & add identifiers(chemical names, systematic names, CAS RNs)
3: Associate to an electronic article via URL link, DOI or PubMedID if available
4:Complete the submitting.

Then you can wait for the approval from the Chemspider's master curator.

Reference:
http://www.chemspider.com/blog/wp-content/uploads/2010/09/CSDocs_ChemSpiderCuratorsManual.pdf
(Xiang Liu)
[Full Marks JCB]

6. Why do some compounds have more than one CAS Registry Number?


"There are two possible reasons for a chemical to have multiple numbers. The CAS numbers could refer to different forms of a chemical where each is considered unique for its particular properties and characteristics. The CAS registry number file includes the registry number, synonyms, chemical structure, and molecular formula for each chemical recorded in the file. If specific research has been done on a particular form of a chemical, a separate CAS number may be assigned to that particular form to facilitate the search process in the CA file. For example, sodium hypochlorite is listed with two CAS numbers, 7681-52-9 and 10022-70-5. The former refers to hypochlorous acid, the sodium salt form of sodium hypochlorite, while the latter refers to the pentahydrate form of sodium hypochlorite. Both forms could be called sodium hypochlorite, thus sodium hypochlorite has, in effect, two CAS numbers.

A chemical also may be listed with multiple CAS numbers when multiple numbers have been inadvertently assigned to the same chemical. This multiple assignment can occur when forms of a chemical are originally believed to be unique, but after further review by chemists are identified as the same chemical. In this case, all the CAS numbers are cross-referenced, allowing the chemical to belocated with any assigned number. The misassigned numbers are deleted as registry numbers, but remain on file for referencing purposes. The CAS number first assigned is the more accurate number to use when denoting the chemical. Although all of the numbers will find the chemical, only the more accurate number will prompt the CAS registry file system to display the name, synonyms, andcharacteristics associated with the chemical. Chromic acid, listed with CAS numbers 1115-74-5 and 7738-94-5, illustrates this situation. After further review by chemists, the second CAS number, 11115-74-5, was deleted as a registry number, but remains on file for future reference. CAS number, 7738-94-5 is the more accurate number to identify chromic acid because it was the first registry number assigned." (Environmental Protection Agency) (Completed Andrew DeVita)
[Dead link - partial marks JCB]

7. What are the advantages and disadvantages of SMILES, InChIs and InChIKeys?


SMILES (Simplified Molecular Input Line Entry Specification)
A major advantage of the SMILES system is the extensive software support of the algorithm. Many molecule editors allow for the conversion of the two-dimensional structure into the SMILES format. Link Other friendly features of this system are it's simple and compact nature, allowing for it to be relatively human understandable. Link In addition, it can also handle the representation of isotopes and reactions. Link

InChIs (International Chemical Identifier)
This is the first major non-proprietary computerized molecular structure representation algorithm that preserves the uniqueness of a particular compound. It was inspired by the IUPAC compound naming system. LinkHowever, this system presented an issue during searches. Link

InChIKeys
This format which is a hashed version of the InChI system was developed for the purpose of easier searching. Link However, this hashed version of InChI allows for duplicate values. Though the probability of finding a duplicate value is very small. Link
(completed by Andrew Buss)
[Full Marks JCB]

8. Give 3 examples of using SMARTS queries.

SMARTS are used to describe molecular structure and patterns. They can be used in designing structures and determining their activity such as in drug designing. Moreover, they can be used in identifying an unknown substance by comparing it to the already identified structure. They can also be used in identifying a specific functional group and/or bonds and/or stereochemistry.
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
[ES - give actual EXAMPLES, not just generalities Partial Marks JCB]

9. Give 5 examples of smartphone applications that allow chemistry searching.

1. Wolfram Alpha – $2.99
This extremely versatile mobile app provides chemistry searching through a sleek and simple user-friendly interface. It offers fast and easy results anytime, anywhere, provided there is internet accessibility. Simply type in a chemical name and gain access to chemical information including structures, synonyms, ID’s, formula, bond information, properties, safety information, and related websites and articles.

2. Wikipedia – Free
This simple, easy-to-use mobile app is 100% open source. It provides fast results anytime, anywhere, provided there is internet accessibility. For added convenience, language-preference capabilities are provided. Simply type in a chemical name to access a vast amount of information. Basic information provided can include, but is not limited to, structures, synonyms, ID’s, formula, properties, hazards, related compounds, and links to MSDS’s. In addition to this information, a full encyclopedia-like article can be found providing detailed information about the chemical ranging from history, to reactions, to applications, and much more. Information found on Wikipedia will vary.

3. ChemMobi – Free
This user-friendly mobile app is organized by tabs to help you quickly find the information you desire. Powered by Symyx, DiscoveryGate, and ChemSpider, it provides chemistry searching within an excess of 30 million chemical structures. It offers fast and easy results anytime, anywhere, provided there is internet accessibility. Search by chemical name or ID to access chemical information including structures, synonyms, ID’s, formula, properties, and safety information. Additionally, chemical sourcing is available through the Suppliers tab.

4. ChemSpider – Free
This mobile app provides chemistry searching within the ChemSpider database through a sleek and simple interface. It offers fast results anytime, anywhere, provided there is internet accessibility. Search by chemical name, ID, or by drawing the structure to access a variety of chemical information including structures, synonyms, ID’s, formula, properties, and predicted properties. Additionally, it offers access to related journal articles and Google searches.

5. ChemDoodle Mobile – Free
This user-friendly mobile app is organized into four main windows to help you quickly and easily find information. It offers fast results anytime, anywhere, provided there is internet accessibility. Search by drawing the chemical structure, or by entering the chemical name to search for the structure, and it will calculate a chemical formula, properties, and interactive spectra. ChemDoodle Mobile can be used in conjunction with a ChemDoodle web account, or using a limited-access guest account.

References:
WolframAlpha
Wikipedia
ChemMobi
ChemSpider
ChemDoodle

(Completed by Mary Paul)
[Full Marks JCB]

10. Give 5 examples of web resources used to teach spectroscopy to high school students.

SpectraSchool
A site hosted by the University of Leicester and the Royal Society of Chemistry that provides a range of resources to help in the understanding of the principles and practices of spectroscopy. The website provides a SpectraGraph program hat enable the user to see the various spectra for a list of certain compounds. Videos and teaching resources can also be found on the site.

Squiggly Lines
This website provides links to aid in the teaching and understanding of light and astronomical spectroscopy at the middle and high school level. The site is broken down by topic, first discussing astronomical distances, then the basics of light, and then finally reaching spectroscopy.

Mysteries of Science
This website is a collection of links to teaching resources provided by various universities as well as NASA which were all compiled by the SETI Institute. The links range from reading to activities to tutorials. Topics include using a spectrometer, building a spectrometer, and spectroscopy.

Cell Phone Spectrometer
Alexander Scheeline at the University of Illinois developed software that can turn any cell phone into a spectrometer. The website provides both instructions and resources for both teacher and student. The site links to the paper about how the software works and allows for free download of the software.

The Science of Spectroscopy
This is a wiki-based site that provides introductory material for advanced high school students. The website provides real world application for the involvement of students and external links for further information.
(completed Jessica Sima)
[Full Marks JCB]

11. What is the compensation for the peer review process in Chemistry Journals?

Peer Review is, for the most part, a voluntary process to uphold standards and accuracy in science. As such, reviewers are not paid for their work in almost all cases.
Wikipedia States: "Because reviewers are not paid, they cannot be expected to put as much time and effort into a review as an audit requires"
[Quote the part of the article that supports your statement about compensation JCB] (Done)
(Citation: Wikipedia)
(Completed Neal Ryan)
[Full Marks JCB]

12. List 5 different ways of specifying chirality in a molecule

A molecule is said to possess chirality if it has a non-superimposable mirror image. These two images of the molecule are called enantiomers, but can be given specific designations to describe them. While there are multiple designations that describe chirality, five “pairs” are discussed below (Wikipedia)
R and S: These labels are generated using the Cahn-Ingold-Prelog system (CIP) and are determined by a ranking of the substituents around a centralized carbon atom (Chemistry.msu) . With the fourth ranked substituent pointing away from the viewer, a chiral molecule is deemed “R” if the remaining numbers create a clockwise circle, and “S” if the remaining numbers create a counter-clockwise circle (Chemistry.msu). The R and S system can label multiple chiral centers.
D and L: D and L designations are assigned to amino acids and sugars and are based off of one configuration, glyceraldehyde. When placing the centralized carbon hydrogen in the backwards direction, the functional groups can be followed in the order COOH, R, NH2, or as this source refers to it, "CORN". A clockwise rotation of CORN will give the D enantiomer, a counterclockwise rotation of CORN will give the L enantiomer (Chemed).
+ and - : + and – designations refer to the rotation of plane polarized light by the chiral molecule. If the light is rotated clockwise it is considered + and if the light is rotated counterclockwise it is considered -. + and – configurations can also be substituted with d and l, respectively, although this sometimes can cause confusion with D and L terminology (Wikipedia).
M and P: M or P designations refer to the helicity, or propeller spin, of a molecule. A chiral molecule that contains a right handed helix is termed P. A chiral molecule with a left handed helix is termed M. The helix, when rotated, will spin in its corresponding direction (clockwise or counterclockwise). (iupac).
Lambda and Delta: the greek symbols lambda and delta can be used similarly to M or P to describe inorganic complexes with helixes (particularly octahedral or dentate complexes) (iupac). The “screw path” or directionality of the “blades” in a Lambda molecule would push material downward, while the directionality of the “blades” in a Delta molecule would push material upward (carleton.edu). An animation is available at (carleton.edu) to show this method.
@ and @@: @ and @@ are SMILES designations. When looking down a tetrahedral molecule from a specific point, the "@" symbol refers to anti-clockwise rotation while "@@" symbol refers to anti-anti (or clockwise) rotation. For example, N[C@](Br)(O)C would refer to looking down a N bond at a C with structures in an anti-clockwise rotation, while N[C@@](Br)(O)C would refer to looking down an N bond at a C with structures in a clockwise rotation. The SMILES notation cannot express all types of chirality. (OpenSmiles)
(Completed: ErinEnnis)
[Full Marks JCB]

13. List 3 sources for database for polymer chemistry
1. Polymerprocessing
Great free database focused on polymer processing. searching polymer data from name, class and repeated formula lists.

2. POLYMERSnetBASE
searching engine covering polymer information via CRCnetBASE made up of about 8000 online books. Polymerdatabase is also a great source for polymer searching and also operated from CHEMnetBASE from CRCnetBASE.

3. MSDS
searching engine for polymer's physical and chemical properties and focused on toxicity and handling information.
(completed by sowonmoon)
[Full Marks JCB]

14. List 5 online sources of Brewing Chemistry.


1. www.asbcnet.org
The American Society of Brewing Chemists’ website is available to anyone interested in learning methods of brewing, handling raw materials of brewing, problem solving in brewing, as well as professional opportunities in the brewing industry.

2. www.mbaa.com
A website of the Master Brewers Association of the Americas that provides interaction with other brewing professionals, resources for better brewing processes, and practical information for companies, as well as home brewers, on a global level.

3. http://www.homebrewersassociation.org
A site dedicated to home brewers explaining in layman’s terms the processes, chemistry, etc. for brewing at home. Zymurgy, the journal of the The Home Brewers Association is also available on the website.

4.www.ibd.org.uk
A professional brewer’s resource, The Institute of Brewing and Distilling provides opportunity for professionals to contact and converse with industry colleagues about processes in fermentation and brewing, take exams and gain certifications, and keep up to date in the brewing industry.

5. www.foodnavigator.com
A website that provides updates and current news in food and beverage science and development.
(Completed Marisa Egan)
[Full Marks JCB]

15. How to evaluate credibility of information when using internet sources.

The World Wide Web is an excellent source for fast and updated information. However, it may be challenging to determine the authenticity of the information. At times, one may have to question the integrity and source of the information. “As numerous writers have pointed out, what chiefly distinguishes the web from traditional sources is that it lacks the filters, which promote reliability in numerous print sources” (1). Since the internet allows individuals to input information, and some sites like Wikipedia allow people to define and add information, people may begin to question if the information is valid. When an individual would like to do this, there are areas to observe when evaluating credibility, such as "peer review, credentials of the author, and writing style"(2). We will see later on if all this information is enough.

For peer review, it is important to denote the company that published the book, if the company is reputable, or if the source is from a well known journal or society. Anonymous internet writers can not be used as valid sources since it is unclear who they are or what company they work for. To test the credential of the author, while it may be unfair and unjust, some individuals may validate credibility if the author has achieved a high degree in that field. However, even though such a high degree is demonstrated, some individuals may tend to talk from a subjective point of view, which may have some bias, but this may not always be the case. Other authors may not have such high degrees but the sources for their information may be valid. But for the most part, if the author has expertise or a high degree and the quality of his writing is in a professional and in high academic standing, it may have more credibility than authors with low academic standing, but both would need further investigation. Another aspect to focus on is the way the information is presented, if it’s from a prestigious individual or company and presented in a clear objective and academic standpoint, it may as well seem credible, but also needs further invesigation.
Lets do an example and see if the above mentioned criteria is suitable; lets look at flash point for carbamazepine (CBZ). Three data entries are obtained, one from a peer review journal (Asian Journal of Pharmaceuticals) and another from a chemical database (Wolfram Alpha) and one from an MSDS (Dorman Laboratories). The peer review journal shows the flash point of CBZ is 169 C, while the chemical database shows 202 C and the MSDS shows <204.4 C. The journal and chemical databases both fulfill the mentioned criteria above, and the MSDS probably takes the information from Sigma-Aldrich, but all have different values. How do we determine the correct value? Lets try another example from Reaxys, which is a chemical database. The melting point of CBZ is obtained from 3 sources, Nist, Sigma-aldrich, and Bioorganic and Medicinal Chemistry Letters, giving values of 189.5-191 C,191-192 C, and 191 C, respectively. All sources fill the criteria above and have a value of 191 C in common, so is it safe to assume the actual value is 191 C? Doing more examples and after checking the values are correctly depicted, it shows that seldom, one source may copy a value wrongly, and other sources copy from that wrong value, which would be appear to be accurate due to the value having precision, however it lacks accuracy. So, if a value is redundant, that does not necessarily mean that the value is correct. It can mean that the 'wrong value' was copied without validating with other sources and without validating where their sources are from.

In this class, we have learned a new approach to validate data. We have learned that even though a journal may have had peer review, the author has credentials, and the writing style is in a professional and academic standing, there is a further step that needs to be done to validate the data. This new strategy will give you a better chance to get an accurate result. If searching for a physical property from a database, such as Reaxys, the database will show values from different sources. If one were to choose a value from the list, the data source should be opened to verify that the value indicated is the one mentioned in the source, since typos or wrong values could be copied. A few things to look at however, is to make sure the units are all the same when comparing values from different sources. It has been shown that a lot of incorrect values occur due to neglected the denoted units. Other important things to look at are patterns in the molecule. If someone is looking at the melting point or boiling point for ethane, it would be essential to look at what is mentioned for methane, and propane, since the melting point should be in a decreasing pattern from methane to propane and increasing pattern of boiling point from methane to propane. So, if the trend is not there, most likely the source values are incorrect or has a typo in one of the values.

After obtaining several sources and after confirming the value's units, one should denote if the value was obtained at STP or at other conditions. It is also important to see if the value is experimental or predicted. In addition, do further verification by looking at other available trends for the compound of interest against other compounds in the same family for valid correlations, as shown in the example above. "After this class, you should feel that you can never blindly trust chemical data sources again"(3). This statement is true, but through this class, we have learned approaches to have more confidence in obtaining accurate results.

So is it better to stick to textbooks? Textbooks may also have the same issues as using the web. There are differnt pros and cons of using the text versus the web, but both are susceptible to the same errors. One advantage of a text, however, is that its information cannot be lost since it is provided in a hard copy format, but if there are any adjustments in data or information, revisions have to be made to new versions of the text. When using internet, the site may have the URL changed or mistyped due to rearrangements of the site by the domain, so it will be difficult to find, but if there are updates or adjustments, the revisions are much faster and just as easily accessible. However, it is important to denote that textbooks are not favorable, since many of their assertions are not referenced. Therefore, the sources of data can not be verified and textbooks should be avoided.

References
1) http://www.rbs0.com/credible.pdf
2) Tony Doyle, John L. Hammond, (2006) "Net cred: evaluating the internet as a research source", Reference Services Review, Vol. 34 Iss: 1, pp.56 – 70 Link DOI 10.1108/00907320610648761
3) Dr. Bradley http://dx.doi.org//10.4016/34604.01
(Completed Michele Alshouli)
[Full Marks JCB]

16. List 5 online databases/resources for students to reference for an instrumental analysis course and some advantages/disadvantages to each.


1. Spectral Database for Organic Compounds SDBS (Web Link)


- Advantages: This is a database filled with many spectra including Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), Infrared (IR), Raman and Electron Spin Resonance (ESR). This also has the ability to search many different ways including open
searches incase you are unsure of the exact compound.

- Disadvantages: As the title suggests, this is organic compounds, leaving out many compounds such as inorganic or organometallic type compounds. Many of the spectra in this database are predicted as opposed to experimental which may be different than
students' actual spectra.

2. NIST Chemistry WebBook (Web Link)


- Advantages: This database has many compounds along with physical, chemical and spectral information. This database also has multiple states of the same spectrum (i.e. solid state vs liquid state IR).

- Disadvantages: Limited help field for searching. Some boolean logic can give overwhelming amount of results.

3. Sigma-Aldrich MSDS Search (Web Link)


- Advantages: Has multiple forms of the same chemical, such as different purities. Gives some similar chemicals along the bottom of a specific chemical's page. Appears to have a mobile phone application as well.

- Disadvantages: MSDS Sheets are not always the best sources for information. Less spectral information than sources 1 and 2. I have also found this website to be temperamental on a Mac computer.

4. Prentice Hall Textbook Chapter Web Material (Web Link)


- Advantages: Well labeled diagrams for understanding infrared spectroscopy. Student friendly IR information for common functional groups.

- Disadvantages: Limited to IR only. No other physiochemical or spectrochemical information.

5. Infrared Spectroscopy Information (Web Link)


- Advantages: Gives background information for IR and associated equations. Has examples of different functional groups and the IR information relating to them.

- Disadvantages: Also limited to IR only. Also no other physiochemical or spectrochemical information. Has a ".com" address, unable to be certain about its reliability over time.

(Completed by Bryan Fulmer [bjfulmer])

[Full Marks JCB]

17. List 3 sources for database for biochemistry.
1. Protein Data Bank
This data bank allows the user to access information about the structure of biological macromolecules. This information can be used to analyze and visualize 3D structures of large proteins. The data bank is free of charge and is updated once a week.
2.Kyoto Encyclopedia of Genes and Genomes
The KEGG database consists of four interconnected data sites which provide data on systems information, chemical information, and genomic information. This includes content on reaction pathways, modeling and simulations, and a database dedicated to information on ligands.
3.Entrez
Entrez is a cross-database search system which allows users to access databases at the NCBI. Instead of searching each biochemical database separately, Entrez search a multitude of databases at once. Entrez offers information on structures and sequencing of biological molecules.
(completed by Leah Pandiscia)
[Full Marks JCB]

18. List different sources for crystal structures, and what types of molecules can be found in each.


Free


Worldwide Protein Databank
Provides access to crystal structures of biological macromolecules, such as proteins, nucleic acids, and polysaccharides.
http://www.wwpdb.org/

Open Access Crystallography
Contains a wide variety of crystal structures, from organic and inorganic molecules to metals and alloys. It is maintained by Portland State University, and has built-in capabilities for viewing crystal structures through a Java applet.
http://nanocrystallography.research.pdx.edu/

Nucleic Acid Database
Focused entirely on nucleic acids, this database has been run by Rutgers University since 1992.
http://ndbserver.rutgers.edu/

Commercial


Cambridge Structural Database
A large database of small organic and organometallic molecules.
http://www.ccdc.cam.ac.uk/products/csd/

Inorganic Crystal Structure Database
This is a nearly complete listing of inorganic crystal structures. It contains data from as early as 1913.
http://www.fiz-karlsruhe.de/icsd_content.html

CRYSTMET
This database focuses on metals, alloys, and intermetallic compounds.
http://www.tothcanada.com/databases.htm

(completed by Noah Johnson)
[Full Marks JCB]


19. Find 5 sources for finding IR spectra to characterize chemical compounds (Excepts those spectra sourses which already been posted in 2010 FAQ).


Excepts those spectra sourses which already been posted in 2010 FAQ, I found these sources for IR spectra:
1. FDM Reference Spectra Databases: A database maintained by Fiveash Data Management, Inc.
2. AEDC/EPA spectral database: This database was under the cooperation of the Environmental Protection Agency Office of Air Quality Planning and Standards (EPA/OAQPS) and the US Air Force.
3. David Sullivan FT-IR Library: By David Sullivan. Last updated on 18 April 1998.
4. Ivo Leito's FT-IR spectra of paint and coating materials: This database foucus on conservation and painting-related materials (pigments, binders, fillers, etc).
5. NICODOM databases.

(Completed by Wenjian Du)
[Full Marks JCB]

20. What are some determination methods for use with inductively coupled plasmas (ICPs) and what are 3 companies that sell the machines?

Inductively Coupled Plasmas are plasmas that are created by electric currents. In specific, the alternating current is passed through coils to create time-varying magnetic fields that excite the electrons in the surrounding gas.

There are two standard methods of determination using inductively coupled plasmas. ICP-MS (indictively coupled plasma mass spectrometry) uses the highly-ionized nature of plasmas to as the source of charged particles normally detected by mass spectrometry. ICP-AES (inductively coupled plasma atomic emission spectrometry) or ICP-OES (inductively coupled plasma optical emission spectrometry) uses the same ionized nature of plasmas to excite atoms and ions.

Some companies that sell ICP-mass spectrometers:

Spectro
"A member of the AMETEK Materials Analysis Division, SPECTRO is one of the worldwide leading suppliers of analytical instruments, employing optical emission and X-ray fluorescence spectrometry technology, used for the elemental analysis of materials in industry, research and academia."

Example: http://www.spectro.com/pages/e/p010402tab_overview.htm

Thermo Fisher Scientific
"Think Thermo Scientific for superior analytical instruments, laboratory equipment, software, services, consumables and reagents. Find better workflow solutions spanning sample preparation, sample analysis, and data interpretation."

Example: http://www.thermoscientific.com/ecomm/servlet/productsdetail_11152_L10978_87279_11961724_-1

Perkin Elmer
"At PerkinElmer, we design, manufacture and deliver advanced technology solutions that address the world's most critical health and safety concerns, including maternal and fetal health, clean water and air, and safe food and toys."

Example: http://www.perkinelmer.com/catalog/family/id/NexION


Some companies that sell ICP-atomic emission spectrometers:

Spectro
"A member of the AMETEK Materials Analysis Division, SPECTRO is one of the worldwide leading suppliers of analytical instruments, employing optical emission and X-ray fluorescence spectrometry technology, used for the elemental analysis of materials in industry, research and academia."

Example: http://www.spectro.com/pages/e/p010313_spectroblue_overview.htm

Perkin Elmer
"At PerkinElmer, we design, manufacture and deliver advanced technology solutions that address the world's most critical health and safety concerns, including maternal and fetal health, clean water and air, and safe food and toys."

Example: http://www.perkinelmer.com/Catalog/Family/ID/Optima%208x00%20ICP%20OES%20Spectrometers

Shimadzu
"Contributing to society through science and technology."

Example: http://www.shimadzu.com/an/elemental/icp/icps8100/icps.html

(Completed by Anthony Lloyd II)
[Full Marks JCB]

21. List 5 different sources for learning NMR.

  1. 1. Wake Forest University H NMR Interpretation Tutorial
The site gives a quick overview of Proton Nuclear Magnetic Resonance (H NMR). It explains the basic of integration, chemical shifts, and splitting. It also has an interactive tutorial for predicting spectrums and assigning peaks.
http://www.wfu.edu/~ylwong/chem/nmr/h1/index.html
  1. 2. Spectral Game
The game presents a new spectrum each round and the player is required to select the molecule that matches the spectrum. You can choose the type of spectrum you want either the H NMR or C NMR. The game continues until you get one spectrum wrong.
http://www.spectralgame.com/
  1. 3. Interactive Web-Based Learning Course: NMR Spectroscopy
The site contains a detailed course on NMR. Each of the page is divided into 3 parts:
1. Learning objective- explains what the student should learn from the contents presented
2. Contents- the contents are divided based on different aspects into subtitles. Each subtitle opens in a new page, the new page contains related graphs and animations to help explain the topic.
3. Learning Tasks- Questions related to the topics presented in the contents that the student should be able to answer.
At the end of the course there is a game titled “Millionaire Game”. The game presents a NMR spectra and the player is required to choose the matching compound. The site also contains an interactive problem set in which the student is presented with spectra and they must choose the matching compound.
http://chem.sci.ubu.ac.th/iNMR/index.htm
  1. 4. Video Lecture on NMR
This is a youtube video on NMR. It explains how NRM works and the principals behind it. It also explains how to read the spectra.
http://www.youtube.com/watch?v=fuU0L0yut4o
  1. 5. Online course book on NMR Spectroscopy
This is the site of Professor James Keeler of the University of Cambridge. He posted the chapters he covered for the course online in PDF format. Each of the chapter covers a different topic. They contain illustration and mathematics related to the topic.
http://www-keeler.ch.cam.ac.uk/lectures/Irvine/

(completed by Sharmin Mollah)
[Full Marks JCB]

22. Find a source or database that lists the molecular symmetry operations and point group of a compound.


3DMolSym
3DMolSym is an online program that allows students to view the molecular structure of a wide range of molecules as well as their symmetry operations and point groups. It provides a 3D animation of the symmetry elements for each molecule to aid in visualization. It also allows students to rotate the molecule, zoom in or out and also adjust the display of the molecule to "Ball n' Stick", "Space Filling" etc. Here's an example of a few of the symmetry elements of ammonia being viewed on 3DMolSym:

3DMolSym_(ammonia).png
3DMolSym_(ammonia2).png
Clicking the button next to "Perform Rotation" will show an animation of the molecule rotating 120 degrees


(completed by Valentine Anyiam)
[Full Marks JCB]

23. Find five sources of finding flash points.

Introduction
Flash Points may be found through two main methods; open cup, and closed cup apparatuses. Open cup apparatuses find flash points by placing a sample in an apparatus that is open to the air and while heating it periodically passing a flame over the cup to find the temperature at which the vapors ignite. Closed cup methods use a sample in an apparatus that is not open to the outside environment, and is periodically opened and a flame passes over it while heating to check for the flash point temperature.

Closed Cup
Pensky-Martens Closed Cup 60C-190C
Tag Open-Cup 93C and above (no upper bound specified)
ASTM D3828 Small Scale Closed Cup Tester Setaflash -30C-300C
Open Cup
Cleveland Open Cup 79C-400C
Automated Devices
There has been much work into finding flash through automated devices. Below is a link to a patent of one of the first automated devices to measure flash points of crude oil and oil lube products developed in 1972.
http://www.google.com/patents?id=rOF8AAAAEBAJ&printsec=abstract&zoom=4#v=onepage&q&f=false
[Cannot assign grade without knowing who submitted JCB]
[Missing links to above info and not 5 sources - Partial Marks JCB]

24. List five online sources that incorporate visualization techniques to enhance teaching and learning chemistry.
Visualization is the process of creating mental images that cannot be seen or may not exist

1. The ChemCollective
http://www.chemcollective.org
The ChemCollective began in 2000 wit the Irydrium Projects Virtual Lab. It was recognized in 2003 with MERLOT's classic award in chemistry and editor's choice for exemplary software across all disciplines. Presently, ChemCollective is a project of the National Science Digital Library (NSDL). The site provides engaging interactive activities in several general chemistry topics such as Thermochemistry, Acids Bases, Periodic Table, Chemical Equilibria and Stoichiometry. The activities are separated into four main categories; Virtual Labs, Tutorials, Scenarios and Simulations. There are several interesting and well thought out activities embedded in those categories such as solving a murder mystery, practice problems that are automatically graded and an interactive period table that shows electron arrangement in energy levels. Instructors are invited to submit ideas and or comment on the existing activities on the site.

2. World Index of Molecular Visualization Resources
http://molvis.sdsc.edu/visres/index.html
This site houses an impressive index of world molecular visualization resources for organic and inorganic molecules. There are fourteen categories listed, examples are Biochemical Structure Tutorials with Rotating Interactive Molecular Displays, K-12 Molecular Visualization Tutorials and Molecular Visualization in languages other than English. The K-12 site includes a link to Proteopedia a 3D interactive encyclopedia of proteins, DNA, RNA and other macromolecules. You can submit a resource and comments without a password or account by simply completing a form.

3. Visualization and Problem Solving in General Chemistry
http://www.chem.purdue.edu/gchelp/
This academic site includes models showing the microscopic behavior of ions in the description of a solution, vapor pressure lowering, freezing point depression and boiling point elevation. In addition, if interested in spectroscopy,with the correct plug-ins you can visualize the vibrational modes of small molecules.

4. Demonstration of a Voltaic Cell
http://content.blackgold.ca/ict/Division4/Science/Div.%204/Voltaic%20Cells/Voltaic.htm
A flash applet was created by the Chemical Education Research Group at Iowa State University that shows how a voltaic cell works including the seeing the transfer of electrons from the anode to the cathode as well as the loss of electrons from the metal electrodes. You can choose the metals as well as the ionic solutions in the separate compartments.


5. Jmol: an open-source Java viewer for chemical structures in 3-D
http://jmol.sourceforge.net/
This site demonstrates what Jmol can do for still images. Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry that can be embedded into website, wikis, etc. There is a gallery of screenshots (still images) of small molecules, macromolecules, crystallography, orbitals as well as reactions and vibrations that can be animated by Jmol. You can also see a few of the interactive applet demonstration pages.
(completed by LSnead)
[Full Marks JCB]

25. 3 Sources for Atmospheric chemical data


1. NATChem database - The Nation Atmospheric Chemistry database archives data from greenhouse gaes, precipitation, particulate matter, as well as other analysis. The database is ran by Environmental Canada. All data is from North American contributors. Data is contributed from many networks, but the network is required to have operated for at least two years with a wide area of coverage with regionally represented sites.
http://www.ec.gc.ca/natchem/

2. PMEL Atmospheric Data Server - The Pacific Environmental Laboratory (PMEL) data server is a National Ocean and Atmospheric Administration project that compiles data from many field experiments affliated with with both PMEL and NOAA.The database represents field experiments that took place in various parts of the world. This open data is allowed to be referenced in other material as long as the principal investigator (PI) is given create for the data. If the data is used for a significant portion of material it is recommended tha the PI receive co-authorship.
http://saga.pmel.noaa.gov/data/

3. IUPAC Subcommittee for Gas Kinetic Evaluation - The Gas Kinetic Evaluation contains data for kinetic and photochemical reactions of many gases. Many of the reactions cataloged are contained in atmospheric studies. All data contained is evaluated by memeber of the IUPAS subcommittee, much of the data can also be found in Atmospheric Chemistry and Physics (ACP) journal publications. The reactions found in ACP are summarized in tables on the website. Any data that is found to be different than the publications are noted.
http://www.iupac-kinetic.ch.cam.ac.uk/
(Completed by HClark)
[Full Marks JCB]