I will mention Jmol in my talk Sunday afternoon, and show a Jmol
script in action.
Jan
CHED 29
Jan H. Jensen, [email protected], Department of Chemistry,
University of Copenhagen, Universitetsparken 5, 2100 Copenhagen,
Denmark
Avogadro is a free and open source graphical user interface for
molecular modeling
(http://avogadro.openmolecules.net/wiki/Main_Page). It runs on all
major platforms (windows, Mac OS X, linux) and is available to
anyone. I will demonstrate the use of Avogadro (including its
combined use with other free programs) in chemical education using a
few simple examples
Jmol users -- Are you presenting anything relating to Jmol at the
ACS meeting next week? Please let us know, if I've missed it here.
Here are three items coming from St. Olaf. Please join us if you
can. -- Bob
MONDAY
CHED 166 Getting the most out of Jmol Protein Explorer
Robert M. Hanson, <mailto:[email protected]>[email protected],
Department of Chemistry, St. Olaf College, 1520 St. Olaf Avenue,
Northfield, MN 55057
Jmol Protein Explorer,
<http://Jmol.ProteinExplorer.org>http://Jmol.ProteinExplorer.org, is
a web application that uses the signed Jmol applet
(<http://Jmol.sourceforge.net>http://Jmol.sourceforge.net) to enable
exploration of biomolecular structures from a user's local or
network drive, from the Protein Data Bank
(<http://www.rcsb.org>http://www.rcsb.org), or from any other
available web site. Based on the widely used Protein Explorer for
the Chime plug-in, Jmol Protein Explorer adds several new features,
including the capability of displaying and working with PDB
"biomolecules", the display of 3D Ramachandran plots, visualization
of amino acid residues and nucleic acid base absolute and relative
orientation using quaternion maps, the ability to save the current
state to the local drive, and the capability to send the current
view as a 3D Jmol model to oneself or a colleague via E-mail. This
presentation will focus on some of the more unusual capabilities of
Jmol Protein Explorer, highlighting ways in which they can be used
in a classroom or laboratory context.
Online Resources for Chemical Education
8:30 AM-11:15 AM, Monday, March 23, 2009 Marriott City Center --
Olympus B, Oral
CHED 167 Open source cheminformatics for teaching and learning chemistry
Gus R. Rosania, <mailto:[email protected]>[email protected],
Michigan Alliance for Cheminformatic Exploration, University of
Michigan College of Pharmacy, Department of Pharmaceutical Sciences,
428 Church Street, Ann Arbor, MI 48109
The advent of open access chemical databases and open source
cheminformatics software packages has created new opportunities for
both teaching and learning chemistry. Modern visualization software
adds the experience of dynamics and the overlay of colour-coded
properties with molecular shape information. Jmol offers such
powerful visualization for free with millions of compounds available
from PubChem to play with. Open-access databases in chemistry remove
the requirement for expensive licenses for commercial chemistry
databases to train students in structure and similarity searching.
Last but not least, we argue that programming with a cheminformatics
library on the source code level will lead to a deeper insight into
structural chemistry than the pure text book experience. This talk
will try to assess the current state of open access databases and
open source software in chemistry and will point out how these
resources may be used for educational purposes.
Online Resources for Chemical Education
8:30 AM-11:15 AM, Monday, March 23, 2009 Marriott City Center --
Olympus B, Oral
CHED 168 Activating computational chemistry via an online presence
Henry S. Rzepa, [email protected], Michael J. Bearpark,
[email protected], Alan Armstrong,
[email protected], and patricia Hunt,
[email protected]. (1) Department of Chemistry, Imperial
College London, Exhibition Road, London, SW7 2AZ, United Kingdom,
(2) Department of Chemistry, Imperial College London, SW7 2AY
London, United Kingdom
Computational chemistry increasingly pervades the taught chemistry
curriculum. Historically, it has been appended to regular laboratory
exercises associated with e.g. organic/inorganic/physical courses.
This year, we have introduced a computational chemistry laboratory
in an integrated form covering many topics (including a novel
spectral prediction module), presenting it as a Wiki, and providing
laptops to each student with all the required software on a readily
maintainable image. We chose this approach for several reasons; the
Wiki is a read/write environment not only for the course team, but
for the students. It also allows 3D molecular models to be
integrated using Jmol (which also supports interesting isosurfaces
such as MOs, MEPs, rho(r), ELF etc), and finally because the
students can have write access to most parts of the course, and
particularly to the discussion areas. The course itself and
associated discussion is visible at
<http://www.ch.ic.ac.uk/wiki/>http://www.ch.ic.ac.uk/wiki/
Online Resources for Chemical Education
8:30 AM-11:15 AM, Monday, March 23, 2009 Marriott City Center --
Olympus B, Oral
CHED 499 Kyle E. Yancey,
<mailto:[email protected]>[email protected] and
Robert E. Belford, <mailto:[email protected]>[email protected].
Department of Chemistry, University of Arkansas at Little Rock, 2801
S. University Ave., Little Rock, AR 72204
This poster will describe a simple way where students and educators
can connect digital text documents and web pages to the interactive
periodic table (PTL! -Periodic Table Live!) of the Chemical
Education Digital Library (ChemEd DL). When documents or web pages
which contain the name of the elements are submitted to our server
through an online form they are returned with the names of the
elements hyperlinked to the dynamic information content of PTL!.
This allows quick access to both textual information like the
description, physical and atomic properties along with multimedia
content like images, Jmol crystal structures and videos that are
associated with the elements. We will describe the open-source
server side script which automates this process and provide students
and educators with the information they need to access to these
tools.
Undergraduate Research Poster Session: Chemical Education
12:00 PM-3:00 PM, Monday, March 23, 2009 Salt Palace Convention
Center -- Hall 5, Poster
CHED 936 Comparison of rules of additivity and DFT in predicting 13C
NMR shifts of anisole derivatives
Emily C. Despeaux, <mailto:[email protected]>[email protected], Amanda
J. Stambaugh, <mailto:[email protected]>[email protected], James B.
Foresman, <mailto:[email protected]>[email protected], and Kathleen M.
Halligan, <mailto:[email protected]>[email protected]. Department of
Physical Sciences, York College of Pennsylvania, Country Club Road,
York, PA 17405
Organic chemists use rules of additivity to determine how electron
density affects the 13C NMR spectra of di-substituted benzene
compounds. Previous research has shown that these rules fail to
accurately predict the carbon shifts for 2-nitroaniline,
specifically carbons 4 and 6. Density functional calculations yield
values that correlate well to the experimental spectra. An
explanation of what causes the simple additivity rules to fail has
yet to be determined and is in part the subject of this study. A
variety of compounds will be analyzed to determine if other cases
can be identified where this breakdown occurs. Interactions between
methoxy electron donating groups and various electron withdrawing
groups in the ortho position will be examined. Carbon NMR shifts
will be calculated for each compound from optimized Gaussian 03
values and compared to experimentally generated 13C NMR and
carbon-hydrogen correlation spectra; different solvents will also be
tested. GaussView and JMOL will be used to visualize what
interactions are present in hopes of explaining the breakdown in the
rules of additivity.
Undergraduate Research Poster Session: Physical Chemistry
12:00 PM-3:00 PM, Monday, March 23, 2009 Salt Palace Convention
Center -- Hall 5, Poster
TUESDAY
BIOL 110 Novel use of quaternions in the analysis of protein and
nucleic acid secondary structure
Robert M. Hanson, <mailto:[email protected]>[email protected],
Daniel Kohler, <mailto:[email protected]>[email protected], and
Andrew J. Hanson,
<mailto:[email protected]>[email protected]. (1) Department
of Chemistry, St. Olaf College, 1520 St. Olaf Avenue, Northfield, MN
55057, (2) Computer Science Department, School of Informatics,
Indiana University, Lindley Hall 215, Indiana University,
Bloomington, IN 47405
In this poster we present a novel method of analysis of protein and
nucleic acid secondary structure using quaternion maps. We show how
two different types of quaternion derivative can be used as
quantitative bases for descriptions of helical straightness and
"structural integrity." Most significantly, we show how quaternion
analysis allows for a completely new method for the visualization of
protein and nucleic acid secondary structure.
Protein and Nucleic Acid Chemical Biology
5:00 PM-7:00 PM, Tuesday, March 24, 2009 Salt Palace Convention
Center -- Hall 5, Poster
BIOL 149 Using quaternions to analyze ligand-protein interactions in
molecular dynamics calculations
Robert M. Hanson, <mailto:[email protected]>[email protected] and
Sean Johnston, <mailto:[email protected]>[email protected].
Department of Chemistry, St. Olaf College, 1520 St. Olaf Avenue,
Northfield, MN 55057
In this poster we describe a novel method of analysis of
protein-protein, protein-nucleic-acid, and protein-ligand
interaction using quaternions. Applied to molecular dynamics
calculations, the method allows visualization and quantitation of
the orientational integrity of such interactions.
Protein and Nucleic Acid Chemical Biology
5:00 PM-7:00 PM, Tuesday, March 24, 2009 Salt Palace Convention
Center -- Hall 5, Poster
WEDNESDAY
CHED 1242 Meeting student needs: An inexpensive internet-based
chemistry textbook
Mark A. Bishop, <mailto:[email protected]>[email protected], Department
of Chemistry, Monterey Peninsula College, 980 Fremont Blvd.,
Monterey, CA 93940
As both the costs of textbooks and student interest in
computer-based instruction rise, it seems to make sense to provide
low-cost, internet-based textbooks. This presentation describes one
such text, An Introduction to Chemistry by Mark Bishop, found at
<http://preparatorychemistry.com>preparatorychemistry.com. There
will be a description of the novel approach to pricing this text so
that the student cost can vary from free to $20 to $79.95, depending
on students' financial needs and whether the student wants the
online version or a printed text. The various components of the
web-text will be described - PDF files of the text and study guide,
flash-based audio presentations, animations, tutorials, glossary
quizzes, concept maps, jmol structures, chapter checklists, and
more. There will also be a description of the tools necessary to
create your own such text.
Online Resources for Chemical Education
8:30 AM-10:55 AM, Wednesday, March 25, 2009 Marriott City Center --
Olympus B, Oral
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
<http://www.stolaf.edu/people/hansonr>http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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--
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Jan H. Jensen Associate Research Professor
Department of Chemistry [email protected]
University of Copenhagen Phone: +45 35 32 02 39
Universitetsparken 5 FAX: +45 35 32 02 14
2100 Copenhagen Denmark
http://propka.ki.ku.dk/~jhjensen
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
------------------------------------------------------------------------------
Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
easily build your RIAs with Flex Builder, the Eclipse(TM)based development
software that enables intelligent coding and step-through debugging.
Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
_______________________________________________
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