Writing scientific paper

Berkeley Lab organized yesterday short workshop focusing on writing for scientific journals. The workshop took 2 hours and it was mainly focused on the “schedule” we should follow during the publication preparation.

The first part summarized the journal selection. I will not go to much details here, because we probably already know in which journals we want publish (Anal. Chem, J. Chromatogr. A and B, J. Sep. Sci., Talanta, Anal. Chim. Acta, Electrophoresis, Chromatographia, Trends in Anal. Chem., to name few of them).

Journal selection is very important, in some cases 95 % of manuscripts is rejected where 50 % are rejected because of wrong journal selection. I have already mentioned it previously in the post from the other side: what editors want.

Very important part of the manuscript preparation is reading the journal’s guidelines. Usually, you can find there a lot of useful information about the content and focus of the journal, format of manuscript, subsections and heading, and references and graphics arrangement.

Next part – the abstract writing – was the most important for me. We have discussed the structure of the freely accessible Nature summary paragraph example.

After one to four general sentences with theoretical background follows section describing general problem of our work together with our results summarized in two three sentences. On the end of the abstract we can put the results into a more general context and (if possible) provide a broader perspective of our work.

Finally, we have focused on the revision and corrections. The better you revise before submission, the less you will revise later. Few simple things usually helps:

1. ask someone to read it for you
2. read it aloud (not always helping, sometimes you read what you want to read)
3. use the computer reading program (can have problems with technical stuff, but will clearly show you problems with your sentences)
4. with writing software, you can also easily find repeating words such as prepositions, be forms, empty qualifiers such as quite, very, really and so on)

Further reading: How to write a scientific paper at Nature website.

At given pressure, the higher is flow through the column the higher is the permeability of the column. More exact definition of the permeability is described as  the volume flow of fluid per unit time per unit area per unit pressure gradient.

In case of liquid chromatography, there is limiting pressure that has practical uses, so if particle s with small diameter are used (to have as low plate height as possible), then the column with limited length and mobile phase with a low viscosity have to be used.

Column permeability calculation

The column permeability can be easily calculated from the flow and column characteristics using the embeded equation. Here the F_m is the mobile-phase flowrate, η is the mobile-phase viscosity, Δp is the pressure drop across the column, L is the column length, and r is the column inner radius.

One can see that the flow of the mobile phase through the column is directly proportional to the pressure across the column and the fourth power of the particle diameter and inversely proportional to the product of the mobile phase viscosity and the length of the column.

This monolithic column affords good separation of uracil and alkylbenzenes in isocratic mobile phase mode (a column efficiency as high as 73 000 plates/m was determined for uracil) and also proved useful for separations in size exclusion mode.

Organic polymer monoliths and small molecules

Compare to silica based monoliths, porous polymer monoliths contain very small or even no concentration of small pores in their porous structure. Therefore, they exhibit much smaller surface areas (tens of square meter per gram) and usually are not suitable for separation of small molecules. Several approaches were explored to improve this drawback of organic polymer monoliths: copolymerization of dimethacrylates differing in the length and branching of the fragment connecting the polymerizable units[2]; the termination of the polymerization reaction at an early stage [3,4] to achieve large surface areas; and the use of high polymerization temperatures [5,6].

However, it has always proven difficult to prepare polymer monoliths possessing both large through pores and a multiplicity of small pores in a single step and alternative approaches needed to be developed.

Hypercrosslinking modification

Separation of uracil (1) and small alkylbenzenes (2-7) with organic polymer monolith. See Ref. 1 for more details.

Hypercrosslinking, pioneered by Davankov several decades ago [7-10] enables the preparation of large surface area materials from preformed polymer precursors. The original implementation used linear polystyrene, which was cross-linked via Friedel-Crafts alkylation to afford materials containing mostly small pores [11].

The typical porous monolithic structure consisting of interconnected microglobules results from phase separation during polymerization of a mixture of monomers and porogens. For poly(styrene-co-vinylbenzyl chloride-co-divinylbenzene) monoliths less than ideal reactivity ratios for monomers such as styrene, chloromethylstyrene, and divinylbenzene lead to polymer microglobules amenable to hypercrosslinking. The divinyl monomer polymerizes faster, and the remaining monomer mixture becomes significantly richer in the monovinyl monomers as the polymerization reaction nears completion. This mixture then affords only slightly cross-linked chains attached to the surface of highly crosslinked microglobular scaffolds. When the pores are filled with a thermodynamically good solvent such as 1,2-dichloroethane, this surface polymer layer is solvated.

Capillary liquid chromatography

The precursor column performs poorly as all alkylbenzenes are less retained and eluted in a single broad peak. In contrast, baseline separation of all alkylbenzenes is obtained with the column after hypercrosslinking (see Figure). On the other hand, gradient separation of the proteins is better on the non-modified column because of negative effect of the small pores on the gradient separation [12]. Finally, because of significant concentration of small pores, these columns can be used for separation of polymers in size-exclusion chromatography.

Our work clearly demonstrates the possibility of postpolymerization hypercrosslinking of the monolithic stationary phase to afford columns for efficient isocratic separation of small molecules in reversed phase and polymers in size exclusion modes.

References

1. Urban, J., Svec, F., Fréchet, J.M.J. Anal. Chem. 2010, 82.
2. Xu, Z., Yang, L. and Wang, Q. J. Chromatogr. A 2009, 1216, 3098 – 3106.
3. Wang, Q., Svec, F. and Fréchet, J. M. J. Anal. Chem. 1995, 67, 670 – 674.
4. Trojer, L., Bisjak, C. P., Wieder, W. and Bonn, G. K. J. Chromatogr. A 2009, 1216, 6303 – 6307.
5. Peters, E. C., Svec, F. and Fréchet, J. M. J. Adv. Mater. 1999, 11, 1169 – 1181
6. Meyer, U., Svec, F., Fréchet, J. M. J., Hawker, C. J. and Irgum, K. Macromolecules 2000, 33, 7769 – 7775.
7. Davankov, V. A., Rogozhin, S. V. and Tsyurupa, M. P. Macronet Polystyrene Structures for Ionites and Method of Producing Same. U.S. Patent 3,729,457, April 24, 1973.
8. Pastukhov, A. V., Tsyurupa, M. P. and Davankov, V. A. J. Polym. Sci., Polym. Phys. 1999, 37, 2324 – 33.
9. Davankov, V. A. and Tsyurupa, M. P. React. Polym. 1990, 13, 27 – 42.
10. Davankov, V. A., Tsyurupa, M., Ilyin, M. and Pavlova, L. J. Chromatogr. A 2002, 965, 65 – 73.
11. Tsyurupa, M. P. and Davankov, V. A. React. Funct. Polym. 2006, 66, 768 – 779.
12. Urban, J., Moravcova, D. and Jandera, P. J. Sep. Sci. 2006, 29, 1064– 73

WebEx is software delivered as a service which you can use it from any computer with an Internet connection. WebEx combines real-time desktop sharing with phone conferencing, so everyone sees the same thing as you talk. And that is exactly what happened.

I asked people from Bruker for advice with my (instrument;) communication problem and we scheduled the WebEx seminar (let’s call it seminar). At exact time I connected to the website they sent me and our online communication started.

For me, it was brand new experience. Ok, I have to say I have no problem with online communication (chat, blogs, social media, …) but it was for first time for me to join the online communiation because of the problem with chromatographic instrument. And I found it very useful.

The online comminication

• saves cost expenses – we all know that it is not always necessary to set up service visit,
• saves time – very important, the seminar can be scheduled on every possible time, which meets requirements of both side
• enhances productivity – majority of the problems can be solve with some kind of advice

I know, all this can be done also using the phone. And for sure, phone is very useful. But using the online communication, you can allow the servicing company the full control over your instrument computer and you don’t have to worry about (almost) anything.

I had this experience with the Bruker company. I am sure others companies offer the same service (or will offer very soon). I belive, that online service is the future of the instrumental service and that majority of the troubleshooting will be solve in this way.

Working on the review

Recently, there was a post about the role of the referees in the science on a The Sceptical Chymist. The post described Nature Physics editorial which focuses on the demands Nature Physics has on the reviewers.

I think, it is not only source of the information for (current and future) reviewers but also for us – scientists trying to publish their work throughout scientific community. No matter if it is Nature Physics, Chemistry, Whatever, …

Therefore, I have chosen seven tips from the editorial and listed them below.

1. First of all, the editor reads the submitted paper with related literature to decide if the paper is good enough to be publish in Nature Physics. Only about one fifth of the submitted papers is chosen for further consideration.
2. The paper should fits into a wider context. Theoretical paper is often assessed by experimentalists and vice versa. As states in the editorial: Science at its best happens where experiment and theory meet.
3. Because of the first selection, they are not primary interested in your opinion whether the paper should or shouldn’t be publish. However, they need to know the strengths and weaknesses of the paper, and in particular contribution of the paper to the field.
4. Does the paper make you think to yourself “Wow! I didn’t expect that!” or “Wow! That could be really useful!” They are looking forward to hearing this kind reaction.
5. Even among paper that do report major results, very few are so perfectly formed in the hands of their authors as to be suitable for publication with little or no revision.
6. Ideally, the significance of every published paper should be clear and accessible to any (physics, chemistry, math, …) graduate. This is one of the main points in the editorial! If even a specialist can’t make sense of it, where is the reason for publication?
7. Finally, as a general rule, keep things collegial and stick to the facts. These are, after all, your peers, who could quite possible soon be reviewing your work.

Even though, this list was written for the reviewers, I think there are several important and interesting ideas, which can help us to write better papers with small or even no problems with their publication.

Agilent 1100

From time to time, we all face problems with HPLC instruments. Then, we all search the internet for the solution for our problem. In this troubleshooting section I would like to point out my problems with instruments and their solutions. Hopefully, it can help also you.

Recently, I was asked to run the HPLC-MS instrument which was off for several months. The LC part was Agilent 1100 and MS was from the Bruker (HCT+). The instruments themselves worked fine, but there was a problem with their connection. At least I thought so. The Agilent HPLC went always to power off mode after couple of minutes. No matter what I have done, no matter what I have tried. It always went to shutdown mode.

As I said, I thought the problem is in their internal (software) connection. The Bruker HyStar software was started by the ChemStation. Because of this I have contacted Bruker company and asked them about the problem. I will speak about the webex communication sometimes in the future, but I have to say it was a nice and new experience. The guy from the Bruker told me, that there is no problem with the connection at all. Therefore I have continued to ask – Agilent this time.

They told me, that the problem I am describing can be caused by the instrument degasser. After the long time, when the instrument is not used at all, the degasser can be broken. It is still working, still degassing the mobile phase, but it can send the wrong input to the instrument and switch it off.

So, if you have a problem with the Agilent instrument (1100) which is going to the power off mode without any reason, check the connection on the back of the instrument. If there is a line between the degasser and the main unit of the instrument (usually pump, but can be autosampler too) than disconnect this line. It is probably different type of connection than the LAN type.

It is probable, that the (autosampler) control light will go red after while. But as soon it can not comunicate with the instrument, it cant tell that something is wrong. And you have still a lot of time to contact the company service to solve the problem with the degasser. Alternatively, you can ultrasonicate the mobile phase or degass it with the stream of helium.

Example of liquids with different viscosity

UPDATED – One of the general property of the liquids is their resistance to change a form. This resistance is called viscosity and can be expressed as a resistance to flow. In case of liquids, the viscosity can be simply expressed as “thickness”. For example, water is “thin” with low viscosity, while honey is “thick” having a higher viscosity (see example on right). More technically speaking, viscosity is classically defined as the tangential force per unit area necessary to maintain unit relative velocity between two parallel plates in a liquid unit distance apart.

Viscosity unit conversion

The unit of viscosity is called the poise (P). The SI unit for the viscosity is Pascal-second (Pa.s).

1 cP = 0.001 Pa.s

Viscosity of the mobile phase

In liquid chromatography, the viscosity of the mobile phase plays crucial role. It influences the maximum pressure used. Clearly, the mobile phase with lower viscosity shows lower instrumental pressure. Thus, higher flow rates of the mobile phase can be used and lead to the shorter analysis time.

Following tables and plots show dependence of the viscosity for a acetonitrile-water and a methanol-water mixtures at different composition of the binary solvent and temperature. Generaly, the viscosity decreases with increase in concentration of the organic modifier, acetonitrile or methanol, respectively. Further, as you can see from the following figures, the viscosity decrease with higher temperature, which forces further research in the field of high temperature liquid chromatography.

Acetonitrile-water mixture

Methanol-water mixture

Source

These data are based on the table presented in Introduction to Modern Liquid Chromatography (L.R. Snyder, J.J. Kirkland, J.W. Dolan, Willey, 2010, 3rd ed.).

For different solvents look in the Mixtures of Water and Organic Compounds file in Landolt-Börnstein Database.

Viscosity of the binary mobile phase

Do you need to know viscosity of your mobile phase composition? Use Chromatographer’s calculator (for methanol, acetonitrile comming soon).

Happy New Chromatographic Year

Not only from the chromatographic point of view, I wish you in the year 2010:

• low pressure
• high efficiency
• sharp resolution
• large capacity
• and satisfactory results

… or (in case you dont want to use chromatographic expressions) you can use any of the translations.

My favorite forum: Chromatography Forum

Chromatography Forum is a public discussion group where you can post questions, news, or messages of interest to chromatographers everywhere.

I have asked Tom Jupile (founder and moderator) for some factual data about the Chromatography Forum. The forum was started in May 1999 as an adjunct to the LC Resources web site, and was updated to its present format in September 2004. Nowadays, it is probably the busiest chromatography site in the world with about 250 new messages every week. The database has over 57 000 messages (plus another 14 000 or so in the pre-2005 archives), all of which can be searched by keyword.

It is truly an international site: in the past month, it had 15 000 visits from 116 countries, of which almost 2/3 were from outside the US (btw. 69 of them from the Czech Republic;).

Chromatographers: nice community

One thing has to be pointed out. More then half of the Tom’s answer is devoted to the mentality of the chromatographic community. It is nice to hear, that the group of people surrounding the 100 years old separation idea is willing to help and share the ideas, advices and thoughts.

I have been the administrator and moderator since the beginning, but apart from occasional issues with the software (and the internet service!) the amount of effort involved has been minor. Unlike other discussion groups with which I am familiar, the Forum is a remarkably civilized place, with a negligible level of sarcasm, rudeness, and “flames”.

I think this is quite a tribute to the professionalism and generosity of the “chromatography community”: as a group they show a remarkable willingness to share their expertise and knowledge. Over the ten years of the Forum’s existence, I have only ever had to “warn” perhaps a half-dozen people about inappropriate posts, and only ever banned one person. (

Tom Jupille, ChromForum.org moderator

Exactly, chromatographers are nice people!

How to write world class manuscript?

Do you know how to write the scientific paper? Are you looking for step by step procedure you should follow? Download Editor’s Presentation on “How to write a world class paper” prepared by the Elsevier.

The presentation covers each step of preparing manuscripts and submitting them to scientific journals for publication, and is delivered by Guowang Xu, Editor of Journal of Chromatography B.

I wanted to prepare outline of the presentation. However, it is full of the very interesting and comprehensive information and I didn’t want to omit any important one. Therefore I have chosen only one slide, which summarize all in one:

What gets you accepted?

• Attention to details
• Check and double check your work
• Consider the reviews
• English must be as good as possible
• Presentation is important
• Take your time with revision
• Acknowledge those who have helped you
• New, original and previously unpublished
• Critically evaluate your own manuscript
• Ethical rules must be obeyed

Nigel John Cook, Editor-in-Chief, Ore Geology Reviews

If you are interested in more information, visit the website with the presentation.