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Author: Subject: The ScienceMadness Guidelines
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[*] posted on 6-3-2012 at 09:04
The ScienceMadness Guidelines

Guidelines for posting on the ScienceMadness forum
… or things you should know before you start posting

1. Amateurism and science

ScienceMadness (SM) is a forum dedicated to amateur scientists with the focus on chemistry. Amateur scientists are those whose interests originate from the love, admiration of, and devotion to science. In this context, the skills, knowledge and resources are not important. What is most important is that you show respect to the scientific method. The scientific method is much more precious than any collection of facts, because humanity can always rebuild knowledge from scratch in a couple of centuries, but it took millennia to develop the scientific method needed to do so. Unfortunately, the scientific method is rarely taught in schools and it takes years of self-discipline and devotion to learn it. If you are not yet a practitioner of this method, the best you can do to constructively participate in the discussions, is to follow these guidelines the best you can. The rest will follow.

On the other extreme, being a professional scientist and a paid researcher does not mean that you can not have honest amateur interests and participate in the discussions. However, in such case avoid abusing SM for solving problems related to your job, problems which you are paid to resolve. You can take it as a noble cause to teach what you learned to others who are in need of such knowledge and your efforts will be much appreciated.

Take notice that discussions motivated by commercial interest and greed have no place on an forum for amateurs.

2. Responsible conduct

Consider that the SM membership is composed of all kind of people, representing a whole spectrum of skills, knowledge, experience and maturity. What you post should therefore be written responsibly, comprehensibly and with regard to good safety practice. Always consider the worst case scenario, that young people with little experience, poor skills and irresponsible tendencies take poorly thought advice, assumptions, or misinterpretations seriously. Therefore, try to make a clear distinction between your assumptions and what is fact. Critically consider the reliability of your references or presented experimental data. This is especially important whenever you are posting information that can potentially lead to injuries and harm to someone who would take it for a fact or misinterpret it.

3. Get acculturated

SM has its own history and a culture that comes with it. Pay attention to the unwritten rules and customs that make the communication easier and have the cohesive function for the forum community. Don't act blindly and destructively. Also, try to leave your own personal baggage behind when you partake the forum discussions. Do not bring in your local culture from your real-life communities into the discussions unless you have reasonable expectations that it can enrich the forum culture. In any case, political discussions from real-life communities have no place on the forum unless they affect the policies in regard to amateur science. Similarly, religious and philosophical discussions are generally inappropriate for a scientific forum.

4. Choose the right place

When you plan to open a new thread, first take some time to consider what forum section the topic and the discourse you will be using belongs to. Nobody will be pleased if you misplace a question about some apparatus acquisition in the "Chemistry in General" forum section, or an inorganic chemistry topic in the "Organic Chemistry" forum section. Sometimes the topic may fit equally well in more than one section, but in such cases you are more likely to be forgiven for your arbitrary choice. The topic is not always the determining factor. Sometimes the discourse you intend to use will determine the right placement. Scientific discourse using accepted scientific terminology is obviously the most desirable, but it is understood that not all are equally versed in it. The "Beginnings" section is the right place for those who are not yet fluent in scientific terminology and prefer an instruction-focused discourse that does not assume implicit knowledge of basic concepts.

5. Hypotheses

Conclusions can only be as valid as the evidence that they are based upon. Do not draw impulsive conclusions based on inappropriate experimental data. For example, if you don't have proper analytical data, do not make improper claims in regard to the experimental results or products identity. Reasonable assumptions can always be made, but make sure that such assumptions leave space to further inquiry on their validity. Do not make deductions by analogy unless you have reasonable argumentation in the form of references or experimental data. It is easy to make faulty deductions on the basis of insufficient evidence coupled with confirmation bias.

6. The use of references

Do not open new topics without providing all the necessary references for whatever you are describing or posing as a fact. Keep in mind that a topic without a single reference to the relevant primary literature, or to sources of your claims, is effectively worthless as it provides no starting point and no reading material for a constructive discussion. It is not expected, though it would be desirable, that you perform a complete literature review on the pertaining topic, but a minimum must be set. Have you ever seen a scientific article without references? Most likely no and for a good reason - an article without references is not a scientific article. SM is a science forum and it can only remain such as long as the members use references. The need for references generally correlates with the obscurity of the claim, but too much references is always better than too little. In any case, do not use phrases of the type “I have read...” or “I have heard...” without providing the source.

The choice of references format is not that important, but enough data must be provided to easily locate the articles or other sources. Wikipedia is not a reliable source and should not be your only reference. Nowadays, the easiest way to cite sources is to use the digital object identifier (DOI) codes when available. Alternatively, when possible, a static URL to the abstract can be provided together with the reference. You can provide references either in the text or as a numbered list at the end of the post.
Never forget to cite sources for citations and make sure to format the cited text in quotations. Failing to cite sources is considered plagiarism which is definitely not an acceptable behavior.

7. Search the forum

The acronym "UTFSE" stands for "use the f****** search engine" and is likely to be the first reply to a commonly posed question. Try to avoid such situations. You can do so by becoming aware that SM is a relatively old forum, with hundreds of thousands of posts, which makes it likely that the topic you want to open was already discussed. Make sure you search the forum and read all the relevant and related discussions. The built-in forum search engine is not very powerful. Using Google with "keywords" is more effective.

Consider if it is more appropriate to continue an old discussion or open a new thread for an old discussion. If you decide that none of the old discussions are worth reviving, make sure to at least include links to these, so that others will comprehend your level of acquaintance in regard to the previous discussions. Adding such a review of previous threads will also allow the interested members to get better acquainted with the topic and contribute to the discussion.

8. Reporting spam

Like any public forum, this site receives its share of link-spam messages from spammers. Please use the 'report' button to report spam to moderators and to the automatic spam-interception system. If you provide consistently valuable spam reports, your reports will be used by the spam-interception system to determine when to automatically remove spam and spammers without moderator intervention. See here for details of the spam interception system and how it uses reports from members.

9. List of things to avoid

  • Avoid posting obsolete replies: Obsolete or off-topic replies are such that their content does not warrant their presence in the discussion thread.
  • Avoid post-whoring: Post-whoring is a behavior where members post meaningless or worthless material, such as one-sentence or off-topic replies, for the sole purpose of showing their presence or increasing their post count.
  • Avoid cross-posting or double-posting: Cross-posting is posting similar topics or replies in different forum sections or threads in order to call for attention or for other reasons. The only attention that this calls for is the attention of the moderators. Double-posting is posting a sequence of replies one after another in the same thread. The forum has an edit function that can be used to add or modify the text of your recent replies, so use this function instead of double-posting.
  • Avoid ignoring important formalisms: For example, chemical elements are represented with symbols composed from the Latin alphabet of both capitalizations and thus “h2so4” certainly does not mean the same as “H2SO4”. Abusing such symbols will make you appear clueless which is likely to repel helpful replies.
  • Avoid appearing kewl or otherwise mentally challenged unless you truly are such: Kewls are people, most commonly troubled teenagers, who feel unaccepted by the society and thus constantly call for other kewls' attention and general pity by pretending illiteracy, criminal intent, self-destructiveness, general irresponsibility and idiocy. The lack of tolerance toward such people is due to their unsurpassed ability to cause a rapid degradation of any forum.
  • Avoid pretending you are a wannabe drug cook or a kewl who wants to "blow things up": The large majority of forum membership frowns upon such attempts at dragging down of the posting quality. There is enough place for discussion of most borderline and socially barely acceptable topics, but only as long as the discourse is kept scientific and the interests are demonstrated to be amateur in origin.
  • Avoid using street slang, vulgarisms, incomprehensible talk, undefined acronyms and beliefs in clairvoyance: Keep in mind that SM is an international, multidisciplinary science forum. The slang from your streets may appear normal to you, but it will most likely make you appear as a fool to those who are not your neighbors. Talking incomprehensibly will certainly not increase the chances that the replies will be of any use to solve the problem you unsuccessfully presented. Only few acronyms are known to the majority of a multidisciplinary audience, so define acronyms at first uses. Believing other members will be able to provide a useful reply even when you present nearly not enough data, is a clear sign that you believe them clairvoyant, which is totally irrational and might increase the chances of them in turn believing you are totally wacko.
  • Avoid emotional responses: Even if you are immature enough to actually believe that it is reasonable to take offense if some anonymous virtual person posts what you perceive as aggressive and offensive replies to your own anonymous virtual incarnation, take a day to calm down and reply correspondingly to the virtual reality, rather than overreact with some pathetic response. However, if someone uses ad hominen attacks or insults instead of scientific arguments (e.g., by calling you a wacko), then report to a moderator rather than escalating it further.

So, this is it, welcome and happy quality posting!

PS: Contact a moderator, if you have suggestions for changes. Your U2U will be forwarded for discussion by the moderators.

[Edited on 7-8-2013 by Polverone]

[bfesser: added anchors; "it took it dozens of milleniums"→"it took millennia"; protocol non-specific hyperlink]

[Edited on 7.10.13 by bfesser]
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22-4-2012 at 04:37
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[*] posted on 22-4-2012 at 04:54

The literature searching guidelines

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.

Dr. Duke's Phytochemical and Ethnobotanical Databases is a free and referenced database for the chemical composition of plants (secondary metabolites only).

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 other chemical resources can be found at WWW Chemistryguide.

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 "" format of URL (where "DOI" is the alphanumerical code, an example of such an URL:

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 Hathi Download Helper is a tool that can do that job.

The 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 Everything on 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" 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 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.

If you have suggestion for additions and changes of these guidelines, please send an U2U.
Thanks to Polverone and others who helped in writing these guidelines.

[Edited on 8-6-2013 by Polverone]
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[*] posted on 6-8-2013 at 07:31

Guidelines for critical thinking
… or skills you should have for protecting yourself and others from nonsense

For most members, there are more occasions of reading posts than writing them, so it is important to have some mental tools for critical thinking in order to discern what is a good idea or a valid argument (also when coming from you). When reading or writing posts, it is crucial to recognize what is nonsense, a fallacious argument, wishful thinking, an unsubstantiated or misleading idea, a dangerous advice, or whatever else that can negatively affect the mind or threaten safety. Most scientists learn these skills as part of the scientific method, but only the minority of the members here underwent such training. Carl Sagan, one of the best science popularizers ever, gives a suitable list of mental tools required for scientific work and critical thinking that can be applied always and everywhere, so I will simply cite from his book The Demon-Haunted World: Science as a Candle in the Dark (1995, from page 197-198):
What sceptical thinking boils down to is the means to construct,
and to understand, a reasoned argument and, especially important,
to recognize a fallacious or fraudulent argument. The
question is not whether we like the conclusion that emerges out of
a train of reasoning, but whether the conclusion follows from the
premises or starting point and whether that premise is true.
Among the tools:

  • Wherever possible there must be independent confirmation of
    the 'facts'.
  • Encourage substantive debate on the evidence by
    knowledgeable proponents of all points of view.
  • Arguments from authority carry little weight - 'authorities'
    have made mistakes in the past. They will do so again in the
    future. Perhaps a better way to say it is that in science there are
    no authorities; at most, there are experts.
  • Spin more than one hypothesis. If there's something to be
    explained, think of all the different ways in which it could be
    explained. Then think of tests by which you might systematically
    disprove each of the alternatives. What survives, the
    hypothesis that resists disproof in this Darwinian selection
    among 'multiple working hypotheses', has a much better
    chance of being the right answer than if you had simply run with
    the first idea that caught your fancy.
  • Try not to get overly attached to a hypothesis just because it's
    yours. It's only a way-station in the pursuit of knowledge. Ask
    yourself why you like the idea. Compare it fairly with the
    alternatives. See if you can find reasons for rejecting it. If you
    don't, others will.
  • Quantify. If whatever it is you're explaining has some measure,
    some numerical quantity attached to it, you'll be much better
    able to discriminate among competing hypotheses. What is
    vague and qualitative is open to many explanations. Of course
    there are truths to be sought in the many qualitative issues we
    are obliged to confront, but finding them is more challenging.
  • If there's a chain of argument, every link in the chain must work
    (including the premise) - not just most of them.
  • Occam's Razor. This convenient rule-of-thumb urges us when
    faced with two hypotheses that explain the data equally well to
    choose the simpler.
  • Always ask whether the hypothesis can be, at least in principle,
    falsified. Propositions that are untestable, unfalsifiable are not
    worth much. Consider the grand idea that our Universe and
    everything in it is just an elementary particle - an electron, say
    - in a much bigger Cosmos. But if we can never acquire
    information from outside our Universe, is not the idea incapable
    of disproof? You must be able to check assertions out.
    Inveterate sceptics must be given the chance to follow your
    reasoning, to duplicate your experiments and see if they get the
    same result.

    The reliance on carefully designed and controlled experiments is
    key, as I tried to stress earlier. We will not learn much from mere
    contemplation. It is tempting to rest content with the first
    candidate explanation we can think of. One is much better than
    none. But what happens if we can invent several? How do we
    decide among them? We don't. We let experiment do it. Francis
    Bacon provided a classic reason:
    Argumentation cannot suffice for the discovery of new work,
    since the subtlety of Nature is greater many times than the
    subtlety of argument.

I suggest to read the whole chapter 12 of Sagan's book. It contains much more on how to recognize baloney (with examples). Actually, the whole book is a good read for any aspiring scientist. From chapter 17 (page 287):
As I've tried to stress, at the heart of science is an essential
balance between two seemingly contradictory attitudes - an
openness to new ideas, no matter how bizarre or counterintuitive,
and the most ruthlessly sceptical scrutiny of all ideas, old and new.
This is how deep truths are winnowed from deep nonsense. The
collective enterprise of creative thinking and sceptical thinking,
working together, keeps the field on track. Those two seemingly
contradictory attitudes are, though, in some tension.
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