8330f16 A09 A10 R10 - University of...

Dr. Rainer Glaser, Computational Chemistry, Chem8330, Fall 2016

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Introduction to Assignments A09 & A10 and the Scientific Peer Review R10 of A10

It is the very purpose of the course Chem8330 ‘Computational Chemistry’ to enable you to

enhance your research with methods of electronic structure theory. Hence, it is the goal of

assignments A09 & A10 to guide you toward the application of computational chemistry in your

own research. You will write a “Project Proposal with Preliminary Results” and this task

entails the definition of an original problem in a well-defined context, the computation and

presentation of some preliminary results, and the construction of a detailed research plan with

justification and project time line. The task is distributed over two assignments as follows: In

A09, formulate specific aims, define your “cast” of systems to study, and obtain preliminary

results from PES analysis. In A10, complete your work on A09 by addition of a section on

background & significance, addition of preliminary results on properties, and completion of all

other parts of the project proposal. The A10 submission will be reviewed by three-fold,

constructive, and un-scored scientific peer review R10.

Every group will write a project proposal on the general theme of Theoretical Studies of

Structure and Function of ‘Your-Active-Compound-Here’. Every group will prepare written

peer-reviews R10 of three A10 submissions. The experience gained in the rubric-based peer

reviews of A01 - A08 and the common general theme of A09 & A10 guarantees well-educated

peer review. Yet, the proposals will vary greatly because of the students’ selections of their

active compound and its compound/property/function triade. This “cast” selection is the first

step of working on A09 & A10 and time spent on careful thoughts in the early stages of the

project will pay off later. Some changes can be made later, of course, if need be.


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Guidelines for the Selection of the “Cast”

[1] There are many options for your selection of an active compound (AC) and its

compound/property/function triade and a few examples are provided to get you going.

The active compound could be a trivalent boron compound, the property could be its Lewis

acidity, and the function could be the use of the Lewis acidity in catalysis (i.e., to activate a

carbonyl compound toward nucleophilic attack).

The active compound could be a transition metal pre-catalyst, the property could be its

transformation into an active catalyst, and the function would be its catalytic function (in

A02, for example, iron heme pre-catalyst, ironoxo heme catalysts, alkane oxidation).

The active compound could be an intermediate, the property could be its molecular vibrations,

and the function would be its spectral signature in IR and Raman spectra (in A05, for

example, hydrated cation, specific solvation, characteristic frequencies in IR and Raman

spectroscopy).

The active compound could be a compound with possible stereoisomers, the property could be

its molecular environment, and the function would be its spectral signature in NMR spectra

(cf. A06 and A08).

The active compound could be a substrate, the property could be that it contains a reactive

center, and the function would be a specific reaction (cf. A07).

[2] Your project proposal must be tightly linked to experimentation. There must exist evidence

in the chemistry literature on the application of the type of AC you will be studying for the

function you will be studying.

[3] In the background and significance section of your proposal, you must compare the

characteristic features of your AC to the respective features of at least two other prominent

chemicals of the same or of similar type in the same or similar application. Such comparisons


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are very much a part of authentic research planning and reporting. Of course, you can make

more comparisons, but you must discuss at least two reference materials.

[4] Your AC and both reference materials must have well-defined structures (may include

disperse polymers, and so on).

[5] As you select your cast, you should create a rough outline of the basic logic of your project

proposal (mind-maps, list of keywords, sketches & cartoons of basic concepts). What is the

primary function of your AC? How does the AC accomplish its primary function? Which

chemical and / or physical properties are / are not desired in AC and why?

Deadline for Topic Selection and Review: Select your cast in the week of October 31, 2016. In

the computer lab on Friday, 11/04/16, review your selections with the instructor. We want to

ensure that you are on the right track or, as needed, consider possible modifications to get you

going in the right direction.

A09: Project Proposal with Preliminary Results. 1. Specific Aims, Cast & PESA

In Assignment A09 you will organize the outline of the project proposal, define your “cast”,

formulate specific aims, and provide preliminary results from PES analysis. Your work on A09

will be evaluated by rubric-based peer-review. Assignments A10 – A12 will build on A09 (or

A09R) and the content of A09 may evolve over time.

(a) Organize the Outline of Project Proposal. Open a Word file “A09_‘your_last_names’.docx”,

set 1-inch-margins all around, type the entire document in Times New Roman, 12 pt, with a line

spacing of “at least 12 pt” (single-spaced!), provide names of author(s) right-adjusted in header.

On page 1, type the project title in bold, type “A. Specific Aims” in the next line with underline

and in bold. Include the subsequent first-level headlines (also underlined and in bold) and they

will be as follows: “B. Background and Significance”, “C. Preliminary Results”, “D. Proposed

Research”, “E. Projected Time Line”, and “F. References”. Number sub-sections of section D as


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“D.1. Subheader-1”, “D.2. Subheader-2” and so on and underline. You may proceed in the same

way for section C; the other sections usually do not have sub-section. References must be cited

in ACS format.

Schemes, Figures, and Tables are integrated with the text. Page limits are strict and they are:

Section A on page 1. Sections A – E limited to a total of 8 pages, no exceptions. Section B

about 2 pages, and certainly no more than 2.5 pages. Section C at least 2 pages. No page limit

on Section F, but Section F may not contain notes or any kind of explanatory details.

(b) Define your “Cast”. Prepare a Scheme 1 that shows the structures of (the parent of) your

active compound AC and of reference compounds RC1 and RC2 and illustrates their major

functions. Use this scheme in Section A to define the problem. Briefly summarize purpose and

advantages of RC1 and RC2, then describe disadvantages of RC1 and RC2, (too toxic, too

expensive, too unstable, low turnover,…). Introduce AC and describe expected benefits.

(c) Formulate Specific Aims. You need to establish that the proposed AC works as you think it

does, that the performance of AC matches and/or exceeds the performance of the reference

compounds, and that AC shows the promised benefits. Address these issues stepwise as separate

specific aims. Usually the “active compound” will be a library of compounds with possible

variations in substitution patterns, variety of transition metals, variety of ligands, variety of

solvents, variety of co-catalysts,…

(d) Preliminary Results, PES Analysis. The peer reviewers of your proposal will need some

evidence that your basic idea does have merit. Hence, you must identify the key concept of your

proposal and present preliminary results in support of the key concept. The evidence can include

discussion of literature. An original proposal will require results of a limited-scope pilot study.

There will be two parts to preliminary results: Results of potential energy surface (PES)

analyses are expected in A09 and results of property analyses will be added in A10.


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Describe what kinds of preliminary results you will present and explain why these data are

important for your project proposal.

Provide a detailed description of the method(s) you used to determine the preliminary results and

cite relevant sources. Search the literature for the publications that have employed these

methods, cite these papers, and comment on the accuracy of the methods.

Show your preliminary results in a Figure (or Figures) and/or a Table. Discuss your preliminary

results and explain the significance of these results to support one or more of the key ideas

expressed in section A on specific aims.

Deadlines: Submit the file “A09_‘your_last_names’.docx” on Tuesday, 11/08/16 by midnight.

Instructor will provide feedback via email and in class on Wednesday, 11/09/16. Submit your

updated electronic file as your first revision “A09R_...” at least two hours before the Friday

meeting; this version will be peer-reviewed. Bring one hardcopy of the updated version to class

on Friday, 11/11/16 for rubric-based peer-review.

A10: Project Proposal with Preliminary Results. 2. A09 plus Background & Significance,

Properties, Proposed Research and Time Line

Assignment A10 builds on A09 (or A09R) and it is your task to complete the project proposal.

Revise and update Section A as needed, write section B, continue to build section C by addition

of preliminary results on properties, write section D while developing a time line in section E,

and continue to build Section F.

(a) Background and Significance. Build on A09(b) and describe the state-of-the-art in the field

with some detail. Strengthen your statements by citation of a good number of key references,

which were published in high-quality journals. You must show that you are fully aware of the

state-of-the-art in that area. You must show that this area of chemistry is relevant (for whom?)


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and significant (why?). You must show that your idea is new, that is, you present a new concept

rather than merely an old concept in new clothes.

This section may have several schemes. Expand on Scheme 1 of section A. Discuss purpose,

advantages, and disadvantages of RC1 and RC2 in depth. Make your case for AC and describe

in detail all of the expected benefits. There might be a Table to compare performance

characteristics. There might be a Figure to illuminate important structural issues or properties of

RC1 and RC2.

(c) Preliminary Results. Continue your work of A09(d) by adding preliminary results to

characterize the function of your active compound.

(d) Proposed Research. Describe a project that you can execute in 3 months assuming that you

will be working 20 hours per week on this project using the resources available to you (Lewis).

Describe the methods you will be using and justify your choices of methods. Describe the

hardware resources you will be using. Describe the software that you will be using. If you need

additional software, then describe what you need and where you can get it (assume you have

enough funding).

Describe the computations you will perform. Explain why these computations are necessary.

Explain what raw data you will collect and how you will analyze this data. Explain how the

results of the data analysis relate to your specific aims. What will success look like? How will

you compare AC to RC1 and RC2? What are possible risks? Are there alternative approaches?

(e) Projected Time Line. Do not make section E too long. The peer reviewers want to see that

you have thought about the execution of the project. Is the scope outlined in D in line with

available manpower and/or hardware?

Deadlines: Submit your file “A10_‘your_last_names’.docx” on Tuesday, 11/15/16 by midnight.

The instructor will provide feedback via email and in class on Wednesday, 11/16/16. Submit

your updated electronic file as your first revision “A10R_...” at least two hours before the Friday


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meeting; this version will be peer-reviewed. Bring three hardcopies to class on Friday, 11/18/16,

for three-fold scientific peer-review.

Guidelines for the Three-Fold, Constructive, Scientific Peer-Review of A10 Submissions

The A10 submissions will be evaluated by scientific peer review R10. The peer review

assignment R10 provides an authentic exercise in writing constructive criticisms. The ability to

provide competent criticism is an important skill and it is not easy to do so in a constructive

fashion. You are required to write at least 250 words of justification in each one of three

reviews. The following items may guide the preparation of your reviews.

(a) Mini-Summary. Write a mini-summary of the project proposal to show that you read the

proposal and that you understand the main points. In this paragraph you demonstrate your

competence and you can make statements about the significance / strengths of the proposal.

(b) List Substantial Criticisms. It is the nature of scientific peer review to focus on issues that

require revision and, hence, this section is key to the review. State and justify your criticisms.

Be direct, honest, and rigorous. Do not disparage. Do not demean. Do not be sarcastic. Show

humility. If possible, suggest a way to resolve or avoid the problem in revision (without forcing

your thinking on the authors). Separate your criticisms and address each in a separate paragraph.

Ask yourself these questions: Did the authors clearly describe the context of existing

knowledge? Is the hypothesis stated clearly? Is the approach logical and appropriate to test the

hypothesis? Are the methods adequate to firmly establish what is being claimed? Is the

hypothesis supported by the preliminary results? Do the authors have clear ideas about the

interpretation of that data? Is the scope adequate? Is the work feasible?

(c) List Minor Issues. List of formatting issues etc.

Peer reviews R10 must be completed with MS Word and each review must begin with the header

shown in the text box below. Write each one of the three peer reviews in a separate file and


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name each file (note different file name convention for R10) “R10_‘authors_last_names’_‘peer-

reviewers_last_names’.docx”.

The peer reviewers will not be evaluated on their performance. Scientists provide competent

peer review for free because the members of the scientific community realize and collectively

accept and value peer review as the backbone of science. However, there will be an instructor

review of your peer reviews before the peer reviews will go to the authors. Authors will not

receive the reviews of their own proposal until they have submitted acceptable peer reviews.

Deadlines: Email the three reviews (DOCX or PDF files) no later than Tuesday, 11/22/16 by

midnight. No hardcopies needed. Dr. Glaser will review the R10 submissions to check whether

they meet expected standards with regard to written justification. Dr. Glaser will then edit the

filenames of the peer reviews by replacement of ‘reviewer-names’ by a ‘reviewer-#’ to maintain

anonymity. The renamed reviews will be emailed to authors by Friday, 11/25/16. Consider the

content of the peer reviews as you prepare your oral presentation (A11) and the final, revised

project proposal (A12).

ProposalTitle:

ProposalAuthors:

Recommendation[(a)Excellent,(b)VeryGood,(c)Good,(d)Poor]:_________

Significance[(a)bottom50%,(b)top50%,(c)top20%,(d)top10%]:______

Scholarlypresentation[(a)bottom50%,(b)top50%,(c)top20%,(d)top10%]:______

Contextwelldescribed?[Yes/No]:______

Clearhypothesis?[Yes/No]:______

Hypothesissupportedbypreliminaryresults?[Yes/No]:_______

Reasonablescopeandfeasibility?[Yes/No]:______

Comments(atleast250words):

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