chemical engineering Mikko Hupa & Dmitry Murzin & Tapio - - PowerPoint PPT Presentation

2011-2015

Article writing in chemistry and chemical engineering

Mikko Hupa & Dmitry Murzin & Tapio Salmi

Åbo Akademi - Department of Chemical Engineering

Experience of the lecturer

Background

Publishing often ”bottleneck” in engineering sciences, but a ’must’ nowadays

• often project work, tight schedule, no extra reporting
• project reports seldom publishable as such
• industrial collaboration and patenting ”disturbs”
• engineers not always ”natural writers”
• language problems

Background

• Producing papers not often ”tought”, just learnt by

doing – often excuses are used:

• We already wrote the project report, why publish more?
• My project is confidential, how could I publish it?
• My work and results do not ”fit” into a typical published

paper format!

• I have too much results, how to cut?
• How to start writing?
• We are many authors – who writes what?

Background

• Main focus in the overall process of producing

publishable papers...

• ...not in linguistic issues
• Based on the experience when helping PhD students

at Åbo Akademi writing their first papers, and, when reviewing manuscripts to journals.

For scientific writing in English...

…many excellent books and guides are available

• Dr. Cathleen Ahonen´s guide is taylor-made for

chemical engineers and can be found at: http://www.ndc.fi/guide/ Click on “guide2003.doc”

Writing Style

By all means, you should write in your own personal style, but keep in mind that scientific writing is not literary writing. Scientific writing serves a completely different purpose from literary writing, and it must therefore be much more precise.

Writing style

• Extreme brevity.

Writing style

• Leo Tolstoi, War and Peace

But Count Rastopchin, who now shamed those who were leaving, now evacuated government offices, now distributed good-for-nothing weapons among the drunken riffraff, now took up icons, now forbade Augustin to evacuate relics and icons, now confiscated all private carts, now transported the hot-air balloon constructed by Leppich on a hundred and thirty-six carts, now hinted that he would burn Moscow, now told how he had burned his own house and wrote a proclamation to the French in which he solemnly reproached them for destroying his orphanage; now he assumed the glory of having burned Moscow, now he renounced it, now he ordered the people to catch all the spies and bring them to him, now he reproached the people for it, now he banished all the French from Moscow, now he allowed Mme Aubert-Chalmet, the center of all the French population of all Moscow, to remain in the city and

• rdered the old and venerable postmaster general Klyucharev, who had done nothing particularly wrong, to be

arrested and exiled; now he gathered the people on the Three Hills to fight the French, now, in order to be rid of those same people, he turned them loose to murder a man and escaped through a back gate himself; now he said he would not survive the misfortune of Moscow, now he wrote French verses in an album about his part in the affair— this man did not understand the meaning of the event that was taking place, but only wanted to do something himself, to astonish someone or other, to accomplish something patriotically heroic, and, like a boy, frolicked over the majestic and inevitable event of the abandoning and burning of Moscow, and tried with his little hand now to encourage, now to stem the flow of the enormous current of people which carried him along with it.

Some important Language points:

• Poor experimentation cannot be masked by brilliant

writing; however, poor writing can mask brilliant experimentation

• Avoid complex sentence structure
• Use simple and clear English
• Always keep in mind that the paragraph is the essential

unit of thought

Read literature

Выход продукта – Product yield or product exit?

Read your own text

A Quick Test of Your “Proof-Reading Accuracy”

There are no tricks in this test. Read the sentence below only once, counting the number of F’s. Count them only once (as you would if you were proofreading). Be honest. Do not go back and count them again or the test will be no fun.

FINISHED FILES ARE THE RESULT OF YEARS OF SCIENTIFIC STUDY COMBINED WITH THE EXPERIENCE OF YEARS.

Answer

There are six F’s in the sentence ! GRADES If you found three, you are of average intelligence. If you found four, you are above average. If you found five, you can turn your nose at most anybody. If you found six, you are a genius.

Correct grammar, spelling, obvious errors (use speller to check) Many mistakes in references, authors’ names are common – correct! Absolute scientific accuracy is required – check data in tables, etc. Avoid repetition. Do not use the same word more than once in the same paragraph Recast sentences – use simple words

Reread What You Have Written Critically

it does not matter in what order the letters are, the

• lny iprmoetnt tihng is taht the frist and lsat ltteer

be at the rghit pclae. The rest can be a total mess and you can still read it without porbelm. The huamn mnid deos not raed ervey lteter by istlef, but the wrod as a wlohe.

40-50% mistakes in the first name Almost never mistakes in the second name Own experience: Dmitry Murzin 1 2 3 4 5

Issues to be discussed

1. Why to write publications – To be or not to be?

• 2. Where to publish - Types of publications
• 3. What to include - “Publishable unit, PU”
• 4. With whom - Question of authorship
• 5. How to write - Structure of the paper
• 6. How to get it published – Rebuttals to reviewers

Why to write publications?

• Only by international publications you become part of the

development of scientific knowledge

• Engineering research absolutely needs scientific

publications and not just patents, reports etc.

• Any new findings not published internationally will be made

again – until they are finally published by someone

• What is not published, does not exist for the scientific

community

Issues to be discussed

1. Why to write publications – To be or not to be?

• 2. Where to publish - Types of publications
• 3. What to include - “Publishable unit, PU”
• 4. With whom - Question of authorship
• 5. How to write - Structure of the paper
• 6. How to get it published – Rebuttals to reviewers

Types of Publications (1)

Theses Project reports, annual updates Conference papers, proceeding books International journals Non-refereed journals Popular articles

Types of Publications (2)

Project reports, annual updates

• summarizes recent work
• essential in collaborative projects with industry
• often local language
• limited access
• no “real publication”, cannot be cited
• no long-term value!
• should in any case be written in a scientific way,

preferably following the structure of an article.

• all technical details should be carefully documented

Types of Publications (3)

Conference papers, proceeding books

• rapid feedback to ongoing work
• easily accepted (review of abstracts only)
• no review of the full paper
• no “real publication”, no scientific value
• should be submitted to a peer review journal

Types of Publications (4)

International journals with referee system

• papers reviewed by unidentified referees
• quality approved by scientific community
• archived and easily accessible for colleagues
• referee comments very useful (don’t give up after

first rejection!)

• the only right place for new results

Impact Factor

• The impact factor (IF) is a measure reflecting

the average number of citations to recent articles published in that journal.

Journal Review

widest circulation, but little chemistry, consider for the very best papers High impact-general chemical journal, large circulation, privately affordable. Broad coverage decreases the number of papers of interest to specialists. High impact. Two languages. Communications and reviews, but no full papers. Full papers and now competes with JACS in impact. Science Nature JACS Angew Chem

• Chem. Euro. J

M Hupa – 2011

Types of Publications (5)

Non-refereed journals –popular articles

• for a broad audience (Kemia-Kemi, …)
• very useful for PR (for industrial people,

teachers, decision makers, public image)

• no real scientific contribution
• not always accessible to colleagues in science
• not suitable for publishing new results for the

first time!

Issues to be discussed

1. Why to write publications – To be or not to be?

• 2. Where to publish - Types of publications
• 3. What to include - “Publishable unit, PU”
• 4. With whom - Question of authorship
• 5. How to write - Structure of the paper
• 6. How to get it published – Rebuttals to reviewers

Publishable Unit

• Projects often bring plenty of results.
• Many journals prefer short, focused papers
• Project reports seldon suitable
• Learn to think in terms of ”Publishable Units”
• Plan PU’s already in your project plan
• Be flexible to new ideas of PU’s

Issues to be discussed

1. Why to write publications – To be or not to be?

• 2. Where to publish - Types of publications
• 3. What to include - “Publishable unit, PU”
• 4. With whom - Question of authorship
• 5. How to write - Structure of the paper
• 6. How to get it published – Rebuttals to reviewers

Authorship Question

Important issue, may easily cause problems. Paper: the final ”product” of research work. Should you include anyone who:

• writes or revises parts of the paper?
• contributes substantially to the work?
• can take responsibility for a part of the paper?
• can defend the entire paper?
• is a good friend/loyal colleague, BB (big boss)?

1992

One author: no problems

Authorship: Order of Names

• Student, others (incl. coach), supervisor, or:
• Supervisor, others, student
• Main author, others, most responsible author
• > PhD Student, MSc Student, Coach, Supervisor

Main author writes first draft!

Simakova et al, Murzin and co-workers

But!

Authorship Question

• Don’t be shy, agree at an early stage (and stick

to the agreement!)

• Be active, initiate collaborative papers. Fun!

Issues to be discussed

1. Why to write publications – To be or not to be?

• 2. Where to publish - Types of publications
• 3. What to include - “Publishable unit, PU”
• 4. With whom - Question of authorship
• 5. How to write - Structure of the paper
• 6. How to get it published – Rebuttals to reviewers

Structuring the Paper

• Title
• Abstract
• Introduction
• Experimental section
• Results
• Discussions
• Conclusions/ Implications
• Acknowledgments

IMRAD Format

• I = Introduction, what question (problem) was studied
• M = Methods, how was the problem studied
• R = Results, what are the findings
• A = and
• D = Discussion, what do these findings mean

Title

• Very important – defines focus of the paper
• Will be the key for any literature searching
• Should be troroughly discussed by all authors
• Specific vs. short
• Depends on the journal

Structuring the Paper

• Title
• Abstract
• Introduction
• Experimental
• Results
• Discussions
• Conclusions/ Implications
• Acknowledgments

Abstract: Indicative vs. informative

Indicative abstract only indicates the subject of the paper. Suitable for:

• review articles
• theoretical papers, and
• symposium abstracts that are due before you

have begun your experiments

Abstract: Indicative vs. informative

Informative abstract describes:

• the problem or purpose of the research, or an

hypothesis

• your methods
• your principal findings (results also in numbers)
• even possibly some conclusions

”Mini Paper” – understandable as such

Abstract

The electronic structures of the first-row transition-metal metallocenes, MCp2 (M = V, Cr, Mn, Fe, Co, and Ni), have been studied using a broad range of d. functional methods with flexible double-z plus polarization (DZP) basis sets. Geometrical parameters of the D5h and D5d conformations (and structures of lower symmetry for CrCp2 and CoCp2) were fully optimized. For the ferrocene system, best characterized experimentally, the B3LYP, BLYP, and BP86 methods give structures in good agreement with experiments. For the D5h-D5d energy difference, the same three methods predict 0.75 kcal/mol (B3LYP), 0.99 kcal/mol (BLYP), and 1.13 kcal/mol (BP86). The cyclopentadienyl rings are very nearly planar; the angles of the C-H bond out of the Cp ring are less than 1° for all metallocenes except ferrocene. The C-H bonds are bent slightly away from the metal for V and Mn, slightly toward the metal for Fe and Ni, and virtually not at all from chromocene. According to the energetic and vibrational analyses, the D5h conformations are the global min., leaving open the possibility that the D5d conformations may exist under certain conditions. However, MnCp2 probably exists as a mixture of both D5h and D5d conformations, because both are genuine min. with only a small energy

• difference. The predicted B3LYP energy differences (D5h-D5d) for the six metallocenes are 0.29 (V), 0.28 (Cr), 0.13

(Mn), 0.75 (Fe), 0.38 (Co), and 0.23 kcal/mol (Ni). A number of reassignments of experimental vibrational bands are

• suggested. The MO energy level diagrams and the electron configurations for the metallocenes are compared. This

information, obtained in a consistent manner across the first transition metal series, is helpful for discussion of the bonding characters and the chem. reactivities of these metallocenes. Systematic Investigation of Electronic and Molecular Structures for the First Transition Metal Series Metallocenes M(C5H5)2 (M = V, Cr, Mn, Fe, Co, and Ni).

Zhen-Feng, Xu,1,2 Yaoming Xie,1 Wen-Lin Feng,2 Henry F. Schaefer III1

1 Center for computational Quantum Chemistry, University of Georgia, Athens, GA, USA. 2 Department of Applied Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China

• J. Phys. Chem. A 2003, 107, 2716

Structuring the Paper

• Title
• Abstract
• Introduction
• Experimental
• Results
• Discussions
• Conclusions/ Implications
• Acknowledgments

Introduction

• A. Give general context (Define who is the reader?
• B. Show that you know the key literature (mention

ALL references dealing with your topic!)

• C. What was missing in the literature, what made you

choose your topic?

• D. End with specific “mission statement” of purpose

and content: “In this paper ...

Novelty and Importance!!!

Novelty and Importance!!!

Structuring the Paper

• Title
• Abstract
• Introduction
• Experimental
• Results
• Discussions
• Conclusions/ Implications
• Acknowledgments

Experimental

• Or: Methods and materials
• Or: Theoretical Basis or Theoretical Treatment
• Write in the past tense. Never use “”I” or “we”.
• Straight forward?

Experimental section-checklist

• Chemicals and materials (report all of them)
• Analysis/characterisation equipment and methods (equipment, columns,

detectors, sample treatment procedures, retention times)

• Experimental (e.g. reactor) equipment (reactor, pretreatment units,

impellers, jackets, temperature and pressure control, data acquisition…)

• Experimental programme (temperature, concentration, pressure

domain, liquid/gas volumes, mass of catalyst, flow rates, residence times)

• Experimental procedure (how the experiment was performed, report all

the steps concisely)

Experimental section-checklist

An outsider should be able to repeat the experiment based on the description – go through each time a checklist of this kind – things are easily forgotten

Structuring the Paper

• Title
• Abstract
• Introduction
• Experimental
• Results
• Discussions
• Conclusions/ Implications
• Acknowledgments

Results

• Tables and figures, make sure you refer to all
• Good figure format (not too much per figure, just make

your point)

• All results should not be reported, just enough of the

relevant ones to make your point (and prove accuracy etc.)

• Just “explain” the results, do not discuss (may be difficult)
• Past tense vs. present tense

Balance: text, figures, tables

1. At final reduction, this lettering is too small to be readable. 2. This line is too thin. At final reduction, this line may not show up at all. 3. These symbols are too small. Different symbols of this size will look the same on the printed page. 4. This lettering is too large when compared with that of point 1. All of the lettering should be of similar size. 5. This line is too broad. Lines of this size will merge when reduced for publication. 6. The patterns that simulate grays will appear blotched when printed.

Better Artwork

This figure will not reproduce well.

1. Larger lettering is used. 2. A thicker line of 1 point is used. This line is thick enough to be effectively picked up by the scanner. 3. Larger symbols are used. Symbols and lettering are of similar size. 4. Smaller lettering is used. 5. A thinner line is used. This line will not easily merge with the other data. 6. The shading is eliminated.

A figure like the one above will reproduce well

Better Artwork

Discussion

• Results and Discussion in one chapter vs. in two?
• Present principles, relationships and generalizations shown by

the results

• Compare with literature data
• Point out exceptions or lack of correlation
• Define unsettled points (don’t try to “explain” everything!)
• Discuss implications of your results: do we need to refine

earlier concepts, theories, practices?

Structuring the Paper

• Title
• Abstract
• Introduction
• Experimental
• Results
• Discussions
• Conclusions/ Implications
• Acknowledgments

Conclusions

• List the key findings with respect to the

“mission statement” in the introduction

• Past tense vs. present tense
• Bring up technical implications

Structuring the Paper

• Title
• Abstract
• Introduction
• Experimental
• Results
• Discussions
• Conclusions/ Implications
• Acknowledgments

Acknowledgments

• Don’t forget! Check once more the list of persons

you give your gratitude

• Remember all parties! Be generous!
• “Gray organizations” also consist of people, don’t

forget to mention (Academy of Finland, EU)

• Primary literature –

Who first lad the basic idea? Who did the most important work before ? Who else contributed significantly? Cite, but do not depend only on reviews. Give credit to originators.

References

Tell your story to the colleagues

• Tell an encouraging story, how you pushed through a

paper

• Never surrender!

Based on MSc thesis done in 1985

Issues to be discussed

1. Why to write publications – To be or not to be?

• 2. Where to publish - Types of publications
• 3. What to include - “Publishable unit, PU”
• 4. With whom - Question of authorship
• 5. How to write - Structure of the paper
• 6. How to get it published – Rebuttals to reviewers

Getting it published

1. Choice of Journal 2. Submission of manuscript 3. Note of receipt 4. Referee comments and recommendation by editor: (A) Not rejected (B) Rejected

Getting it published (A)

1. Choice of Journal 2. Submission of manuscript 3. Note of receipt 4. Referee comments and recommendation by editor: (A) Not rejected (B) Rejected A: Not rejected 5 A. Rebuttals- take it seriously 6 A. Final decision by editor 7 A. Final manuscript 8 A. Proof version 9 A. Galley proof 10 A. Publication

Getting it published

1. Choice of Journal 2. Submission of manuscript 3. Note of receipt 4. Referee comments and recommendation by editor: (A) Not rejected (B) Rejected

Getting it published (B)

1. Choice of Journal 2. Submission of manuscript 3. Note of receipt 4. Referee comments and recommendation by editor: (A) Not rejected (B) Rejected B: Rejected 5 B. Take it easy 6 B. Resubmit after changes 7 B. Submit to other journal 8 B. Go to 2.

Contesting the rejection decision

Consider it only if you honestly think and at least

• ne night‘s sleep, that the editor and referees

have made a superficial or wrong judgement. In this case write a polite letter explaining as briefly as possible why you think the editor should reconsider his/her decision

Some final remarks

1. Think about publications, articles from the first beginning

Some final remarks

1. Think about publications, articles from the first beginning 2. Perform experiments in such a manner that systematic entities are formed (e.g. determination of kinetic trends, temperature/concentration/catalyst effects)

Some final remarks

1. Think about publications, articles from the first beginning 2. Perform experiments in such a manner that systematic entities are formed (e.g. determination of kinetic trends, temperature/concentration/catalyst effects) 3. Keep a very good documentation of experiments; avoid uncontrolled accumulation of experimental data

Some final remarks

1. Think about publications, articles from the first beginning 2. Perform experiments in such a manner that systematic entities are formed (e.g. determination of kinetic trends, temperature/concentration/catalyst effects) 3. Keep a very good documentation of experiments; avoid uncontrolled accumulation of experimental data 4. Take it very seriously, when the supervisor/colleague tells that now it is time to write – Power Point presentations are not an article!

Some final remarks

1. Think about publications, articles from the first beginning 2. Perform experiments in such a manner that systematic entities are formed (e.g. determination of kinetic trends, temperature/concentration/catalyst effects) 3. Keep a very good documentation of experiments; avoid uncontrolled accumulation of experimental data 4. Take it very seriously, when the supervisor/colleague tells that now it is time to write – Power Point presentations are not an article! 5. Start the writing with the part you feel easiest (typically from the experimental part; Introduction should be written last or at least checked once more very carefully when the manuscript is ready)

Some final remarks

1. Think about publications, articles from the first beginning 2. Perform experiments in such a manner that systematic entities are formed (e.g. determination of kinetic trends, temperature/concentration/catalyst effects) 3. Keep a very good documentation of experiments; avoid uncontrolled accumulation of experimental data 4. Take it very seriously, when the supervisor/colleague tells that now it is time to write – Power Point presentations are not an article! 5. Start the writing with the part you feel easiest (typically from the experimental part; Introduction should be written last or at least checked once more very carefully when the manuscript is ready) 6. Think carefully where to publish

Запомнили что-нибудь?

Homework: Analysis of Structure of Selected Papers

Total presentation time 10 min Introduce briefly the whole subject of the paper Give critical comments on:

• Title (specific-short)
• Abstract (indicative-informative)
• Introduction (context/purpose!)
• (Experimental/Results/Discussion just briefly)
• Conclusions (vs. purpose)
• Other aspects