Sciencemadness Discussion Board

Guidelines - a call for participation

Nicodem - 13-3-2012 at 09:10

Some of you might have noticed that we are in the process of supplementing the Forum Matters section with guidelines for new and inexperienced members. The guidelines for posting were already done. You can read them and send your suggestions via U2U. They might be occasionally revised, but essentially they are fine as they are now.

What is currently most needed are the guidelines for searching the literature and guidelines for good safety practice. Other guidelines can also be considered.

The moderating crew is already terribly busy with other work, such as real life and other such annoyances. So, here is a call for some volunteering work you could do to contribute with your experiences and skills, to do something for which you will not get paid, not even one cent. Nonetheless, some of you might be smart enough to find some other type of satisfaction in such a participation.

Those interested should reply here with a proposal. This could be a joint effort, so you should address which guidelines you would want to do. You should propose the structure of the text (sections based on all relevant topics, perhaps with some draft content). You can chose to do the whole work or volunteer for specific sections only. The proposals will then be evaluated and I, or some other moderator, will pretend to be an editor delegating work to the most promising authors.

There are some info on the forum in regard to the literature search and safety issues that can be used as a starting point, but I would suggest to do something original and effective for all kind of maturity and experience levels. Bellow are just a couple of hits given by the search engine, but there are many more.

Literature search:
https://www.sciencemadness.org/whisper/viewthread.php?tid=39...
https://www.sciencemadness.org/whisper/viewthread.php?tid=12...

A good starting point in regard to the safety issues is the accidents threads:
https://www.sciencemadness.org/whisper/viewthread.php?tid=13...
http://www.sciencemadness.org/talk/viewthread.php?tid=3698
...and this one: https://www.sciencemadness.org/whisper/viewthread.php?tid=11... ... where I even found this little prophecy by watson.fawkes:
Quote: Originally posted by watson.fawkes  
Quote:
Originally posted by Nicodem
Scaling up is the science behind chemical technology.
You know, this would make a great little four-page introductory document for beginners, as part of an advocacy to start with microscale experiments.

@Nicodem: Not that I'm advocating <i>you</i> write it, but it comes up often enough that a referable document would be a boon.


We have several members well skilled in searching the literature and finding ways to obtain articles. I hope some of them are interested in sharing their knowledge. These guidelines are allowed to contain some general suggestions on how to bypass corporative obstacles and use pirated material, but should not encourage such behavior (it should be taken that it is a totally personal responsibility on when it is ethical to step over the law in the name of science and education).

I know also that there are several members who have enough experience with practical work to recognize the issues that beginners face in regard to safety. Please take some time to participate.

zoombafu - 13-3-2012 at 13:53

I would be interested in writing up a safety post. Ill start working on one for general lab safety. Also I think it would help if some of the threads in the forum matters section were un-stickyed or combined. It is somewhat messy looking, and I think newbies would be more likely to read through things if there was less clutter. For example the two public advisory posts could be condensed in with the guidelines for posting. The welcome section could be un-stickyed as well, as It really isn't used by many people. Just my opinion though.

Nicodem - 17-3-2012 at 02:39

Quote: Originally posted by zoombafu  
I would be interested in writing up a safety post. Ill start working on one for general lab safety.

Thank you. Please send a proposal on its structure, so that suggestions can be offered before you start.
Quote:
Also I think it would help if some of the threads in the forum matters section were un-stickyed or combined. It is somewhat messy looking, and I think newbies would be more likely to read through things if there was less clutter. For example the two public advisory posts could be condensed in with the guidelines for posting. The welcome section could be un-stickyed as well, as It really isn't used by many people.

Once we will have all the reading material for new members finished it will indeed be best to combine it into a more organized form, but for now let's see what we can get.

Anybody interested in doing the literature searching guidelines?

Nicodem - 14-4-2012 at 03:08

Please help me completing the literature searching guidelines by suggesting additions and corrections to the draft bellow. It desperately needs additions from inorganic and material science chemistry viewpoint. I'm an organic chemist by profession, so the draft is heavily biased in that direction. This is why it needs contributions from other people. Polverone just gave an excellent contribution, which can give you an idea on what kind of additions are expected. Proof reading suggestions from native English speakers are also welcome. Please suggest also URL's for keywords to be linked to. As you see there is much to be added to this draft, so you have plenty of space for suggestions.

---------------------------------

1. General aspects

All the known information in regard to synthetic procedures, chemical properties and chemical science, as well as literature reviews and scientific discussions, can generally be found in the literature. Pointers to such literature are called references and are the very essential elements of the scientific method.

Literature can be a very wide concept (essentially everything that was ever written is considered “literature”). Its most important distinction is into categories called primary literature, secondary literature and tertiary literature.

Primary literature is where the researchers originally published their findings, most commonly in the form of reports, scientific articles (full paper, communication or letter type), disclosures in patent applications, or eventually as posts in this or some other forum. Primary literature contains, as the minimum, the description of the experiments performed, the results, and the conclusions drawn. Typically, a full paper type of an article contains the detailed description of the experimental work and all the analytical data, while a communication or a letter type of an article does not necessarily contains such detailed information.

Secondary literature is most commonly presented in the form a of review of the primary literature in regard to a specific topic. It does not necessarily contains detailed data. However, it is very valuable because secondary literature contains organized collections of references to primary literature, often with an expert commentary and hypotheses that might be worth considering, if doing related research.

The tertiary literature is usually in the form of a large volume of information organized as a book, an encyclopedia, a dictionary, or some similar form. These usually offer only superficial reviews of the topics, illustrated with exemplary or selected cases, often just the enough needed to provide support to the established theory. They commonly contain references to secondary and primary literature, though textbooks often don't. Tertiary literature should always be verified by checking its references before the information they present can be considered reliable. Textbooks, and other literature for educational only purposes, are also considered tertiary literature, though it should always be kept in mind that they do not necessarily contain reliable and referenced information. The aim of textbooks is to teach concepts. Due to this they are allowed to contain misinformation and fabricated data (from the scientific perspective) as long as they are considered correct (from the educational perspective).

Another distinction that is commonly used is between scientific literature and patent literature.

The scientific literature is written in accordance to the scientific method, should be peer reviewed by definition, and is generally published in scientific journals. The most common format is a scientific article which must have references to other scientific articles. Articles typically first present the topic of the research with a short review, followed by the hypothesis, the discussion of the experimental work and the results obtained. They often present also the detailed experimental and analytical data, and end with the conclusions which resumes the article's main contribution to science. Scientific literature can generally be found in the scientific libraries (such as university libraries or research institution's libraries). Nowadays, and if you have access, most of it can be obtained from the publisher's Internet sites in the electronic PDF formats. Some journals give free access, but most are held by publishing corporations that require paid institutional access (usually via IP address recognition) or on a pay-per-view basis.

The patent literature is written in the form of a patent application. This is a legal document with which the applicants request the governments for concessions on exclusive commercial uses of the disclosed invention. When eventually granted by the national patent examiners, these applications become patents. Patents are thus a trade between the private enterprises and the public, with which the applicants offer the disclosure of the invention to the public and in exchange receive legal protection against competitors for the period of up to 20 years. The disclosures of the invention that the patent applications contain, can often represent a valuable scientific contribution even though this is not their primary goal. Patent applications became public 18 months from the filling date and can be obtained trough numerous national patent offices or certain international patent cooperations. Patent documents are referred by a two-letter country code, the succession number, a letter (A or B), and a single number (for example: US20070043072A1). The letter and number A1 at the end signifies the document is the first version of a patent application, while B1 would signify the document is already a patent. For informational purposes, this document statuses are usually not relevant.



2. Searching for references or information


2.1. Reference databases

Chemists have long since recognized the need for reference databases that would allow for searching the references by topics, keywords, properties, structures or reactions. There are several such databases available for the researchers.

The German scientists in the 19th century started the Beilstein database, which is a database that abstracts a lot of factual information from the scientific literature, in particular physical and chemical properties of compounds. It also abstracts the published structures and reactions, and allows thorough (sub)structural searches. It abstracts chemistry, pharmacology and material science journals. Beilstein was originally a paper volumes based database, but is available electronically as CrossFire Beilstein for many years already. It can be used for searching all kind of topics, but its structural search capabilities are particularly suitable for organic chemistry.

A related database focused on inorganic chemistry is Gmelin. It is essentially an enormous paper volumes index. Nowadays, Beilstein and Gmelin have been combined into the electronic database Reaxys.

A very important database which only started at the beginning of the 20th century by the American Chemical Society is the Chemical Abstracts. This is best known for its valuable abstracts, which are authoritative alternative references to the articles written in languages you do not understand or are published in obscure journals you can not obtain. It is also known for its CAS system of attributing numbers to any new published compound or chemical material. It is extremely efficient when it comes to searching by keywords and structures. The quality of the abstracted structures and reactions is very good, but the abstracted chemical properties, especially from the older literature, fades in comparison to Beilstein. Chemical Abstracts is electronically available under the title SciFinder. Until this year, SciFinder was available as a Citrix application, but unfortunately this was discontinued and a less practical web based interface is now offered as the sole option.

The most widely used science bibliography database is ISI web of knowledge which can also be used for finding references by searching for authors, topics and keywords. It allows easy navigation through citation maps, which can be of use in finding related articles. Unfortunately, it requires institutional access through IP recognition.

The joint cooperation of the East German and Soviet chemists yielded the SPRESI database, which was maintained up to the year 1989. It can often surprise you by giving you references that other databases missed, but is of little use for the very old and the most recent literature. It is currently commercialized by a German company as a web based application that allows topic and structural searches (a free trial period is available). A pirated riped version in the form of a ChemFinder database file was also made available a couple of years ago.

Google Scholar is one of the best keyword based search engines that uses the archives of all scientific publishers who provide digital versions of articles as its reference database. The publishers allow Google to index also articles that have otherwise limited access, so that searching for keywords works also for phrases that are not present in the abstract. Its advantage is to directly point to the original location of the abstract and the full paper. Its disadvantage is its limitation to the keyword search and the limitation to electronic documents only. Since most journals have now digitized their pre-computer archives, this limitation has grown less serious over time. A final advantage is that Google Scholar will give links to complete free copies of articles if Google finds a free copy of the article anywhere, even if the original was published in a closed-access journal.

Google Patents can perform keyword searches of the United States of America patents (patents with the US prefix). The search engine is quite unique in that it can search the body text of the patent documents, but its huge limitation is in that it is limited to only this one country's patents. Luckily, most companies commonly nationalize their patents also in the USA. This means that a large proportion of all the patents have their US equivalent which can thus be searched through Google Patents.

Two interesting new reference database projects are ChemSpider and ChemSynthesis by the Royal Society of Chemistry (RSC). It is becoming a very useful free resource for organic synthesis and is supposed to contain 25 milion structures abstracted from 400 sources. The only little drawback is in that ChemSpider is focused on commercial vendors. It appears that for now, these prevail over the information abstracted from the scientific literature (a lot of entries don't have any references to articles). Still, it is a database very rich in information and is also able to provide references to the patent literature. Additionally, ChemSynthesis does a good job at abstracting chemical reactions from a dozen of major organic chemistry journals.

A free database that offers several searching and metasearching features on organic and inorganic compounds is ChemIDplus. It lists physical, chemical and toxicological properties, but is poor in chemical references.

Another free web based resource is the WebReactions database. It allows searching organic reactions by a structural search.

A very good database focused on pharmacology and medicinal chemistry is PubMed. It incorporates the Medline database and information from other sources. It offers a keyword and structural search. It also gives abstracts together with the references and direct links to the articles on the publisher site.

A good reference database for biosynthetic topics is BRENDA. It allows searching for references about enzymes, biosynthetic reactions, taxonomic information and protein affinity data.

The Merck index is meant to be a small, single book, reference database for quick laboratory use (a digital version is also available). It is indeed practical, but limited to only about 10,000 short monographs on common organic and inorganic compounds. Each monograph contains the essential referenced data on a specific compound (chemical properties, preparation, toxicology and other topics). The index also contains 450 micro-reviews on name reactions.

A good reference database for searching toxicology information is TOXNET. It performs a metasearch trough several toxicology databases.


2.2. Measurement repositories and factual databases

The Protein Data Bank (PDB) is an excellent database for searching protein biochemical references. It is also a repository for X-ray diffraction (XRD) derived protein structures which can be downloaded.

The Cambridge Structural Database (CSD) is a reference database and a repository for structures determined by single crystal XRD, as well as for data obtained from powder XRD and neutron diffraction. The related database for inorganic compounds is the Inorganic Crystal Structure Database (ICSD). The Powder Diffraction File (PDF) is a repository for powder XRD data. All of these can also be used as reference databases.

The Spectral Database for Organic Compounds, SDBS has become the best repository of NMR, IR, MS and other spectral data. It covers the spectroscopic data of a huge collection of organic compounds and offers a variety of search options.

Cheméo offers free access to high quality thermodynamic and other physical properties collected from (and referenced back to) heterogeneous collections of fundamental data compiled by various public-funded efforts such as the National Institute of Standards and Technology, International Uniform Chemical Information Database, and Korea Thermophysical Properties Data Bank. It allows search by properties, molecular descriptors, and names. Molecular structures can be saved as 2D mole files and properties can be saved as spreadsheets.

Williams' pKa data compilation is a list of mostly aqueous pKa values for most common acids and bases. Evan's pKa table is a shorter list of aqueous and DMSO pKa values. Bordwell pKa Table is a larger compilation of acidities in DMSO.

Handymath Calculators is a site with calculators and density charts for a wide variety of subjects. FACT Phase Diagram Database is a collection of specialized factual databases like phase diagrams for alloys, salt mixtures and related technical data. Azeotrope Databank gives compositions of many binary azeotropes (Horsley's review in Anal. Chem. 1947, 19, 508–600 is otherwise a classic for azeotrope data).

The Lange's Handbook of Chemistry (several editions, printed & web) and the CRC Handbook of Chemistry and Physics (several editions, printed, web & e-book) are the classical works where to search for the factual data about compounds, materials and mixtures.

The International Union of Basic and Clinical Pharmacology (IUPHAR) offers a free database of molecular affinity measurements to proteins (ligand/receptor interactions) that is additionally useful also as a reference database for pharmacology and biochemistry. Its focus is mainly on the neuronal and hormonal receptors and ion channels, while the data for enzymes is poorly represented. The Binding Database is a better place for searching affinities on enzymes.

Factual data, such as physical and chemical properties of compounds, or their spectroscopic data can often easily be obtained from the vendor catalogs. These are rarely referenced, so their reliability can be questionable, but experience shows vendors usually provide accurate data nevertheless. All the major chemical vendors have their catalogs freely available on their web sites, equipped with a keyword or structural searching tool. In particular, the Sigma-Aldrich catalog provides spectroscopic data along other information for most of their products (e.g., physical properties, NMR, IR). Available are also numerous metasearch engines that provide combined search results for most vendors (ChemExper, eMolecules, etc.).

A list of chemical databases and catalog metasearch engines can be found at WWW Chemistryguide. This site lists several other useful resources as well.


2.3. Literature reviews

Science of Synthesis (ex Houben-Weyl) is an excellent collection of concise organic synthesis reviews, easy to search or browse trough the hierarchically organized topics.

Organic Chemistry Portal is the best known organic chemistry Internet portal. It has a wealth of referenced information. Another good collection of links and tutorials for organic chemistry is Organic Chemical Resources Wordwide.

e-EROS Encyclopedia of Reagents for Organic Synthesis (printed, web & e-application) is a large collection of reviews on 4000 reagents. It is very useful if you have a reagent and want to know what it can be used for.

A Comprehensive Treatise on Inorganic and Theoretical Chemistry (Mellor, 1922-1937) is a very old but extremely thorough series of volumes reviewing the inorganic chemistry of its time. It is available in full from the Sciencemadness library.

An extensive collection of reviews on various aspects of organometalic and coordination chemistry is the Encyclopedia of inorganic chemistry. This has been recently merged with another reference work to form the Encyclopedia of Inorganic and Bioinorganic Chemistry.

Name reactions reviews are useful when you get the feeling of being lost among the hundreds names of top chemists. The Name Reactions section at the Organic chemistry portal or the similar Merck index Name Reactions chapter are two good starting points. Strategic applications of named reactions in organic synthesis (Kürti & Czakó, 2005, printed & e-book) is very practical book where two pages are dedicated to every named reaction, giving its scope, limitations, and mechanism. Provides plenty of references to further reviews, seminal papers and exemplary uses. The book Organic synthesis based on name reactions and unnamed reactions (Hassner&Stumer, 1994) lists even the most obscure reactions (available as e-book). Other available books are Named Organic Reactions (Laue&Plagens, 2005) and Name Reactions: A Collection of Detailed Reaction Mechanisms (Li, 2006).

March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure (several editions, Smith&March; book, printed & e-book) is the legendary review of organic chemistry mechanism studies.

If the material you are interested in is commercially significant, a good first stop is the Kirk-Othmer Encyclopedia of Chemical Technology (printed, web and CD) or Ullmann's Encyclopedia of Industrial Chemistry (printed, web and CD). These sources will give technological overviews plus citing the most important patents (and sometimes papers) relating to industrial practice. Then you want to find those papers and patents; patents are convenient because they are available at no charge. The RÖMPP Encyclopedia (printed, web and CD) is a huge reference work in German with topics focused in applied chemistry and process technology. A good older source is Thorpe's Dictionary of Applied Chemistry. There were 4 editions, the last finished in the 1940s, and the earlier editions are available from Google Books and other digital book collections.

Synthetic Organic Chemistry (Wagner&Zook, 1953; book, printed & e-book) is an early single-volume review of organic syntheses organized by functional group formations. It is limited to the relatively basic classical reactions, therefore suitable for the beginners and amateurs.

Many books in the Sciencemadness library can be used as reference works.

Review series are extremely useful reference works with the ambition of covering entire research fields. These come in a multi-volume format, with the volumes commonly published over several years. Here is a list of those series that are available digitally (or at least partially):
ACS Advances in Chemistry; ACS Symposium Series; Advances in heterocyclic chemistry; Advances in Organometallic Chemistry; Aliphatic, Alicyclic and Saturated Heterocyclic Chemistry; Chemistry of Heterocyclic Compounds; Comprehensive Heterocyclic Chemistry (I, II & III); Comprehensive Medicinal Chemistry (I & II); Comprehensive Organic Functional Group Transformations (I & II); Comprehensive organic synthesis; Fieser's Reagents for Organic Synthesis; General and Synthetic Methods; Organic reactions (the first 5 volumes are available in full from the Sciencemadness library); Organic Reaction Mechanisms; Organometallic chemistry; Organophosphorus chemistry; Rodd's Chemistry of Carbon Compounds; The Alkaloids; Topics in Catalysis; Topics in Current Chemistry; Topics in Heterocyclic Chemistry; Topics in Stereochemistry.

Most journals publish review articles besides scientific reports, but some journals are specialized in publishing only literature reviews: Accounts of Chemical Research, Chemical reviews, Chemical Society Reviews, Coordination Chemistry Reviews, Natural Product Reports, Quarterly Reviews of the Chemical Society, Russian Chemical Reviews, and many others.

The Thieme publishing company provides a free bibliographic database Synthesis Reviews that can be consulted when searching for review articles.


2.4. Practical chemistry and laboratory manuals:

Organic syntheses (series, printed & web) is the legendary collection of independently checked organic synthetic procedures. Each synthesis of a compound features also a review of the previously published syntheses. The similar Inorganic syntheses (series, printed & e-book) are checked inorganic synthetic procedures for useful inorganic or organometallic compounds.

Handbook of Preparative Inorganic Chemistry (several editions, Brauer, printed & e-book) is a collection of inorganic syntheses complete with references. A similar work is Inorganic laboratory preparations (Schlessinger, 1962). The Vogel's Textbook of Practical Organic Chemistry (several editions, Vogel et al.; book, printed & e-book) is the legendary organic synthesis laboratory manual. It is also very useful for getting acquainted with the common laboratory techniques and apparatus setups. Organikum (several editions, Schwetlick, book, printed & e-book) is an excellent organic synthesis manual, very popular among the European organic chemists. Unfortunately, most editions are available only in German language, but check the libraries for translations in your native language.

The Synthetic Organic Chemist’s Companion (Pirrung, 2007) is an excellent book to learn sophisticated organic synthesis techniques.

Synthetic Pages is a web based compilation of experimental procedures with the focus on experimental details that are usually not mentioned in the literature examples. For these reasons, the procedures are suitable also for less experienced chemists.



3. Practical aspects


3.1. Searching for references

Searching the scientific literature is hard work and can take from hours to days to achieve the review of even one narrow topic. Prepare to invest a serious effort into such an endeavor and don't give up before you have used all the relevant resources. Some of the reference databases are freely available even without any institutional access. For the others, remember that there are scientific libraries that offer access and have skilled librarians who can offer you assistance. In fact, not only is it important to try out as much reference databases as possibly, it is also important to learn some essential searching skills. Choosing the right keywords and drawing the right structures with the right specifications is extremely important. If you don't have the skills and intuition on what are the proper keywords to use, the search output can either consist of no useful reference at all, or of an overwhelming list of references requiring a lot of time to review. Therefore, you need to either learn better the terminology in regard to the researched topic or try as much options as humanly possible.

Do not rely solely on reference databases. Make good use of the secondary literature and check for reviews on the research topic. Review articles, books and series exist on nearly any imaginable topic, so it is unlikely that nothing was written on what you are interested in. Review articles can also be found by checking scientific articles on related topics, as these commonly point to some authoritative review. Even if the articles you find during your literature search are not exactly what you look for, make sure you check their list of references, because some might be just what you look for, or can further point you in the right direction.


3.2. Locating and accessing articles

Finding the publisher's Internet site and locating the journal is generally as easy as using the journal title as the keyword in an Internet search engine. Most still active scientific journals already have an Internet based access to articles as PDF files. A database of scientific journals like Genamics JournalSeek can also be useful to check the status of a journal. Some journals will require a visit to a real library. Keep in mind that even when your nearest library does not have the journal you look for, they can easily order articles using the interlibrary loans. Alternatively, you can e-mail the authors requesting them a copy of the article. Most will be happy to oblige.

Most scientific journals are published by private corporations and are thus obviously not freely accessible. However, journals that are published by chemical associations, often have a free access policy to the articles as PDF files (check the list of freely accessible journals).

Scientific journals are commonly abbreviated to keep the citations short. Many lists of journal abbreviations exists, but the Chemical Abstracts abbreviations are now considered to be the norm.

The newest format of citations is the use of Digital Object Identifier (DOI) codes. Essentially, the whole citation is reduced to an alphanumerical code (for example, DOI: 10.1016/j.jhazmat.2012.01.085). The DOI web site stores the location of a digital version of the article in its database. The advantage of such a citation format is in that the actual location of the digital object (usually an article) is very easily found, for example by using the the "dx.doi.org/DOI" format of URL (where "DOI" is the alphanumerical code, an example of such an URL: dx.doi.org/10.1016/j.jhazmat.2012.01.085)


3.3. Accessing patents and patent applications

Patents and patent applications need to be available to the public due to their particular legal status. Nowadays, this accessibility is easily ensured by the Internet. In fact, most if not all countries have their own patent office Internet site where they facilitate the accessibility of the patent documentation. These sites can be easily found via search engines by using the country name and “patent office” as keywords. A few international intellectual property organizations provide a centralized access to worldwide national patents or patent applications examined trough the patent cooperation treaty (PCT). These sites are generally the best single location where you can download patent documents as PDF: Espacenet or Wipo. Both sites also offer a keyword based search engine.


3.4. Obtaining copyrighted material illegally

A large portion of all chemical scientific literature has been pirated. Entire volumes of scientific journals, series and thousands of e-books are available to those who don't have constraints in using them. In fact, most of the above mentioned reference works or books are available also illegally. Additionally, institutional access to publisher's sites can be compromised from the passwords obtained in hyperspace. It is not the policy of this forum to encourage breaking of any law, but it is obvious that the copyright law can be in conflict with certain ethical aspects regarding the intellectual and educational needs of the people. It is thus solely to your discretion to decide whether to use pirated material, or not.


3.5. Public digital libraries

The Sciencemadness Library is a modest collection of some very useful books. The focus is on laboratory chemistry and older works that are more engaging and relevant for chemists who do not have access to modern analytical instruments. New users often overlook the site library, perhaps because they discovered the forum through a search engine and don't know there is more. These books are generally 40+ years old and provide convenient references to older primary literature.

Google Books is an effort to digitize the contents of many libraries and make the material easy to search (and sometimes easy to view) online. The partner libraries are mostly academic and they have a good selection of books and journals. Older materials that are definitely out of copyright are freely visible to users, and available for download to some users. With the publisher's permission, some newer books can be (at least partially) read through Google Books though they cannot be downloaded. Google Books appears to use IP address geolocation to impose stricter visibility and download constraints on users outside the United States. It may be significantly more useful to non-US visitors who use an Internet proxy with a US endpoint.

The Hathitrust is an effort between partner libraries to provide a permanent repository for works digitized through the Google Books program and other digitization programs. The Hathitrust is more aggressive about making public domain materials available, so if you find a work on Google Books that seems like it should be free but isn't, try checking Hathitrust. Hathitrust also uses IP address geolocation to limit access, so get yourself a proxy. Hathitrust does not offer a convenient way to download complete copies of public domain works, but HathiHelper is a tool that can do that job.

The Archive.org is engaged in their own digitization effort of public domain works. Additionally, many public domain texts originally scanned by Google have been cross-shared to archive.org. Everything on archive.org is available for download in full, and they do not impose any geolocation restrictions. You can use their internal search tool or find relevant texts with "search terms site:archive.org" on Google.

The Bibliothèque nationale de France, Gallica is an especially rich resource if you can read French, but it also hosts a fair number of English-language works. It offers search of titles, authors, and abstracts but not full text search. It is a superior resource if you already know the book or journal you want to look at but can't find it from other sources. Gallica hosts some materials that have either not been scanned or not displayed to the public in full on other sites. It does not appear to use geolocation restrictions.

The Digital Library of India (also at http://202.41.82.144) does not have good search tools. There are many data entry errors in author names and book titles. The site is often slow. The reason I still recommend it is that Indian copyright restrictions are more relaxed than those you will find elsewhere, and DLI does not use geolocation restrictions. It hosts many English-language works from those shadowy years between the 1920s and 1990s, where material is not out of copyright in the West but often is not for sale either.







Edit 1: Thanks to turd for his suggestions, which are now included. Anybody else?

Edit 2: Added the pKa compilations, e-EROS, azeotropes, Lange, CRC and a couple of biochem/pharma databases.

Edit 3: Added a list of review series and journals. Expanded some topics.

Edit 4: Merged with Polverone's material.

[Edited on 4-14-2012 by Polverone]

[Edited on 19/4/2012 by Nicodem]

[Edited on 21/4/2012 by Nicodem]

froot - 14-4-2012 at 09:08

Slightly off the discussion here but it would be good to have guidelines for chemical disposal for home experimenters.

Edit, I would be happy to oblige but my efforts would basically be a regurgitation of what I find on the net. If that's sufficient for now let me know.

[Edited on 14-4-2012 by froot]

Polverone - 14-4-2012 at 13:21

I have edited your excellent material in place, Nicodem. I added the Cheméo database, hyperlinked some of the books that are available in our own Sciencemadness library, and made some minor textual revisions.

Nicodem - 21-4-2012 at 03:53

I made several additions to the above draft. I would like to thank those couple members that helped and ask again for a final review.

Polverone - 21-4-2012 at 12:50

Very nice, Nicodem. I have nothing to add to the above. Since you have merged it with my earlier contribution, I think I will retire my post in the sticky thread once this one has been added.

Nicodem - 22-4-2012 at 05:22

I moved the guidelines to the old thread that is now renamed into "The ScienceMadness Guidelines" and saved your reply there as a quote bellow for the record.
Now, for the next goal, somebody could write the safety guidelines? Perhaps something more general like "experimental work guidelines" would be even better? I noticed many members are pretty much clueless on how experiments are to be performed. I'm not talking only about basic skills like stoichiometry and laboratory techniques. I bet many don't even know how to keep a laboratory notebook, how to evaluate results (analysis and reaction monitoring), or what reaction scale the preliminary experiments are generally run. With all the teenagers on board, some such information should be made available...
Quote: Originally posted by Polverone  
The following was asked in another thread, but the answer has broad relevance:

Quote: Originally posted by GreenD  
How can you find older references on making simple molecules. If you google it, you usually get the most cutting edge/specifically made materials.

I was looking for poly lactic-acid / glycolide hydrogels, but everything is so specific!

How do you guys find the "original" papers?


If the material you are interested in is commercially significant, a good first stop is The Kirk-Othmer Encyclopedia of Chemical Technology* or Ullmann's Encyclopedia of Industrial Chemistry*. These sources will give technological overviews plus citing the most important patents (and sometimes papers) relating to industrial practice. Then you want to find those papers and patents; patents are convenient because they are available at no charge.

Google has a nice patent search tool, but only for US patents: http://www.google.com/patents
Espacenet does not have such good search or interface, but it covers many more nations: http://www.epo.org/searching/free/espacenet.html

If you are interested in an industrial product too new, old, or minor to rate an entry in the industrial encyclopedias, you can start by searching patents directly. If you want to find a material's early origins, sort search results by date, oldest first. Patents may cite other patents, books, or papers relevant to your search.

Your hydrogel example is fairly modern, but the amateur chemist is often interested on now-obsolete chemical technologies, because many of these technologies are more suited to a home lab than the hot, pressurized, catalytic methods that are now most economical on an industrial scale. You can try to search older editions of Kirk-Othmer and Ullmann's, but they are likely to be available in paper at the library only. A good older source is Thorpe's Dictionary of Applied Chemistry. There were 4 editions, the last finished in the 1940s, and the earlier editions are available from Google Books and other digital book collections.

The Sciencemadness Library: http://library.sciencemadness.org/library/
This is a modest collection of some very useful books. The focus is on laboratory chemistry and older works that are more engaging and relevant for chemists who do not have access to modern analytical instruments. New users often overlook the site library, perhaps because they discovered the forum through a search engine and don't know there is more. These books are generally 40+ years old and provide convenient references to older primary literature.

Google Books: http://books.google.com

Google Books is an effort to digitize the contents of many libraries and make the material easy to search (and sometimes easy to view) online. The partner libraries are mostly academic and they have a good selection of books and journals. Older materials that are definitely out of copyright are freely visible to users, and available for download to some users. With the publisher's permission, some newer books can be (at least partially) read through Google Books though they cannot be downloaded. Google Books appears to use IP address geolocation to impose stricter visibility and download constraints on users outside the United States. It may be significantly more useful to non-US visitors who use an Internet proxy with a US endpoint.

Hathitrust: http://www.hathitrust.org/

Hathitrust is an effort between partner libraries to provide a permanent repository for works digitized through the Google Books program and other digitization programs. The Hathitrust is more aggressive about making public domain materials available, so if you find a work on Google Books that seems like it should be free but isn't, try checking Hathitrust. Hathitrust also uses IP address geolocation to limit access, so get yourself a proxy. Hathitrust does not offer a convenient way to download complete copies of public domain works, but I have written a tool to do that job: http://library.sciencemadness.org/library/hathi/

Archive.org: http://archive.org/details/texts

Archive.org is engaged in their own digitization effort of public domain works. Additionally, many public domain texts originally scanned by Google have been cross-shared to archive.org. Everything on archive.org is available for download in full, and they do not impose any geolocation restrictions. You can use their internal search tool or find relevant texts with "search terms site:archive.org" on Google.

Bibliothèque nationale de France, Gallica: http://gallica.bnf.fr/?&lang=EN

The BNF is an especially rich resource if you can read French, but it also hosts a fair number of English-language works. It offers search of titles, authors, and abstracts but not full text search. It is a superior resource if you already know the book or journal you want to look at but can't find it from other sources. Gallica hosts some materials that have either not been scanned or not displayed to the public in full on other sites. It does not appear to use geolocation restrictions.

Digital Library of India: http://www.dli.ernet.in/ or http://202.41.82.144/

The Digital Library of India does not have good search tools. There are many data entry errors in author names and book titles. The site is often slow. The reason I still recommend it is that Indian copyright restrictions are more relaxed than those you will find elsewhere, and DLI does not use geolocation restrictions. It hosts many English-language works from those shadowy years between the 1920s and 1990s, where material is not out of copyright in the West but often is not for sale either. DLI is where I obtained the otherwise-unavailable book Autoclaves and High Pressure Work and where I filled in the missing volumes of JW Mellor's Comprehensive Treatise on Inorganic and Theoretical Chemistry.

*Expensive, but free copies available via the usual peer to peer and one-click file host methods.

DDTea - 24-4-2012 at 08:52

Can we separate the Literature Search guidelines from the general community posting guidelines?

I ask because the Literature Search guidelines was one of the best introductions to the organic chemistry literature that I've seen. It would be convenient to have a stand-alone topic/thread to refer people to. In fact, I can think of a few professors and TA's that would love to show that to their students.

Magpie - 24-4-2012 at 09:29

Quote: Originally posted by froot  
Slightly off the discussion here but it would be good to have guidelines for chemical disposal for home experimenters.


I agree. I have often wondered how we could best do this. Although most jurisdictions (federal, state, & local) have laws regarding waste disposal I don't think that a regurgitation of these laws is what's needed. For one thing they likely differ widely from place to place. More importantly, who could afford to follow them to the letter? It seems that most of the posters here can barely afford basic labware and chemicals, let alone afford to be sending their waste off site to licensed waste disposal companies.

So, if we take the approach that we will recommend some disposal methods that will help protect the environment then perhaps that is the best that we can do.

I would like to know what others think about this subject. One concern I have is: By publishing these recommendations are we (the forum or authors) in any way liable for unlawful conduct in the eyes of the authorities (EPA, etc)? For this reason I have always regarded this a touchy subject.

Nicodem - 24-4-2012 at 11:15

Quote: Originally posted by DDTea  
Can we separate the Literature Search guidelines from the general community posting guidelines?

I ask because the Literature Search guidelines was one of the best introductions to the organic chemistry literature that I've seen. It would be convenient to have a stand-alone topic/thread to refer people to. In fact, I can think of a few professors and TA's that would love to show that to their students.

I already did change the tittle of that thread to something as general as "The ScienceMadness Guidelines" so that the location is appropriate. The ambition is to have all the guidelines in one location for the new member to read them all.

You can refer people to it by using the URL of the post:

https://www.sciencemadness.org/whisper/viewthread.php?tid=19...

or

http://www.sciencemadness.org/talk/viewthread.php?tid=19143&...

I'm glad you found the guidelines so useful.