From owner-chemistry@ccl.net Mon Aug 6 10:53:01 2012
From: "John McKelvey jmmckel^-^gmail.com" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: Comment on Algebra, etc
Message-Id: <-47326-120806104737-17240-4kBjG/p0FA1nNy/TX2mVSw(-)server.ccl.net>
X-Original-From: John McKelvey <jmmckel!=!gmail.com>
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Date: Mon, 6 Aug 2012 10:47:30 -0400
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Sent to CCL by: John McKelvey [jmmckel(_)gmail.com]
Folks,
I forwarded the previous missive on this to a local chemistry faculty
member, Pr Ron Duchovic, who has been fighting an uphill battle, but
gaining some, on math requirements for freshman chemistry courses.
Pr Duchovic's response:
My take on the article is that it makes some very important points, but
misses some equally critical ideas.
For anyone who is preparing for a career that demands quantitative
skills -- science (physical, biological, social), engineering, computer science,
numerical manufacturing -- the requirements of algebra, geometry, trigonometry,
calculus, linear algebra, and differential equations are crucial.
These tools are
too important to be ignored. In fact, I think that the current level
of mathematics
required for the biological and social sciences is inadequate.
However, I agree with the author of the article that there are lots of
people for whom the ability to compute (basic arithmetic) and to understand
probability and statistics is much more important than algebra or calculus.
For health science people it is the ability to do arithmetic that is
crucial (drug
dosage). For the informed citizen, the ability to understand statistics is much
more important than algebra and calculus. I agree with the author of
the article
that the math curriculum should be revised to note these distinctions.
However, I disagree with the author when it comes to geometry. Geometry
is not so much about computation as it is about logic. In teaching
geometry there
is the opportunity to teach ordered, logical thinking and problem
solving. These
are critical skills for everyone. [and so says Pascal, (inserted
here by JMcK)]
I would argue that computation, geometry, and, statistics
should be required of
everyone. In addition, including a component of the history and
conceptual foundations
of mathematics would enrich everyone's understanding of the power and
limits of human
reasoning.The subjects of algebra, trigonometry, calculus, linear
algebra,and differential
equations are requirements that are much more field/career-specific.
Ron Duchovic
Dr. Ronald J. Duchovic
Associate Professor of Chemistry
Indiana University Purdue University Fort Wayne
2101 Coliseum Blvd. East
Fort Wayne, IN 46805-1499
260-481-6293 (Office)
260-481-6070 (FAX)
--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel]-[gmail.com
From owner-chemistry@ccl.net Mon Aug 6 12:24:01 2012
From: "John McKelvey jmmckel]*[gmail.com" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: Apologies... the article I read was in the NYT, not CCL, but the issue is still valid...
Message-Id: <-47327-120806113816-5417-usxS4qVCIS3f7UlSwkzbZQ*server.ccl.net>
X-Original-From: John McKelvey <jmmckel-#-gmail.com>
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Date: Mon, 6 Aug 2012 11:38:10 -0400
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Sent to CCL by: John McKelvey [jmmckel.]_[.gmail.com]
http://www.nytimes.com/2012/07/29/opinion/sunday/is-algebra-necessary.html?WT.mc_id=NYT-E-I-NYT-E-AT-0801-L14&nl=el
--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel]_[gmail.com
From owner-chemistry@ccl.net Mon Aug 6 17:52:01 2012
From: "Amy J Austin docronindaemon(-)gmail.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: Apologies... the article I read was in the NYT, not CCL, but the issue is still valid...
Message-Id: <-47328-120806175022-615-EV16zmG/JrE6hstG/BVXJA^_^server.ccl.net>
X-Original-From: "Amy J Austin" <docronindaemon*gmail.com>
Date: Mon, 6 Aug 2012 17:50:09 -0400
Sent to CCL by: "Amy J Austin" [docronindaemon- -gmail.com]
Hi John,
I agree with you that Chemistry students should have to take more Mathematics as a prerequisite for the major. Further, I believe the lack of these required courses places undergraduate students lacking an education in higher level Mathematics at a disadvantage. Imagine learning the concepts involved in Physical Chemistry or Theoretical chemistry if one simultaneously struggles with the tools involved.
A descriptive Chemist wouldn't need the same command of Mathematics as a Physical/Theoretical Chemist. Then again, how would an undergraduate student know if they had an interest in the latter without the fundamental Mathematical knowledge to master the material.
Best,
Amy
> "John McKelvey jmmckel]*[gmail.com" wrote:
>
> Sent to CCL by: John McKelvey [jmmckel.]_[.gmail.com]
> http://www.nytimes.com/2012/07/29/opinion/sunday/is-algebra-necessary.html?WT.mc_id=NYT-E-I-NYT-E-AT-0801-L14&nl=el
>
> --
> John McKelvey
> 10819 Middleford Pl
> Ft Wayne, IN 46818
> 260-489-2160
> jmmckel]_[gmail.com
>
>
From owner-chemistry@ccl.net Mon Aug 6 18:26:01 2012
From: "Michel Petitjean petitjean.chiral*gmail.com" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: Comment on Algebra, etc
Message-Id: <-47329-120806144114-17091-kjJKlInnLsz39nQr1JHhWg_._server.ccl.net>
X-Original-From: Michel Petitjean <petitjean.chiral:_:gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Date: Mon, 6 Aug 2012 20:41:05 +0200
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Sent to CCL by: Michel Petitjean [petitjean.chiral__gmail.com]
About geometry: how many chemists are able to write a rotation matrix ?
That is just elementary level calculus, but the knowledge of molecular
modeling reduces often to play with graphic softwares.
More seriously, chemists (and in general, scientists) deserves to
receive a good general education of all basic disciplines, and that
includes maths (without maths, modeling is quasi inexistant, only
experiments).
Alas, some VIP (Very Important Professors) decided that students must
be primarily trained in their own research fields, not to receive a
pluridisciplinary education thought to face to a variety of situations
in the market.
Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral[A]gmail.com (preferred),
michel.petitjean[A]univ-paris-diderot.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html
2012/8/6 John McKelvey jmmckel^-^gmail.com <owner-chemistry[A]ccl.net>:
>
> Sent to CCL by: John McKelvey [jmmckel(_)gmail.com]
> ...
> However, I disagree with the author when it comes to geometry. Geometry
> is not so much about computation as it is about logic. In teaching geometry there
> is the opportunity to teach ordered, logical thinking and problem solving. These
> are critical skills for everyone. [and so says Pascal, (inserted here by JMcK)]
> ...
From owner-chemistry@ccl.net Mon Aug 6 19:01:01 2012
From: "Irene Newhouse einew|*|hotmail.com" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL: Is algebra necessary?
Message-Id: <-47330-120806153342-19913-peijPlaOKHMmUHtwjNbSiw||server.ccl.net>
X-Original-From: "Irene Newhouse" <einew-.-hotmail.com>
Date: Mon, 6 Aug 2012 15:33:38 -0400
Sent to CCL by: "Irene Newhouse" [einew-*-hotmail.com]
The high failure rates in math aren't due to so many people being unable to learn math. They're due to the sorry state of math teaching. A large part of the problem is that education is all too subject to fads, and that teachers aren't given enough training in the method du jour. I say this as someone who has regularly tutored students in grades 1-12 in math since 2006. I have had to decode math homework for 3rd graders because their tutors, who passed algebra, geometry & algebra II in their day, had no clue. It took the extra math that comes with a Ph D in physical chemistry to be able to wrap my head around the assignments in the absence of training in the approach. When there are such abrupt changes in educational practice, not even parents who did well in school in their day are able to help their children with homework.
The math tutor in this area for whom I have the utmost respect has taught an autistic student whose public high school deemed incapable of getting a diploma, enough math to pass the Compass test to the Math 100 level for the local community college. He has also taken another autistic student, who tested at grade 4 math before tutoring, to grade 7 math, **in one summer**, and summer vacation around here is only 6 weeks - modified year-round schedule. Both sets of tests were done by the student's public school, so they're about as objective as you can get. The student's parents told him the results caused quite a stir at school. He regularly teaches kids under 10 how to factor quadratic equations & other similar algebra concepts. He works with the kids who come to him, usually because they're struggling in math at school, not with child prodigies.
On the other hand, there are still many occupations that don't require one to be able to do upper level high school math, and it's been silly to try to merge what in my day were the vocational, business, and academic high school tracks into one curriculum that doesn't serve anybody particularly well.
A lifetime ago, my first boss explained that he had very competent primary & high school teachers because in his day, a woman who wanted a career had pretty much only 3 choices - teacher, nurse, or secretary. Now that women had more choice, the most intelligent young women were no longer choosing teaching, which, as a 'woman's job' was historically grossly underpaid. He ended by stating that for about 150 years, the US had a pretty good general education system only because it was solidly based on the exploitation of the brightest American women. Since the end of that era, we've been getting the teachers we've been paying for all along. Around here, experienced condo cleaners get the same or higher wages as starting teachers, so it's not going to be easy to solve the problem.
Irene Newhouse
From owner-chemistry@ccl.net Mon Aug 6 19:36:00 2012
From: "Joy Ku joyku||stanford.edu" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: Workshop: MD Prototyping & Simulations on GPUs with OpenMM
Message-Id: <-47331-120806183956-31986-JlOA4M4wJZnnt4F7XuOKdg#,#server.ccl.net>
X-Original-From: "Joy Ku" <joyku~~stanford.edu>
Date: Mon, 6 Aug 2012 18:39:53 -0400
Sent to CCL by: "Joy Ku" [joyku::stanford.edu]
Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM)workshop.
Where: Stanford University
When: Sept. 6-7, 2012
Registration: Free but required and spaces are limited. To register or for more information, visit http://simbios.stanford.edu/MDWorkshop.htm.
OpenMM is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs).
A well-designed framework provides an application layer and a library, so that non-programmers can easily and quickly run MD simulations and develop custom algorithms on GPUs, while programmers are simultaneously able to integrate OpenMM cleanly into their own programs.
For the workshop, no programming background is required, though programming topics will also be covered for those who are interested in them.
During the workshop, you will gain hands-on experience using OpenMM's new application layer and application programming interface (API). Learn to:
* Set up and run an MD simulation on your GPU using both PDB and AMBER files
* Create a custom force to apply to your simulations
* Customize the simulation through Python scripting
You will also have time to work with the OpenMM development team on your own research project.
________________________________________
OpenMM is supported by Simbios, an NIH National Center for Physics-Based
Simulation of Biological Structures. To learn more about Simbios and its
research and software tools, visit http://simbios.stanford.edu.
[1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS
Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics
Processing Units," J. Comp. Chem., 2009, 30(6):864-872.
[2]Eastman, P. and Pande, V.S., Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit, J. Comp. Chem., 2010, 31(6):1268-1272.
From owner-chemistry@ccl.net Mon Aug 6 20:12:00 2012
From: "Hugo Alejandro Jimenez Vazquez hjimenez[]woodward.encb.ipn.mx" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: Negative Barrier Height
Message-Id: <-47332-120806184528-3903-d4yAQ6mM4ErCG2aUwzOX9g[*]server.ccl.net>
X-Original-From: Hugo Alejandro Jimenez Vazquez <hjimenez|*|woodward.encb.ipn.mx>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Date: Mon, 6 Aug 2012 17:14:05 -0500 (CDT)
MIME-Version: 1.0
Sent to CCL by: Hugo Alejandro Jimenez Vazquez [hjimenez a woodward.encb.ipn.mx]
On Fri, 3 Aug 2012, Dr. Bhupesh Kumar Mishra bhupesh_chem(_)rediffmail.com wrote:
>
> Sent to CCL by: "Dr. Bhupesh Kumar Mishra"
> [bhupesh_chem__rediffmail.com] Dear All, I am doing some calculation on
> reaction mechanism. I have optimized transition states. But the problem
> is that it is characterized by low vibrational frequency (<100 cm-1).
> The calculated barrier heights are negative. Whether it is possible? May
> negative barrier heights for TS are acceptable for understanding of any
> reaction mechanism?
> Any suggestions is highly appreciated.
>
> Sincerely
> Bhupesh Kumar Mishra(Ph.D.)
> UGC-Dr. D. S. Kothari Post Doctoral Fellow
> Department of Chemical Sciences
> Tezpur University
> Tezpur- ASSAM
> INDIA
>
Hello,
I've followed the messages in this thread and I do have a few comments
based on whan I consider my long (about 15 years) personal experience in
locating transition states.
As some have mentioned, there is no information on the type of reactions
that you are studying. You don't even mention whether you are working with
inter- or intramolecular reactions.
As others have already mentioned, you need a single imaginary ("negative")
vibrational frequency (actually, a negative force constant) in order to
say that you have found a transition state. Even if you have found a
geometry with that single negative frequency, you cannot state that you
have found THE transition state for your particular process. Many systems
have low vibrational modes corresponding to rotation of single bonds and
the search of your TS can go the wrong way and your software can locate
the TS for other process rather than that you're looking for. Usually,
imaginary vibrational frequencies with low values (say between -20 and
-100 cm^-1) correspond to conformational changes, while absolute values
higher than that may correspond to the formation of bonds. For example,
the TS of Diels-Alder reactions have values for the imaginary frequencies
of about -500 cm^-1, depending on the particular reaction and the level of
theory you are using to locate it. After you find a TS you still have to
find out whether it corresponds to the TS you are looking for or not. The
simplest way to do this is to visualize the normal mode corresponding to
the imaginary frequency, and see if the molecular motion is related to the
reaction you're studying. As others in this thread have said, the other
way which would be the preferred one and at the same time the most
expensive, is the determination of the Intrinsic Reaction Coordinate,
starting from the transtion state found.
As for your question concerning whether it is possible to have "negative"
reaction barriers, assuming that you have indeed located the correct
transtion state, the answer is YES. One of the participants in this thread
has even hinted an answer to this puzzle. If we look at the description of
a reaction coordinate for a concerted reaction (just to give a simple
example) in a textbook, what we see is a simple curve for "reactants" on
the left side, products on the right, and a TS somewhere along the way, at
the highest poing of the curve. However, the description of the
"reactants" is, in many, many cases, left to your imagination,
particularly in the case of intermolecular reactions. We usually assume
that this point in the reaction coordinate corresponds to the isolated
reactants at their ground state geometries, but have we seriously thought
about this matter? After all, the reaction coordinate IS the description
of the geometrical/energy changes the system suffers as the reaction takes
place. So, the initial point SHOULD BE a particular geometry.
We have to think that it is likely that for many intermolecular reactions,
the reactants can form a stable complex corresponding to a minimum,
stabilized by noncovalent interactions, even by some form of charge
transfer (sound familiar?) before the reaction takes place. We can even
think that there are several ways in which two molecules can associate to
form stable complexes. The stabilization energy for this complexes can be
substantial, depending on the nature of the forces involved. We are
talking of even a few tens (tens, not tenths) of kcal/mol in the gas phase
BEFORE the actual reaction takes place.
If your reaction has a small activation energy, then it is likely that the
energy of the TS be still "lower" than that of the sum of the energies of
the isolated reactants, which are the values that we usually take as a
reference, leading to "negative" activation energies. However, here the
"reactants" would have to be the molecules forming the most stable
complex, and you would have to measure the activation energy taking the
complex as your reference, and not the isolated reactants. This would lead
you to the expected "positive" activation energy.
Of course, there are other things to think about, such as the inclusion of
solvent effects if your actual reaction is carried out in solution which
will usually decrease the stabilization of the complex; the effect of
zero-point energies, and the effect of temperature which will affect the
thermal energy, enthalpy, and free energy contents of the system...
Regards,
---
Hugo A. Jimenez Vazquez
hjimenez#%#woodward.encb.ipn.mx
Departamento de Quimica Organica ENCB-IPN
Mexico
From owner-chemistry@ccl.net Mon Aug 6 20:47:01 2012
From: "Hanneke Jansen johanna.jansen/./novartis.com" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: Innovative computational workflows for drug discovery
Message-Id: <-47333-120806190326-19626-6wKlPeCehOBljORFADvong/./server.ccl.net>
X-Original-From: "Hanneke Jansen" <johanna.jansen]=[novartis.com>
Date: Mon, 6 Aug 2012 19:03:23 -0400
Sent to CCL by: "Hanneke Jansen" [johanna.jansen[A]novartis.com]
Dear Colleagues,
The Teach-Discover-Treat ("TDT") initiative is a call to action for our computational chemistry community which seeks to address major gaps in drug discovery education while developing targeted efforts against neglected diseases. As part of TDT, we have kicked off a competition that solicits submissions of tutorials for state-of-the-art drug discovery workflows with the requirement that all computational tools and models used in the workflows are freely available.
Three competition categories are focused on neglected diseases. Experimental follow-up in all three categories is being made possible through partnerships for compound acquisition, synthesis and biochemical testing. This is where you can have a real impact on drug discovery for neglected diseases!
A fourth "open innovation" category seeks innovative drug discovery workflows that do not fall into one of the other three categories and are either exemplified on a neglected disease project or adaptable to a neglected disease application.
Please visit our website, www.teach-discover-treat.org, for more information, including additional competition details and presentation slides from the kick-off symposium at the ACS Spring 2012 National Meeting in San Diego.
The datasets for the various challenges are available for download:
https://sites.google.com/a/teach-discover-treat.org/web2012/downloads
The readme files that are included for each of the four challenges contain specific instructions; please read them carefully!
We invite and encourage each of you to join us in this effort. Submission closes on September 5 th.
Good luck!
The TDT Steering Committee
Hanneke Jansen, Rommie Amaro, Jane Tseng and Wendy Cornell
From owner-chemistry@ccl.net Mon Aug 6 22:46:00 2012
From: "Salomon Turgman Cohen sturgman.:.gmail.com" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: Apologies... the article I read was in the NYT, not CCL, but the issue is still valid...
Message-Id: <-47334-120806205852-19768-Sy98B3Vq+Z2Yre6NIXrOWg*_*server.ccl.net>
X-Original-From: Salomon Turgman Cohen <sturgman.*_*.gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Mon, 6 Aug 2012 20:58:45 -0400
MIME-Version: 1.0
Sent to CCL by: Salomon Turgman Cohen [sturgman()gmail.com]
Dear All,
My memories of the required Physical Chemistry course for the
cheme degree are still fresh in my memory. I remember struggling with
some of the tools and missing their relation to previous work in math
classes. Eventually, some of us just got it. Perhaps, a piece of this
puzzle is teaching department specific math classes (at higher costs
obviously) where mathematical concepts are connected immediately to
future topics to be taught in the (chemistry) field.
Salomon
On Mon, Aug 6, 2012 at 5:50 PM, Amy J Austin
docronindaemon(-)gmail.com <owner-chemistry:+:ccl.net> wrote:
>
> Sent to CCL by: "Amy J Austin" [docronindaemon- -gmail.com]
>
> Hi John,
>
> I agree with you that Chemistry students should have to take more Mathematics as a prerequisite for the major. Further, I believe the lack of these required courses places undergraduate students lacking an education in higher level Mathematics at a disadvantage. Imagine learning the concepts involved in Physical Chemistry or Theoretical chemistry if one simultaneously struggles with the tools involved.
>
> A descriptive Chemist wouldn't need the same command of Mathematics as a Physical/Theoretical Chemist. Then again, how would an undergraduate student know if they had an interest in the latter without the fundamental Mathematical knowledge to master the material.
>
>
> Best,
>
> Amy
>
>
>
>
>
>
>
>
>> "John McKelvey jmmckel]*[gmail.com" wrote:
>>
>> Sent to CCL by: John McKelvey [jmmckel.]_[.gmail.com]
>> http://www.nytimes.com/2012/07/29/opinion/sunday/is-algebra-necessary.html?WT.mc_id=NYT-E-I-NYT-E-AT-0801-L14&nl=el
>>
>> --
>> John McKelvey
>> 10819 Middleford Pl
>> Ft Wayne, IN 46818
>> 260-489-2160
>> jmmckel]_[gmail.com>
>
--
Salomon Turgman Cohen
Postdoctoral Associate
Cornell University
(919) 341-9650