May 1998 - chemweb - imperial.ac.uk

Ph.D. Studentship Available
by Dr. Derek M. Bloor 19 May '98

19 May '98

********************************************************** **** Ph.D. Studentship AVAILABLE FROM SEPT 1998 ****** ********************************************************** THE OPTIMISATION OF MACROMOLECULE/SURFACTANT INTERACTIONS This 3 year Ph.D fully funded studentship (Course fees + Subsistence allowance) in Physical Chemistry is available from September 1998 at the University of Salford in association with Dr. Derek M. Bloor Description As a result of their unique structure, surface active agents often display various degrees of specificity with respect to their association behaviour with macromolecules. The addition of a polymer to an aqueous solution of a surfactant sometimes dramatically affects the physicochemical properties of that solution. It is these properties which render such systems amenable to commercial exploitation. For example; rheology control of hydrophobically modified polymers; gels formed by the addition of ionic surfactants to neutral polymers; combinations of proteins, natural gums and surfactants found in food products which contribute to the control of texture. Attempts to reduce empiricism by producing formulation guidelines have met with various degrees of success. This project is aimed at providing further significant improvements in these guidelines using a novel experimental approach to obtain a better understanding of the factors influencing optimisation of systems for specific applications. For each type of system, experimental parameters will be measured using a surfactant selective electrode (SE) and isothermal titration calorimetry(ITC) to enable the manipulation of the equilibrium position between the bound and aggregated surfactant to be achieved in a systematic way. The SE measurements will be carried out at Salford University whilst it is anticipated that the ITC measurements will be carried out at Unilever Research (Port Sunlight) and/or the Fritz Haber Institute (Berlin, Germany). This work will lead to enhanced flexibility in product formulation, in particular minimising the amount of experimentation required to achieve improved environmentally friendly products. For further information please contact Dr. Derek M. Bloor, University of Salford, Department of Chemistry, The Cockcroft Building, Salford M5 4WT UK D.M.Bloor(a)chemistry.salford.ac.uk -------------------------------------------------- Dr. Derek M. Bloor University of Salford Chemical Sciences Science Research Institute Salford M5 4WT UK Tel: 0161 295 5192 Fax: 0161 295 5111 -------------------------------------------------- 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)

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Announcing the SDPD Round Robin
by Armel Le Bail 19 May '98

19 May '98

STRUCTURE DETERMINATION BY POWDER DIFFRACTOMETRY ROUND ROBIN Organisers: Armel Le Bail (University of Le Mans) and Lachlan Cranswick (Daresbury Laboratory). (Deadline for submission of solutions - June 30, 1998) http://fluo.univ-lemans.fr:8001/SDPDRR/ This is to announce the availability of powder diffraction data as part of the Structure Determination by Powder Diffractometry Round Robin (SDPDRR). Participants have the option of solving one or both of two samples: i) An Inorganic Phase ii) An Organic Pharmaceutical Compound The data and information on the samples can be emailed, if web links are too slow or congested. A poster for pinning on department bulletin boards is available on the web-site. Background and protocol are available from the website. A summary of results will be presented at an invited talk on "Trends in Structure Determination from Powder Diffraction" at the August 1998 ECM-18 meeting in Prague. Armel Le Bail (E-mail: armel(a)fluo.univ-lemans.fr) Lachlan Cranswick (E-mail: l.cranswick(a)dl.ac.uk) 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)

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Alternate Base Pairing
by Rzepa, Henry 16 May '98

16 May '98

An article in New Scientist (May 16, p32) describes a radical alternate base pairing for CG and AT, which would if correct lead to a quite different DNA structure. The proponent of this theory (Mark Curtis, an artist) came to his conclusions on geometric grounds. Energetic grounds were not considered. For my evaluation of this theory, see http://www.ch.ic.ac.uk/newscientist/curtis/ The alternate AT pairing seems not that unreasonable, but the alternate CG pairing seems unlikely. Comments anyone? It will be interesting to see what, if any, science emerges in any subsequent New Scientist debate! I did send them a letter, but suspect they will consider it a "bit too technical" to publish. Shame that the New Scientist, despite my pleadings over the years, has always considered Chime models "too complicated" to put on their Web page. Any yet their own diagrams (p 34) obscure a vital aspect of the new base pairing, no doubt in the interests of "not making it too complicated for the reader". Henry Rzepa. +44 171 594 5774 (Office) +44 171 594 5804 (Fax) http://www.ch.ic.ac.uk/rzepa/ 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)

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Chemical Certification
by Rzepa, Henry 15 May '98

15 May '98

We are completing the process of getting our chemistry server certified by Verisign/Belsign. This will enable it to, inter alia, issue signed Java applets etc. The process, whilst cheap, is interesting, since it involves the institutional lawyers signing an interesting pile of paperwork certifying in essence that e.g. I exist. Arguably, its something that might become essential in the future. Is this something anyone else has undertaken/heard about others undertaking, or whose company has gone through the process for Internet Commerce? Apart from enabling some aspects of Java, we did it because we wanted to increase the "authenticity" of the origin of the documents coming from out site, and because its an interesting learning curve getting a university group certified (its done per server, and against a named individual). Perhaps people at the other end could not care a brass monkey about the certified authenticity of documents coming from us. Certification as such of course does not prove anything of the quality of the chemistry so emanating! Does anyone in industry, or behind a firewall care about our authentication? 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/ 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)

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Publishing chemical resources on the WWW
by Mark Winter 13 May '98

13 May '98

Dear colleague First, apologies to those of you see more than one copy of this message. I have the honour of giving the 6th ChemWeb Virtual Lecture in a couple of weeks time. The idea is to complement some of the earlier lectures in the series. Abstracts of those earlier lectures are at http://chemweb.vei.co.uk/ and details of my lecture are: Title: Publishing chemical resources on the WWW Date: May 27th, 1998 16h BST (15h GMT) Place: ChemWeb Auditorium [http://chemweb.vei.co.uk/] (an abstract is at that site) This is a request for a little assistance. In additions to examples of my own work, I should like to mention some good examples of work from other individuals or groups. I should like to hear from chemists who are doing the following, and who have some open-access materials in those areas. What I want to do in the appropriate "slides" in the lecture is to indicate a few URLs for viewers to follow up after the lecture. 1. Writing materials in an integrated course package such as Web-CT or related for chemistry course delivery. Clearly for a participant to find a link useful you would have to have a guest login enabled. 2. Writing chemistry materials using portable data format files (.pdf) and integrating those materials into WWW pages. 3. Using VRML and/or 3DMF files to do something related to chemistry other than display molecular structures. 4. Projects involving undergraduates writing WWW-based chemistry course materials as part of their assessment for degrees. 5. So-called "non-programmers" using packages such as HyperCard as cgi applications on a Macintosh web server to do something to do with chemistry. Or the equivalent on PCs. 6. Any other innovatory publication of chemistry material via the WWW which could be done by relative non-experts If anyone would be prepared to allow me to place a link to their appropriate materials in the lecture "slides" please contact me by e-mail before 20 May 1998. Thank you in advance Dr Mark J Winter (Director of Studies) Department of Chemistry, The University, Sheffield S3 7HF, England tel: +44 (0)114 222 9304 fax: +44 (0)114 222 9303 e-m: mark.winter(a)sheffield.ac.uk http://www.shef.ac.uk/chemistry/staff/mjw/mark-winter.html WebElements is the periodic table on the world-wide web: http://www.shef.ac.uk/chemistry/web-elements/ The Sheffield Chemdex is a listing of chemistry sites on the world-wide web: http://www.shef.ac.uk/chemistry/chemdex/ 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)

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Re: WANTED - cyclodextrin .CAR files
by Julianne M. Braun 09 May '98

09 May '98

I don't know about .CAR files, but the pdb and Xplore files are readily available for both alpha and beta-cyclodextrin from a number of servers. If you can use some other file format besides .CAR, perhaps you would find Babel useful - it's a program that can convert between a number of different file formats. Unfortunately, it is unable to write .CAR files despite being able to read them. The URL for the Babel Home Page is: http://mercury.aichem.arizona.edu/babel.html Hope this is helpful. Julianne At 05:56 PM 5/9/98 +0100, fragoso(a)icmcb.u-bordeaux.fr wrote: >Hi! > >I'm a PhD student and I'm looking for a .CAR file of alpha-cyclodextrin >and beta-cyclodextrin. Have looked in some sites but nothing. >Can anybody help me? > >Thanks a lot in advance, > >Alex > >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) > > 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)

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WANTED
by fragoso＠icmcb.u-bordeaux.fr 09 May '98

09 May '98

Hi! I'm a PhD student and I'm looking for a .CAR file of alpha-cyclodextrin and beta-cyclodextrin. Have looked in some sites but nothing. Can anybody help me? Thanks a lot in advance, Alex 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)

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Molecule-of-the-Month at Imperial: Viagra
by Rzepa, Henry 06 May '98

06 May '98

The drug Viagra is typically of the "Internet age", with prescriptions for the pill being taken on-line (http://thepillbox.com/buyviagra.htm, 10 pills - $105.09 ) and much other information such as side effects etc being so documented. Being unable to find any structural information, I created http://www.ch.ic.ac.uk/motm/viagra.html Of some minor interest is that two of the CAS hits on this system appear to show the wrong tautomer. Anyone found an exemplary page on the role of nitric oxide in the metabolic sequence? Finally, I might note with interest an anecdote by a 2nd year student here. Part of their degree consists of a "chemical IT" course, in which they are trained to use a variety of chemical information tools, and then demonstrate their skills by creating a project. Quite a few students mount the project on their personal web site provided by ISPs. This student came to tell me that in about 4-6 weeks on-line, their particular project had notched up about 4000 hits (they had inserted a counter), and he was now being sent emails from what appeared quite senior researchers asking about details. It certainly seemed quite a motivator for him! I wonder how many laboratory notebook writeups have had a similar impact! 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/ 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)

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(Help) AMBER for esters?
by John W. Cox 04 May '98

04 May '98

I'm working with Insight/Discover and using AMBER to model DNA-metal adducts. One of the metal compounds I hope to minimize has an ester ligand and AMBER does not have the adequate parameters (regarding the C-OS-CT portion, an additional oxygen atom type seems necessary). I'm familiar with adding atom types to AMBER, but have not been able to track down those specifically for esters. Are they available? Any leads are appreciated. Cheers, John Cox John W. Cox Department of Chemistry Virginia Commonwealth University (804) 828-0276 che5jwc(a)titan.vcu.edu 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)

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Software for review
by Stephen R. Heller 04 May '98

04 May '98

4 May, 1998 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I have four (4) new software products. I am looking for people who are willing to review these software products. In return for the review which is published in JCICS you get to keep the software or database. The review should be completed in 1-3 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. I have tried this approach for about the past six years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e-mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 6 May, 1998 (Wednesday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER(a)GIG.USDA.GOV) PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I often send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The packages I now have are: 1. NIH SBIR Phase I and II forms software from GDI - Grant Forms (www.grantform.com) 2. LogP dB 3.5 software from ACD Labs (www.acdlabs.com) The ACD/LogP Calculator will accept most neutral structures ontaining 50 or fewer atoms and only the elements H, C, N, O, F, Cl, Br, I through the ChemSketch interface. Then it will calculate n accurate Log P (octanol/water partition coefficients). 3.ChemSketch 3.5 drawing program software from ACD Labs (www.acdlabs.com) (includes Dictionary, Tautomers and 3D Viewer) including Chemsketch, Dictionary, Tautomers and 3D Viewer) 4. NMR Processor 3.5 software from ACD Labs (www.acdlabs.com) This includes Chemsketch, Dictionary, Tautomers and 3D Viewer) Steve Heller Steve Heller, NIST 820 Diamond Avenue, Room 101 Gaithersburg, MD 20899 USA Phone: 301-975-3338 FAX: 301-926-0416 E-mail: srheller(a)gig.usda.gov WWW: www.hellers.com/~steve 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)

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