November 24, 2014
Chemistry 5: Scientific Computing Skills
Homework Assignment 8: Chemistry Databases
Four out of eight problems will be graded
YOUR SCORE FOR THIS ASSIGNMENT: 94/100 points
• Upload this Word document into the Homework 8 drop box before the deadline.
• If you haven’t done so already, you must register to use SciFinder Scholar.
• IMPORTANT For the SciFinder and Web -of-Science problems, use “ Edit → Paste Special →
Unformatted Text” when pasting information copied from web browsers and SciFinder Scholar in order to
avoid inserting web links, formatting, and other unnecessary objects into this document. Students who
ignore this simple request will lose quite a few points for the clutter in their answers.
• IMPORTANT In the part on NIST database, you will be asked to insert an image. One way to do this is to
save the image from the browser on your computer hard drive and then and inset it using “Insert →
Picture → From File” command.
Several assignments in this homework deal with locating research papers in scientific journals. A mind -
boggling number of papers are published each year by hundreds of journals. Each paper can be uniquely identified
by specifying the following informati on.
• The journal’s name
• The volume of the journal in which this paper appeared
• The issue of the journal in which this paper appeared
• Page numbers on which this paper was printed
• The publication year
In addition, it is customary to provide the following info rmation:
• The name(s) of the author(s)
• The title of the paper
• The DOI (digital object identifier) number; refer to http://www.doi.org/ for more information
Here is an example of a full citation:
Finley, B. D.; Saltzman, E. S., Measurement of Cl2in coastal urban air. Geophys. Res. Lett. 2006, 33 (11),
In this example, the paper was written by two authors, Finlay and Saltzman. The title of the paper is “Measurement
of Cl2in coastal urban air”. Geophys. Res. Lett. stands for a journal called “Geophysical Research Letters”. 2006 is
the publication year; 33 is the volume number; 11 is the issue number; L11809 is the starting page; and the number
at the end is the doi number. If you search fo r this doi number, you will be referred to this link
where you can view the paper’s abstract and, if you have a subscriptioto this journal, the entire paper. 1. Use Web-of-Science to find all articles authored by your Chem 5 professor (Douglas J. Tobias) on the topic
“water” that were published in 200 1. List these publications below in the same format as in the sample answer.
Be sure to include the full list of author names; do not use “et al.” to truncate the list of authors.
SAMPLE ANSWER (this reference format must be followed in problems 1, 2, and 3):
1. The publication title in italic
The full list of author last names and initials, separated by commas
The journal name
The volume, issue, pages, and publication year, in this order
2. Addition of amines to conjugated dienes catalyzed by solid base catalysts
Kakuno Y, Hattori H , Tanabe K
Volume: 34, Issue: 12, Pages: 2015-2018, Published: NOV 1 2006
1. Short wavelength collective dynamics in phospholipid bilayers: A molecular dynamics study
Tarek M, Tobias DJ, Chen SH, et al.
Physical Review Letters
Volume: 87, Issue: 23, Article Number: 238101, Published: DEC 3 2001
2. Effects of solvent damping on side chain and backbone contributions to the protein boson peak
Tarek M, Tobias DJ
Journal of Chemical Physics
Volume: 115, Issue: 3, Pages: 1607 -1612, Published: JUL 15 2001
3. Electronic polarization and hydration of the dimethyl phosphate anion: an ab initio molecular dynamics
Kuo IF, Tobias DJ
Journal of Physical Chemistry B
Volume: 105, Issue: 24, Pages: 5827 -5832, Published: JUL 15 2001
4. Surface solvation of halogen anions in water clusters: An ab initio molecular dynamic study of the Cl -
Tobias DJ, Jungwirth P, Parrinello M
Journal of Chemical Physics
Volume: 114, Issue: 16, Pages: 7036 -7044, Published: APR 22 2001
2. Roughly 30 years ago, UCI Chemistry professor A. J. Shaka published a very important paper on nuclear
magnetic resonance that was cited more than a thousand times by other researchers. Here is what we know
about this paper:
Published sometime around 1984 (p lus or minus one year) by A. J. Shaka and others
Use Cited Reference Search in the Web-of-Science to locate this reference, and find out how many times this
particular publication has been cited by other researc hers.
In addition, find the latest publication that appeared in the Journal of Biomolecular NMR and cited the Shaka
paper in question. Use the same format for your answers as described in problem 1 above. Do not use “et al.” to
truncate the list of authors; you must include a complete list.
YOUR ANSWERS: (use the same format as in Problem 1)
Full reference to Shaka’s paper:
1. Computer-optimized decoupling scheme for wideband applications and low -level operation Shaka AJ, Barker PB, Freeman R
Journal of Magnetic Resonance
Volume: 64, Issue: 3, Pages: 547 -552, Published: 1985
Number of times this publication was cited:
The latest reference in the Journal of Biomolecular NMR that cited it:
1. Characterization of the Ashbya gossypii secreted N-glycome and genomic insights into its N-
Aguiar TQ, Maaheimo H, Hesikanen A, et al.
Volume: 381, Pages: 19-27, Published: NOV 15 2013
a. Use Web-of-Science to find a publication about isotopic fractionation in nitrous oxide authored by
researchers at Caltech, which appeared in a journal called “Science” within the last 20 years. Provide a
citation to this paper below.
YOUR ANSWER: (use the same format as in Problem 1)
1. Isotopic fractionation of stratospheric nitrous oxide
Yung YL, Miller CE
Volume 278, Issue: 5344, Pages: 1778 -1780, Published: DEC 5 1997
b. Follow the UC e-Links to get to the PDF file of this publication. Paste the link to this P DF file below.
c. Open this PDF file. To prove that you have successfully opened this file, r etype the first sentence in the