From owner-chemistry@ccl.net Sat Sep 2 02:51:00 2006 From: "Joaquin Barroso Flores joaco_barroso*o*yahoo.com" To: CCL Subject: CCL: DPD solubility parameters Message-Id: <-32466-060902024009-24290-AXyajigzB5AlKtdlLxt8ig|,|server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-2115484242-1157179202=:9440" Date: Sat, 2 Sep 2006 01:40:02 -0500 (CDT) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso^_^yahoo.com] --0-2115484242-1157179202=:9440 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello, Does anybody know if there is a way to calculate DPD solubility parameters for molecular fragments using quantum mechanical methods? I need to define some fragments and their relative interactions for the later implementation of a DPD code. By the way, and while im at it, is it correct to call DPD a molecular dynamics method? I've got a bit of a controversy on that one. Thanks to all in advanced! Cheers ********************************************************** Q. Joaquin Barroso-Flores Departamento de Quimica Teorica Instituto de Quimica UNAM Correo Alterno: joaquin_barroso===correo.unam.mx joaquin.barroso===gmail.com ********************************************************** --------------------------------- Do You Yahoo!? La mejor conexión a Internet y 2GB extra a tu correo por $100 al mes. http://net.yahoo.com.mx --0-2115484242-1157179202=:9440 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hello,
 
Does anybody know if there is a way to calculate DPD solubility parameters for molecular fragments using quantum mechanical methods? I need to define some fragments and their relative interactions for the later implementation of a DPD code. By the way, and while im at it, is it correct to call DPD a molecular dynamics method? I've got a bit of a controversy on that one.
 
Thanks to all in advanced!
 
Cheers


**********************************************************
Q. Joaquin Barroso-Flores

Departamento de Quimica Teorica
Instituto de Quimica UNAM

Correo Alterno: joaquin_barroso===correo.unam.mx
joaquin.barroso===gmail.com

**********************************************************

Do You Yahoo!? La mejor conexión a Internet y 2GB extra a tu correo por $100 al mes. http://net.yahoo.com.mx --0-2115484242-1157179202=:9440-- From owner-chemistry@ccl.net Sat Sep 2 20:07:00 2006 From: "Sengen Sun sengensun]|[yahoo.com" To: CCL Subject: CCL: A global convention or an international joke? Message-Id: <-32467-060902175916-30275-mpQ/JbN93R05gk+a3BGWbw[]server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 2 Sep 2006 13:59:10 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun~~yahoo.com] Professor Boyles clearly recognizes a mis-use of the word "cause,".... "they can be exceptionally confusing to students on the linguistic level alone." . But he explained in several different ways in PHILCHEM_L why such a "mis-use" is justified in text books and in literature. . >> "good scientists are aware of these things"... >>"Empirical scientists work with many >>presuppositions and take many things >>for granted to simply 'get the job done,'". . Then, why are we a group of people who claim to be emerging philosophers of chemistry? What emerging for? Just follow experimentalists, "get the job done", make money, pound on the decades-long confusions, and make the confusions more and more solid? Are we willing to think "how philosophy is practised" uniquely? Further, it is a screaming sound to me that Shahbazian and Zahedi called for a "global convention"(!!!!!) in their conclusion of a 15 text page article in FOCH, although I absolutely have no idea what they want specifically. I guess, during a possible "global convention," some one is going to say something like: "we got to enjoy the beauty of mistakes (or mis-uses) created by our older generations. Please do not say that "the sp3 hybridization of the carbon atom in methane DOES NOT cause its tetrahedral geometry", as it is not language-economic by adding two more words "DOES NOT". A single word "cause" is much more convenient as the meaning of "cause" has never been vigorously defined and as there is no causal relation here.... " Please enjoy the "clear chemical language", a new emerging philosophy, and finally a funny international joke, my friends! Sengen > From: "Boyles, David A." > Subject: Re: PHILCHEM Digest - 28 Aug 2006 to 31 Aug > 2006 (#2006-30) > > Sengen: > > In the statement "The sp3 hybridization of the > carbon atom in methane causes its tetrahedral > geometry" as cited, we find a mis-use of the word > "cause," and a prevalent one, at that, in textbooks, > not to mention for example which of Aristotle's four > causes are being invoked--if any. Not presuming to > know with precision what Shahbazian and Zahedi > think, it is clear nonetheless that they are saying > that in a circular way we have two propositions--a > statement on hybridization, and a quite separate one > on geometry--which are referentially linked so as to > provide explanatory power. These two statements > have become linked, even though historically their > origins are very separated in time. What is > particularly interesting, perhaps, is that the most > recent proposition--hybridization theory--is used as > an explanatory cause of an earlier proposition, the > geometry of carbon (albeit with the caveat carbon in > some compounds only, and not all, although the > textbook statement does not sa! > y as much). Why this is the case and not the other > way around warrants its own scrutiny, but in any > case the impression is thus given of the > supervenience of earlier ideas which are apparently > obvious (geometrical objects) on later ideas which > are not at all overtly obvious (orbital theory), as > though the latter were the "cause" or perhaps more > correctly (?) the explanation of (?) or reason for > (?) the former. I believe good scientists are > aware of these things, while others are unaware of > them, or at least unaware of the philosophical > issues engendered by them, including their > ontological and epistemological implications to our > understanding of phenomena themselves. > > These kinds of statements are typically found in > 'textbooks' which conflate separate ideas. > Evidently this has several purposes, including > economy of verbiage on one hand, and reinforcement > of related concepts in student minds on the other. > Far from intellectually rigorous, such level books > attempt with economy to present language statements > first and foremost as tools, as code-words which > students will hopefully realize are only that as > their academic careers develop. > > Apart from the scientifically utilitarian purpose > such statements might have on the 'textbook' level, > they can be exceptionally confusing to students on > the linguistic level alone. I recall very vividly > how my undergraduate years foundered on puzzlement > not so much on the fact that there are many ideas > (propositions)in chemical space, but on the very > words used to relate one to another. Words such as > 'cause' which were never defined, but put into the > background 'created' much consternation to my own > learning experience. > > Far from trying to do the impossible and purge or > rework the language of textbooks, however, one would > do better to realize that textbooks are only > textbooks, and that for all the philosophical > problems present, that such problems are inherent in > any explanation, in any proposition, in any language > as philosophy is preeminently appreciated in making > us aware. Empirical scientists work with many > presuppositions and take many things for granted to > simply 'get the job done,' (including atomic theory > in my case--I weigh out compounds for my chemical > reactions in slavish subordination to the "count" > model of John Dalton whether or not it corresponds > to atoms makes little difference--a pianist must > likewise perform on something and in that case it > can by definition be but a keyboard of a piano) > presuppositions that require and deserve analysis in > philosophy. One begins to realize that after formal > education, perhaps, and not during it. Formal > education is a slice of reality, a pl! > atform of understanding, but not das Ding itself. > > Best Wishes, > > David A. Boyles > Professor of Chemistry > Department of Chemistry > South Dakota School of Mines and Technology > Rapid City, SD 57701 > > From: Ivan Antonowitz > Subject: Re: Comments on A Critique of Chemical > Language > > David A. Boyles posted: > >> > [snip] > Not presuming to know with precision what > Shahbazian and Zahedi think, it > is clear nonetheless that they are saying that in a > circular way we have two > propositions--a statement on hybridization, and a > quite separate one on > geometry--which are referentially linked so as to > provide explanatory power. > These two statements have become linked, even though > historically their > origins are very separated in time. > [snip] > << > > The keystone phrase in the above sentences is > "referentially linked". In the > Ordinary Language of Chemists, Philosophy and > Psychology are so > "referentially linked" as to be indistinguishable > from each other [thus > turning David's concept inside-out]. > > Many are taken aback to find that few people Read > what the author Wrote. > Even if people agree on the same Denotations, their > Connotations can diverge > into incomprehensibility. On the other hand, unless > one is a post-modernist, > we conventionally agree that the word "Unicorn" > connotes a magical > horse-like creature with no Denotation; Unicorns do > not exist. > > The catch is that Connotations and Denotations are > only pre-1920 > psychological concepts unique to human beings, and > as such are subject to > Formal Symbolic logic scrutiny to unravel their > muddled usages. In Formal > Symbolic logic we now instead distinguish Statements > from Propositions, > post-1980. Some systems still confuse the two as a > pedagogical short-cut > which is only unraveled much later on in the course. > > A further example of Dualism at work. In the > classroom, Teaching and > Learning are designed to be "referentially linked". > However, many on this > list would find it insulting to be 'taught a > lesson', but certainly expect > to learn from the other participants ideas. This > capability of 'unlinking' > is essential in any analysis. > > David could as well have used the historical > examples of electricity and > magnetism whose 'hidden unity' [J.C. Taylor] > involved just how information > was transmitted between them, despite their rather > divergent physical > characteristics. If David tried to espouse the > 'magnetic' approach, I have > tried to show the equivalent 'electric' shock. > > Ivan Anotonowitz > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Sat Sep 2 22:15:00 2006 From: "Jeff Nauss jnauss.:.accelrys.com" To: CCL Subject: CCL: Accelrys Customer Training for October 2006 Message-Id: <-32468-060902211857-7355-RwpEagErFwFbICpQH7r4ng]|[server.ccl.net> X-Original-From: Jeff Nauss Content-Type: multipart/alternative; boundary="=_alternative 0006EBB6882571DE_=" Date: Sat, 2 Sep 2006 18:18:51 -0700 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss]=[accelrys.com] This is a multipart message in MIME format. --=_alternative 0006EBB6882571DE_= Content-Type: text/plain; charset="US-ASCII" Accelrys Inc. are holding the following training workshops during October 2006. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs for the scheduled workshops are $500 per day for all customers. For the on-line presentations, the price is $175 per three hour session for all customers. SAN DIEGO, CA Introduction to Discovery Studio 2 Oct Structure-Based Design in Discovery Studio 3 Oct Protein Modeling in Discovery Studio 4 Oct Simulation in Discovery Studio 5 Oct CAMBRIDGE, UK Introduction to Crystal Structure Modeling 3-4 Oct Introduction to Nanomaterials Modeling 5-6 Oct Introduction to Quantum Mechanics Modeling 9-10 Oct Introduction to Polymer Modeling 11-12 Oct Introduction to Life Science Modeling with InsightII 17-18 Oct Homology-Based Protein Design 19-20 Oct CHARMm 23-24 Oct Structure Based Drug Design with InsightII 25-26 Oct PARIS, FRANCE Structure Based Drug Design with Cerius2 23-24 Oct Pharmacophore Generation with Catalyst 25-26 Oct Further details can be found on our website at http://www.accelrys.com/training/general/calendar.html and http://www.accelrys.com/training/general/calendar_online.html Questions regarding scheduling and content should be directed to workshops_-_accelrys.com -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training --=_alternative 0006EBB6882571DE_= Content-Type: text/html; charset="US-ASCII"
Accelrys Inc. are holding the following training workshops during October 2006.  These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals.

Costs for the scheduled workshops are $500 per day for all customers.  For the on-line presentations, the price is $175 per three hour session for all customers.

SAN DIEGO, CA

Introduction to Discovery Studio                2 Oct
Structure-Based Design in Discovery Studio      3 Oct
Protein Modeling in Discovery Studio            4 Oct
Simulation in Discovery Studio                  5 Oct

CAMBRIDGE, UK

Introduction to Crystal Structure Modeling              3-4 Oct
Introduction to Nanomaterials Modeling                  5-6 Oct
Introduction to Quantum Mechanics Modeling              9-10 Oct
Introduction to Polymer Modeling                       11-12 Oct
Introduction to Life Science Modeling with InsightII   17-18 Oct
Homology-Based Protein Design                          19-20 Oct
CHARMm                                                 23-24 Oct
Structure Based Drug Design with InsightII             25-26 Oct

PARIS, FRANCE

Structure Based Drug Design with Cerius2     23-24 Oct
Pharmacophore Generation with Catalyst       25-26 Oct

Further details can be found on our website at http://www.accelrys.com/training/general/calendar.html
and http://www.accelrys.com/training/general/calendar_online.html

Questions regarding scheduling and content should be directed to workshops_-_accelrys.com

--
Jeffrey L. Nauss, Ph.D.
Lead Training Scientist
Accelrys
10188 Telesis Court, Suite 100
San Diego, CA 92121-4779

Phone: +1-858-799-5555
Fax: +1-858-799-5100
http://www.accelrys.com/training
 --=_alternative 0006EBB6882571DE_=-- From owner-chemistry@ccl.net Sat Sep 2 23:59:01 2006 From: "Venuvanalingam Ponnambalam convener^^tcs2006.in" To: CCL Subject: CCL: THEORETICAL CHEMISTRY SYMPOSIUM 2006, BHARATHIDASAN UNIVERSITY, INDIA Message-Id: <-32469-060902225809-25843-s0jrMEsDJcN5WUWzoWsWzQ]~[server.ccl.net> X-Original-From: "Venuvanalingam Ponnambalam" Date: Sat, 2 Sep 2006 22:58:09 -0400 Sent to CCL by: "Venuvanalingam Ponnambalam" [convener_-_tcs2006.in] Dear Colleagues, The Tenth Theoretical Chemistry Symposium (TCS 2006) will be held during December 11-13, 2006 at Bharathidasan University, Tiruchirappalli, Tamil Nadu, India (http://www.tcs2006.in/). This National Event is convened also as a part of the Silver Jubilee celebrations of Bharathidasan University. Usually held once in two years, the TCS provides a forum for discussing emerging trends in theoretical chemistry in India and in the whole world. The symposium will have technical discussions through invited lectures by leading experts and poster presentations by young researchers in the field. Recently theoretical chemistry has gained immense importance in view of its applications in material and life sciences. TCS 2006 tries to cover all areas of theoretical chemistry, with special emphasis on the following. Theoretical & Computational Methodologies in Chemistry Density Functional & Wave function based Quantum Chemistry Statistical Mechanics & its Applications in Chemistry Classical & Quantum Simulation of Complex Systems Electronic Structure & Spectroscopy of Molecules & Clusters Chemical Dynamics, Reactivity & Catalysis Chemistry at Surfaces and Interfaces Nonlinear Phenomena & Dynamics in Chemistry Molecular Materials & Nano-Systems, Soft Condensed Matter Biology-inspired Theoretical Chemistry Equilibrium & Non-equilibrium Processes in Condensed Phase Chemo & Bioinformatics, Drug Modelling The conference will begin in the morning on Monday, December 11 and will end in the noon on Wednesday, December 13. There will be totally six lecture sessions and two poster sessions and in that one lecture session is earmarked as a special session in honor of Professor Debashis Mukherjee, IACS, Kolkata a world-renowned theoretical chemist on the occasion of his sixtieth birthday. The conference website is now open for registration and abstract submission. The deadline for all contributions is September 30, 2006. Please visit the conference website http://www.tcs2006.in/ for more information and details. Totally 200 participants, including few foreign delegates, are expected for TCS 2006 and this would be a wonderful opportunity to know the latest trends in theoretical chemistry and to initiate newer collaborations worldwide. We look forward to meeting you at Tiruchirappalli during TCS 2006. With best wishes, P.Venuvanalingam Convener, TCS 2006 School of Chemistry Bharathidasan University Tiruchirappalli 620 024, INDIA E-mail: convener^tcs2006.in