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, [email protected], Department of Chemistry, St. Olaf
College, 1520 St. Olaf Avenue, Northfield, MN 55057
Jmol Protein Explorer, http://Jmol.ProteinExplorer.org, is a web application
that uses the signed Jmol applet (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), 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, [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/
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, [email protected] and Robert E. Belford,
[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, [email protected], Amanda J. Stambaugh, [email protected],
James B. Foresman, [email protected], and Kathleen M. Halligan,
[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, [email protected], Daniel Kohler, [email protected], and
Andrew J. Hanson, [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, [email protected] and Sean Johnston, [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, [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 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
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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