November 1998 - chemweb - imperial.ac.uk

Molecule Editor in Java
by Denis M. Bayada 18 Feb '99

18 Feb '99

Dear all, I have just finished writing a molecule editor in JAVA. If anyone is interested, it is available at : http://www.chem.leeds.ac.uk/ICAMS/people/denis/moledit.html You may freely download the Java source code and modify it. Any comments are indeed welcome. Thank you Denis --------------------------------------------------------------------- Denis M. Bayada e-mail: denis(a)mi.leeds.ac.uk ICAMS voice: (44) (0)113 233 65 95 School of Chemistry fax: (44) (0)113 233 65 63 University of Leeds http://www.chem.leeds.ac.uk/ICAMS/people/denis Leeds LS2 9JT ENGLAND ... but as I proceeded in my labour, it became every day more horrible and irksome to me. Sometimes I could not prevail on myself to enter my laboratory for several days, and at other times I toiled day and night in order to complete my work. It was, indeed, a filthy process in which I was engaged. Frankenstein (Mary Shelley) --------------------------------------------------------------------- ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

2 1

Chemistry teaching and Internet
by Dr. Wendy A. Warr 30 Nov '98

30 Nov '98

In preparing my chemweb (the list) filter for ChemWeb.com (The Alchemist at http://ChemWeb.com) I noticed the message about the use of the Internet for teaching science and it reminded me that I had intended to reply. At least two of the ChemWeb/VEI events have concerned education - check out the Library at http://chemweb.vei.co.uk/ Also, I have written a (free) report at http://www.warr.com/chemint.html about the Chemistry and the Internet conference held in Irvine in September. Some of the presenations in Irvine were related to education. Wendy -- Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 wendy(a)warr.com http://www.warr.com chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

1 0

MDPI's Molecules and Springer's "Molecules Online"
by Shu-Kun Lin 30 Nov '98

30 Nov '98

Dear colleagues: Thanks for the concern regarding my trouble from Springer. In answering many requests, I would like to put the open letter to Springer's "Molecules Online" editor here, where I have presented some simple facts. I already contacted with Springer's "Molecules Online" editor before. But he never gave me a reply. I am very busy and do not really have time to bother anyone or to prepare such long letter to anybody. Thanks again. Shu-Kun Lin --------- Open letter to the editor of Springer's "Molecules Online" http://www.mdpi.org/molecules/protest/indexp.htm Dear Dr. Stephen Hanessian: In order to protect the basic freedom of press and information exchange of so many of our fellow scientists who are the authors, the subscribers, and the supporters of our journal Molecules (vol.3, 1998, http://www.mdpi.org/molecules/) from further damage by Springer Verlag, on a very basic ethical ground and in light of the following reason, please consider whether you resign from the editor-in-chief position of Springer's "Molecules Online". MDPI's Molecules and Springer's "Molecules Online" could have been published separately as two independent journals. However, Springer created the problem by insisting that "Molecules Online" is not a separate journal, and started this year to launch it as a "continuation" of our journal Molecules. Springer claimed in a hegemonic manner that MDPI's Molecules is not allowed to publish and only its journal can publish. The fact is that Molecules is not Springer's trademark of publication. (History will witness that Springer will finally loss this case generated by itself because it violated the basic human rights of free press.) Please also be reminded another simple fact that the founding editor (Dr. Shu-Kun Lin) of Molecules is still alive, active and has been continuously and successfully editing this journal and has never invited anybody to replace him. It has been demonstrated that I have credit to run Molecules, even though I never pretended to have any great achievement in organic synthesis (I only imagined a little bit to have chance to win a Nobel prize, I mean Nobel Peace Prize, due to my novel theoretical work on diversity assessment, my practical work on diversity preservation of both substance sample and information, and my strong advocacy on press freedom). Molecules is started as the first journal to support the preservation of molecular diversity by samples deposit. It has been treated as MDPI's official journal since 1995 as you may find from MDPI paid advertisement published in scientific journals in 1995, including several issues of "Synthesis" in 1995. We also used MDPI fund to pay all the editorial work, including paying a guest editor. Springer never paid me a penny during the whole year of 1996. Springer only provided publication service for the journal edited by me and for vol.1 publication only, before Springer unilaterally and suddenly terminated the contract of publication service at the end of 1996. Because of the ruthless harassment from Springer, we cannot make our papers published by MDPI in 1997 and 1998 available to the public for months and cannot publish any of the recently accepted manuscripts. During recent six months, Springer even insisted on deleting all of our papers published already in Molecules vol.2, 1997 and vol.3, 1998. Published papers are very much like born babies. Can you put them back into their mother's body? From this case, as you might have also realized, Springer's present executive in this division of publication has no respect on our scientists' basic rights. Like many of your colleagues in Basel, Switzerland, I have attended your lectures and I like them very much. You are a good scientist. You should have no difficulty to launch your own new journal successfully. To our scientists in organic chemistry, Springer might be a great company because it was the publisher of Beilstein database (This database is definitely no longer published by Springer now). However, it is not so great as to risk one's reputation and to let Springer continue to use your name and to put you on a position only to try to destroy your fellow scientists' established journal Molecules. The case of Molecules already caused public anger against Springer. My colleagues and I will greatly appreciate it if you support our Molecules instead of collaborating with Springer to destroy it. We want to go on with our unique publication policy of Molecules and continue our great efforts to preserve and exchange chemical samples and experimental data. With best regards, Sincerely, Dr. Shu-Kun Lin Editor-in-Chief, Molecules (ISSN 1420 3049) http://www.mdpi.org/lin/ Basel, 30 November 1998, via e-mail chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

1 0

Re: ORGLIST: Challenge: To find Reaction with most bond forms/cleaves (fwd)
by G.P.Moss 30 Nov '98

30 Nov '98

If you include enzymic reactions then an 11-bond example is the cyclisation of squalene epoxide to a number of triterpenoids such as hopanol. In the laboratory this type of acid catalysed cyclisation does occur but I doubt if an 11-bond example is known. Gerry Moss _________________________________________________________________________ Dr GP Moss Telephone: +44 171 775 3262 Department of Chemistry Queen Mary & Westfield College Facsimile: +44 181 981 8745 Mile End Road London E1 4NS, United Kingdom E-mail: g.p.moss(a)qmw.ac.uk World Wide Web server: http://www.chem.qmw.ac.uk/ IUPAC chemical nomenclature data base: http://www.chem.qmw.ac.uk/iupac/ IUBMB biochemical nomenclature data base: http://www.chem.qmw.ac.uk/iubmb/ chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

1 0

Workshop in Cuba - Call for Papers
by Tito Diaz Bravo 26 Nov '98

26 Nov '98

International Workshop TIAP99 - Call for papers Call for papers Dear Colleague, I have pleasure in announcing the Second International Workshop on Process Analysis in Chemical Engineering, TIAP99, which will be held in Havana, Cuba, from 27 to 30 April 1999. This Workshop is organized by the Chemical Engineering Department of the Higher Polytechnic Institute "Jose Antonio Echeverria" (ISPJAE), Havana, Cuba. We cordially invite you and members of your staff to participate in this Workshop. For further information you can visit our website at http://redquimica.pquim.unam.mx/internacional/cubaenglish.htm or contact me: Dr.Tito Diaz Bravo Facultad de Ingenieria Quimica. ISPJAE. Marianao CP 19390. C. Habana. Cuba. E. Mail: tiap(a)quimica.ispjae.edu.cu Fax: (537) 272964 Tel.: (537) 207220 IMPORTANT DATES Abstract due 15 Jan 1999 Author Notification 30 Jan 1999 Submission of Final Manuscript 20 Feb 1999 Notification of Final Acceptance 1 March 1999 Deadline for registration 27 April 1999 Please pass forward this e-mail to all your staff members and thank you in advance for helping us to publicise this announcement. chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

1 0

From my very unfortunate experience with Springer ...
by Shu-Kun Lin 26 Nov '98

26 Nov '98

My dear colleagues: During recent months of suffering from Springer Verlag's lawsuit regarding the journal MOLECULES (http://mdpi.org/molecules/) I thought a lot and concluded that the internet publication and electronic conference really give all of our scientists' unprecedented freedom of press and we all should love it: Now the technical part of publication is extremely easy and cheap. Every scientists can be a publisher himself. I tell you frankly we published 20 issues of MOLECULES (Vol.2, vol. 3) by ourselves with very easy-to-use software. Before that, publication must be done by a publishing company. Now it is not necessary at all. The only remaining part of publication is peer review of the manuscripts, which has been done exclusively by scientists themselves anyway. My MOLECULES vol.2 and 3 was published not by any publishing company. However, I received more supports and I have more manuscripts than I can publish. The quality (layout, etc.) is very good. This is recognized by the fact that all the major abstracting and indexing services covered my two volumes. Therefore, I believe in near future publishing companies will be vanishing. Long live the Internet!! If they want to survive, the only chance might be to become humble database manager, because Internet makes everything related to information nothing but database. >From my very unfortunate experience with Springer Verlag, I would like to tell all of those dear colleagues who plan to launch a new journal, particularly an internet one, think at lest twice before collaborating with a "famous" professional publisher, it might be predatory one! I also want to use this chance to protest openly against Springer Verlag. I am not used to this kind of thing but I will fight against this injustice. As basically only a poor boy from a remote village in China, I have already luckily enjoyed many, including internet, which I never expected before. Springer: you believe me, I have nothing evil to fear. I believe the principles in the world still exist and the basic human rights of free press will be protected. I thank many colleagues who encouraged me. Sincerely, Shu-Kun Lin http://www.mdpi.org/lin/ --------------------------------------------------------- Dr. Shu-Kun Lin Molecular Diversity Preservation International (MDPI) Saengergasse 25, CH-4054 Basel, Switzerland http://www.mdpi.org/ E-mail lin(a)mdpi.org Tel. +41 79 322 3379, Fax +41 61 302 8918 -------------------------------------------------------- chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

1 0

A java based 3d Molecular viewer
by Paul May 23 Nov '98

23 Nov '98

Hi, You might like to look at: <http://pw1.netcom.com/~gpurvis/Dendron.html> which gives details of another 3D molecular viewer used to see chemical structures on web pages. This one's called ChemApp and is Java based, so doesn't require plug-ins, and is configured to use CAChe chemical sample files (.csf). It's free to download and use so long as appropriate credit is givento the author (John Purvis, Pomona College, Claremont, CA). Regards, ------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 928-9927, fax: +44 (0)117 925-1295 <mailto:paul.may@bris.ac.uk> <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> "Ha! Your superior intelligence is no match for our puny weapons" Simpsons ------------------------------------------------------------------------- chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

1 0

Report on Chemistry and The Internet
by Dr. Wendy A. Warr 22 Nov '98

22 Nov '98

Some of you may have seen my FREE report about the Chemistry and the Internet conference held in Irvine in September. If you haven't, do visit http://www.warr.com/chemint.html You may want to print the report for reading later - it runs to about 40 pages - but there are no graphics and access should be fast. Apologies for duplicate messaging. Wendy -- Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 wendy(a)warr.com http://www.warr.com chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

1 0

Springer-Verlag acquired
by Dr. Wendy A. Warr 22 Nov '98

22 Nov '98

The following is a preview of part of my Warr Zone page for November 27 (in The Alchemist at http://ChemWeb.com) Bertelsmann A.G. signed a 1 billion German mark ($597 million) deal on November 20, to buy an 82 percent stake in Springer-Verlag G.m.b.H., Germanys largest publisher of scientific journals and technical books. The acquisition will allow Bertelsmann to make new inroads into the United States market. Almost 25 percent of Springers annual revenues of 615 million marks comes from the United States. More than 60 percent of the company's publications are in English. The acquisition, which is subject to approval by European regulators, is part of an aggressive push by Bertelsmann to become a dominant player in science and technical publishing - a market that is expected to grow faster than consumer or popular books in the next few years. Bertelsmann took over Random House earlier this year and in October struck a deal with Barnes & Noble to participate in a joint venture in the chains online bookstore. Part of the appeal of Springer was Springer LINK, the electronic network, which offers more than 400 technical and medical journals. Bertelsmann has an expanding infrastructure of Internet investments, from its electronic bookstores in the United States and Europe to its interest in the search engine Lycos and the on-line service, America Online. It believes that its own strength on the Internet can add something important to Springer. The latter is expected to increase its sales of scientific and technical books through Barnes & Nobles electronic bookstore, placing additional pressures on Amazon.com. It is claimed that, using the information highway, which is built for mass consumer markets, Bertelsmann can deliver scientific, technical and medical contents for incremental costs. The professional and scientific publishing market is being consolidated: to compete requires a lot of capital and resources. Springer, a privately owned, independent company, had a profit margin of about 10 percent. The new majority owners expect a future return on sales of 15 percent to 20 percent. The new chairman to head the supervisory board of Springer, Jürgen Richter, is the former chairman of Axel Springer, a Berlin-based newspaper conglomerate which has no connection with Springer-Verlag. -- Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 wendy(a)warr.com http://www.warr.com chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

1 0

E-Journals, Databases small and large, and Copyright
by Rzepa, Henry 21 Nov '98

21 Nov '98

My recent posting to this forum addressed the interesting trend that publishers are starting to create and distribute tools to assist authors in creating and validating "database" entries to be associated with electronic versions of articles they are preparing. Given that such "Added value" or "enhanced" articles might contain up to 100 or so molecules, perhaps with a great deal of associated property and spectral information and perhaps expressed in eg XML/CML, this must constitute by recent rules a copyrightable database. Created by the author, the initial copyright at least must presumably reside with the author. Of course, a publisher would wish to use such individual microdatabases to aggregate into much larger databases, this being part of their own "added value" contribution to the publishing process. Presumably then, the publisher will wish the copyright owners to transfer that copyright to them, the publisher. This of course many (not all) publishers already do with the text and images associated with more conventional articles. It will be interesting to see how this process might evolve. For example, in recognition that each microdatabase will add value to the publishers larger database, should the author charge the publisher for the transfer of the database? Presumably, in turn the publisher will charge the e-journal reader for the right to access and use any larger database. If its accepted that authors might be able to "sell" their microdatabase to the publisher, then what might the going rate be? Per molecule? Is a sensible formula even possible? Perhaps of course the publisher might instead ask that if the author wants to gain from the database accretion process, they should hand over the microdatabase free of charge to the publisher. I wonder if these issues have been resolved anywhere, by any publisher, of chemical or indeed non chemical journals. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; mailto:rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ If my digital email signature is invalid, download a new root at http://www.belsign.be/en/services/receive/install-ca.html chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

2 1