Fetzthechemist’s Weblog

Part 4 – Hydrocracker red death, alternate storylines by others (not!) July 20, 2025

In the many years since the coronene dimerization by the Scholl condensation was found to make the hydrocracker deposits, others have put forward alternatives as explanations. The 2 that have been the most visible have been a sets of papers by the Saudi Aramco research group in Dhahran and by UOP-Honeywell.

The Aramco group has published papers, Saroj K. Panda, Hendrik Muller, Thunayyan A. Al-Qunaysi, Omer R. Koseoglu, Journal of Chromatography A, 1533 (2018) 30–37 and Nadrah A. Alawani, Hendrik Muller, Saroj K. Panda, Adnan A. Al-Hajji, and Omer R. Koseoglu, Energy and Fuels, 34, 179-187 (2020). In these, their focus is on only the compounds of 7 rings or more created by the one-ring additions, such as coronene and ovalene. They do not even mention the dimerization reaction.

The Uop work, sold to refineries as part of a remediation package, relies on this chemistry and then further claims that a fluorecence monitoring with specifics of around of 510 nm excitation and 525 nm emission will monitor these types of large PAHs that cause the plugging and catalyst deactivation. These, from my extensive research in the 1980s, are not true or at best not the full story.

I had real pure standards of many of the large PAHs these two groups claim. (In fact, in the first Aramco paper, their chromatogram peak 5 is incorrect – it is not benzo[a]coronene, but an isomer that I isolated and reported in the early 1990s). From my fluorescence work, partly given in the appendix of my book on large PAHs that shows fluorescence spectra of many pure samples. Ovalene might give such fluorescence through its secondary emission bands, but most of the large PAHs these groups show do not fluoresce at such high wavelengths. Only the dimer, dicoronylene, does with intensity.

In my work on the deposits, I had extracted these large PAHs with dichloromethane. They were only a few percent, less than 2% of any Red Death deposit out of the many dozens I had studied. A good source for isolation to identofy specific PAH, but not a major cause.

Part 3 Refinery hydrocracker Red Death June 21, 2025

• leapfrogging to very large PAHs

Things were moving forward after only 3 years of planning, set up, studying, and experimenting. But was the deposit just a mix of the one-ring additions?

Another addition to the lab capabilities had been getting a spectrofluometer. This allowed looking at very low concentrations of PAHs, parts per billion in the oils, rather than parts-per-million. 3DE fluorescence allowed simple mixtures (like liquid chromatography fractions) to be analysed and individual PAHs to be seen.

Fluorescence spectra for a single PAH are “pure” in the x and y axes of excitation and emission, giving a pattern for each PAH. This illustration shows a mixture of 2 isomers of 11 rings.

The red deposit was slightly soluble in 1,2,4-trichlorobenzene.

The fluorescence spectrum looked exactly like dicoronylene and when thermal probe mass spectrometry was used also looked like dicoronylene.

So, red death was a simple mix of dicoronylene and its methyl and dimethyl derivative. It was made by the Scholl condensation where the catalyst acidic alumina sites fused 2 coronenes (in the original organic chemistry by Scholl in 1905, aluminum (III) chloride had been used.So, the one-ring buildup made coronene and then that was turned into minute amounts of dicoronylene that precipitation once its parts-per-billion range solubility was exceeded.

Simple chemical reactions, a simple product.

Prepping for grad school to get the advisor you want July 9, 2023

Most students think that getting accepted by the grad-school program they wanted is the last major step before the on-site tasks that lead to being in their hoped-for research group. This often lets them be surprised by one step tht can be a great help or a great hindrance – the exams that most chemistry departments give to incoming grad students before the school year begins (that is their main reason for having beginning grad students show up a week or so before the term begins. They caqll it orientation or some such, but they have a battery of exams, usually focused on the main branches of chemistry. Thgeir goal is to assess each student’s real knowledge level since every college or university worldwide has different requirements, emphases, and course offerings, with the added differences of each student’s choice of courses to take or not take, their aptitude in each discipline. Each grad student may or may not be ready for the graduate-level courses offered. They may or may not be reacy for cumes or whatever qualifying tests for a doctoral program the department has.

Not knowing this, most students just show up expecting an orientation and get hit by these exams. They have nor refreshed their knowledge since taking the GRE. Some do miserably and the result is having to take the specified undergrad courses in order to prove capability for this department[‘s graduate courses. That can be time added onto the grad0-school duration. It can give a false image to the professors of that student’s possibilities.

The contrary is also true. Doing well on them gets a student noticed. They might find more doors open when they are choosing a research advisory. (I did extremely well on mine, years ago, and the professors knew who I was out of the more than 25 other beginning grad students.

A caveat, too. Do not assume beforehand that you will get into the research group you want. Big names can be choosy. Research funding is limited. The professor may not be who you thought you would find – they are people and you might find that a big name has a personality than you are not compatible with or that may not like you.

Getting into a chemistry grad-school program – things before applying July 3, 2023

Chemistry grad-school programs operate in a familiar way that most students do not know. It is very much like undergrad sports programs – a limited number of slots, lots of funds for support that are given out based on potential and the desire of the program to have the best people it can, and there are clocks ticking.

Each chemistry department has a target number of opening. You as a student do not know how many this is, so you do not know how easy or hard it may be to get in. You are not guaranteed any monies when applying – the department decides what type of support you are offered and at what amounts.Teaching assistantships are the most common form, but there are levels in amounts of money offered. There also are fellowships and other funding that require different roles for the student, often with very much smaller time requirements. Instead of teaching for several hours per week, you might be a grader or proctor for exams. You might be a tutor for undergrads who need help. You might only have to help ewnroll students on registration days.

With all of this, the better you look to a grad school, the more you may be offered. If you have a strong transcript, loaded with advanced and especially graduate-level courses, you look stronger. As soon as is possible as an undergrad you ought to be taking, or even just sitting in on grad courses for no grade or only a pass-fail mark. Doing honors research is also a plus.

Since grad schools have limited numbers of openings, take any exams, such as the Graduate Record Exam, as early as you can. That helps you apply earlier. A very strong candidate might get an offer early and that leaves fewer slots for late-appliers to try to win. Applying in January is way too late.

As far as where to apply, that is not just what research is being done by certain professors. You do not know if that professor will even be there the following year when you arrive. Professors to move around. Have contingencies. Choose a department where there are several possible good research groups besides those of the “big-name” you might dream of working for.

Do not just aim for your ideal few schools. You do not know who your competition is or how they look to those departments. Apply to a few good departments that you know you should get into in addition to the ones you know are more competitive. If you are not accepted by all of the latter group, you will still be in grad school the year you want to be – if not you have one whole year to retry for those who rejected you – and you lose one year in getting your advanced degree when you might have.

If you do get accepted by several strong schools, you may be desirable enough to get in a recruiting battle. Schools might change their offers to attract you, changing teaching assistance into one of the other forms that will demand less time and work on you. They will often offer to give you a trip to see their department and meet their faculty.

Getting a great grad school position is not just applying and waiting to see how it plays out. You can influence your chances and what goes on.

(Although I went through this a long time ago, the overall process has not changed very much. I had lots of grad-level classes on my transcript – which did affect my GPA and some schools did not take that into account, but most did. I had a 99 percentile in the Chemistry GRE. I had a fellowship for most of my offer from the school I went to – which also made me more attractive to professors because their research funding did not have to support me.)

How to get into the chemistry grad program you want July 1, 2023

This is a heads up that I will be writing several pieces aimed at undergraduate chemistry students as advice in advancing their careers. I am composing 2 or 3 articles on the first topic of getting into your desired grad school – the things to do and the things to expect.

Academia (in the USA) and US patent law May 30, 2022

Once upon a time…..I was the main writer and editor of a career-development column in a scientific journal was called “Building a Professional Career” and was publish regularly in the Springer Verlag journal Analytical and Bioanalytical Chemistry. I had had carte blache from the editor and editorial board to write on any topic or to solicit articles from people on topics I thought they could contribute. I wrote over 50 such articles. Occasionally I would use this to review books that I thought were useful to research chemists. One such was: “Book review: Chris P. Miller and Mark J. Evans The Chemist’s Companion Guide to Patent Law”, J. C. Fetzer, Anal. Bioanal. Chem., 399, 1009-1010 (2011).

Having worked in industry and being inventor or co-inventor on 3 US patents, I knew pretty well how a lot of patent law worked. Employees doing research and development were exposed to the patent process and to patent law, and companies train their employees on how to conduct research to comply with those.American academia has never been very aware of this until the past couple of decades when professors and universities realized the immense wealth involved in patenting research.

But academia had a history and mindset that was not attuned to generating patents. Who was the generator of ideas was often not documented, let alone with detailed proof of the ideas, the proofs, and especially their timing was nowhere near what was done in industry. As academia moved into applying for and gaining patents, they also found that competitors, both in industry and in other academic institutions, were going to the US Patent Office or to the courts to contest patents on numerous grounds.

Some of these involved the timing, as the shoddy record-keeping in academic research groups often did not have proof of a legal standing (notebooks were not organized clearly to prove their validity, little or no dating and even less for witnessing was done as proof, changes and erasures abounded with no explanation or clarity as to why and what had been there previously, et cetera. Assignation of inventors was mirky and had little record-keeping, a holdover from the research professor’s power to assign authorships for submitted research papers that allowed whims, biases, and preferences. All of these led to numerous judgements invalidating patents that universities and professors held. So, thus, the need for the book.

The article generally was met favorably, but some American academicians were upset, and one (a prominent atomic spectroscopist who was a member of the advisory board of the journal, which I had also been for over a dozen years prior to becoming the column editor and I will call Gary H. for the purpose of this story) was livid. He thought the whole parts about patent law saying that since graduate students and post-docs were working on projects where a professor had generated funding for the research, then they were in the same role as an employee in private industry, particularly if they are paid to do the research (the case for many grad students and almost all post-docs). This contrasts with the old-school mentality in academic research that everyone is a team member, blah, blah, blah.

Gary H. contacted the journal editor and complained that I had too much freedom to publish personal opinions without review. He opined that my articles should be reviewed by members of the advisory board in a form of peer review (there were many dozen of advisory board members, so he suggested a small committee which he volunteered to initially lead). Gary H. was wrong in that there had been review by the editor and editorial staff for my articles, as well as any others from guest contributors that I had invited to write for the column.

The editor contacted me. I explained that it was not personal opinion, but from a section of the book meant to inform professors that as far as in writing and applying for US patents, members of a research group work for the professor. I then also offered to only write a small number of future articles and to rely on guest authors much more. I had been growing more tired of writing these articles after several years. I decided to shift to that role and only wrote a small handful of articles over the next decade of being an editor for that column and its successors. Thanks, Gary H.

The weirdest research I ever did May 14, 2022

I have done a wide variety of research. I have had both a curious mind and one that thinks of how to extend the current knowledge. The fields of this have been mainly in chemistry, but in a range of topics that is much wider than is usual. I will touch on one of the most arcane ones.

Saturated hydrocarbons can occur in 2 main forms, chains and rings. In both a carbon atom’s 4 single bonds are connected to either other carbon atoms or to hydrogen atoms.

I read somewhere that unlike other common hydrocarbons, cyclohexane had a very small amount of what chemists call polarity. (Wikipedia says “In chemistry, polarity is a separation of electric charge leading to a molecule or its chemical groups having an electric dipole moment, with a negatively charged end and a positively charged end”. The others have either none are an infinitesimally amount. The ring structure warps the bonds enough that their electrons can interact that little bit more.

So, I had the idea that I would try to separate saturated ring compounds, like cyclohexane but with more rings, by their polarity differences. Separation by polarity while using a liquid medium is commonly done by normal-phase liquid chromatography (LC). Routine normal-phase LC is done with a saturated hydrocarbon liquid phase.

What I needed was a very non-polar liquid phase and an extremely polar column-packing phase to accentuate those tiny differences. The liquid phase needed to be even less polar than a saturated hydrocarbon. Freons are such molecules, being a carbon skeleton surrounded by fluorine atoms instead of hydrogens. Pure Freons, however, are too non-polar and the ringed saturated hydrocarbons would not dissolve in them. Trifluorotrichloroethane (TFTCE) will dissolve them and mixes with Freons. So, I used a blend of TFTCE and a perfluoroheptane.

These are some of the compounds I used to develop the separation.

I needed a highly polar column material. ES Industries sold a tetranitrofluoreni phase at that time, an aromatic moiety with 4 nitro groups on its periphery. This was extremely polar column.

The combination of a very non-polar fluorinated solvent sytem and a very polar column phase meant that compounds of even the tiniest of polarities would interact and be retained by the column. So that’s what I did, relying on the very miniscule polarity of cyclohexane-type rings to separate these multicyclic hydrocarbons.

My best time at being an expert-witness April 19, 2022

I was reminded of this by a “memory” post I made on Facebook 10 years ago. It was a case were the plaintiffs, the side I was hired to work for, claimed health effects from their workplace.

This was probably my hallmark expert-witness case, out of the couple of dozen or so that I have been involved in. My Facebook comment was that the expert report that I was writing had reached 50 pages in length. The report ended up being 59 single-spaced pages with a lot of chemical structures inserted when needed. A 12-hour deposition followed a few months later, with the defense having a team of 3 attorneys – which led to both the length of the deposition and to it meandering and changing topics often – from PAH volatility to how the aromatic carbon – carbon bonds form and break to dozens of topics.

The topical matter was the chemistry of large polycyclic aromatic hydrocarbons (LPAHs), the subject of my first book (published in 2000). The opposing side’s experts said a lot about reactions either happening or not happening in ways that supported their legal points. My role was to point out how this was wrong. I used numerous examples from my and the research of others.

At one point, the opinion of one of their experts was brought up. It had a basis on work Dr. Maximillian Zander has published, calling him the “world’s leading expert on LPAHs”. Max was a very close friend and we had 4 published papers together on collaborations, we had freely exchanged the rare LPAH pure compounds we had, and just brainstormed my email and in person. We even exchanged Christmas cards every year.

Max had told me once that he thought I was the current generation’s Erich Clar, who had been Max’s PhD advisor and had essentially founded the field of LPAH research back in the 1920s and built it up over the next 60 years.

When I pointed out that their expert had misinterpreted Max’s work, this all came out, essentially leaving a strong refutation of their experts. A month later, there was a settlement – this was after almost 6 years of very contentious litigation (I was brought in for the last 2 years and the tide turned).

I might start and off & on writing project here April 15, 2022

I have the idea of writing a series of posts that amount to episodes that I find of significance or interest in my life, a sort of disjointed and scattered autobiography. I will try to have a preamble that gives each context both then and overall and when there was any later significance, what that was that the episode had.

I have already written a few and might rewrite each of those with these new emphases and aims.