## How to EXCEL in PCHEM?

I have begun a new tutorial series on Excel I’m calling my EXCEL Boot Camp.

Why host an EXCEL Boot Camp for PCHEM?

Many of my students have never used EXCEL. Years ago, I added videos to the lab materials showing them how to complete the many data analysis tasks in Excel, but these were very cook-book in nature. The students were successful in following the recipe, but if they made any small mistakes along the way the process dragged on, consuming the whole FOUR-HOUR lab period (or longer).

In this situation, when it came time for the student to answer some simple and basic questions about the SCIENCE behind the Excel data analysis, they were unable to do so.

Therefore, I am adding some Excel tutorials that are skills-based. This will train the students in the useful spreadsheet skills so that they can bring them to the data analysis exercises and fully participate in the SCIENCE.

The Lessons will be added to this blog as they become available on YouTube. You can subscribe here and on YouTube to be notified when new content is posted.

Happy pchemming!

DW

Posted in D L Williams, Philosophy

## DW’s Favorite Quotes (and Why)

### A work in progress

I continue to read and be impacted by the thoughts of others.

He who loves to read, and knows how to reflect, has laid by a perpetual feast for his old age. (Uncle Esek, “Scribner’s Monthly”, September 1880)

No idea who Uncle Esek is, but I have been infinitely blessed by the ability to read and reflect. I was extremely proud of my children when they read their first chapter books. I announced that from that day onward they would never be bored!

The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble. It therefore becomes desirable that approximate practical methods of applying quantum mechanics should be developed, which can lead to an explanation of the main features of complex atomic systems without too much computation. (http://rspa.royalsocietypublishing.org/content/royprsa/123/792/714.full.pdf , Quantum mechanics of many-electron systems, P. A. M. Dirac, Proc. R. Soc. Lond. A

This is the charge that I have taken up in preparing a manuscript that teaches Spectroscopy in One Dimension. The book proposal is 90% completed, and I aim to send it to the publisher in late August.

Study without desire spoils the memory, and it retains nothing that it takes in [sic]. (Leonardo DaVinci)

This was an epiphany for me. I realized that a huge percentage (>90%?) of my students could not learn chemistry because they did not desire the CHEMICAL KNOWLEDGE. They desired a grade, a checked box on their transcript, a degree, or a future job, but NONE of those things will help them with point groups, wave functions, phase diagrams, etc. To learn CHEMISTRY they have to desire CHEMISTRY. A large part of my job as a professor is awakening the desire for CHEMISTRY, thus opening their ability to RETAIN what they STUDY.

“Of all tyrannies, a tyranny sincerely exercised for the good of its victims may be the most oppressive.” (C.S. Lewis, God in the Dock, 1948)

So much could be written about this quote, but it will get political very quickly. I’ll pare it down to one question. Are policies being made because they actually (with evidence and data) produce good outcomes, or are policies being made because they make the policy makers FEEL good?

I believe in Christianity as I believe that the sun has risen. Not only because I see it, but because by it I see everything else.” (C.S. Lewis, Is Theology Poetry? 1945)

Christianity is a World View as is Naturalism, Deism, Confucianism, etc. World Views are lenses through which one sees EVERYTHING. What is your world view? Why do you have it? How did you get it? Do you have reasons for keeping it? And what would it take for you to change it?

I have told you these things so that in Me you may have peace. You will have suffering in this world. Be courageous! I have conquered the world.” (Jesus of Nazareth, John 16:33)

I love this quote even though it promises suffering. The best quotes tell you something true. They are like an accurate compass. They point North ALL THE TIME, and as long as you have North, you can get un-lost.

## PCHEM and Forensic Chem Lecture Videos

I frequently have seniors who want to revisit the concepts in pchem sit in my 8AM lectures the year after they have had my course. It’s a privilege to have them and an encouragement to see their natural curiosity in action. They seek to firm up their understanding of the quantum world and how we interact with it (i.e. spectroscopy).

In the fall of 2017, I put these students to work videoing the lectures and posting them on the Physical Chemistry at Sam Channel. These videos are essentially raw footage of lecture. The videos could have been greatly improved by adding in the PowerPoint Slides, captioning, cleaning up the audio, and cutting out my “ums” and “uhs”. But these volunteers did not have time to do that, nor did I. I had a CLEANING WORKSHOP to plan and execute!

### CHEM 4380 – Forensic Chemistry

The students appreciated the fall lecture videos so much, there was a great amount of interest in capturing the Forensic Chemistry Lectures. So we created a Forensic Chemistry at Sam Channel, too.

The lecture playlist is only one piece. Jessy also created other playlists of videos on the Forensic Chemistry at Sam Channel that should interest Forensic Science and Forensic Chemistry students and enthusiasts. She performed these tasks as an SHSU Honors Contract for the course – an activity that supplements the material for the student and enhances the skills that they take away from the course.

## Thanks to the Student Team!

Even raw footage must be stitched together, uploaded, described, tagged, and set up on YouTube. This takes TIME and time is a valuable commodity for our chemistry majors.

I thank William Fernandez for videoing CHEM 4448 and CHEM 4449. His videos were so well-received by the students that Jerome Butler decided to sit in and video my Forensic Chemistry course CHEM 4380. Thanks Jerome!

I thank Matthew Peavy for producing the videos for CHEM 4448 and CHEM 4449, and for uploading them. I thank Jessy Stone for producing and uploading the CHEM 4380 videos for Forensic Chemistry.

You students who are willing to go beyond the minimum give us hope for the future.

You people in industry and in graduate programs, hire these students! You won’t be sorry!

-DW

Posted in D L Williams, Education, Physical Chemistry

## Brainstorm Session on 3D Printer Waste

Friends, Romans, Countrymen, lend me your ideas. Look at the picture of the dual extruder tip cleaning fences and give me your thoughts on what they could be used for.

Background: I have recently added a 3D printer to my lab to prototype chemical laboratory accessories.

I purchased a dual extrusion Makerbot and I love it. I will blog a review of its performance sometime soon.

Technical Details: Aside from the waste produced from being a noob at 3D printing, there is also a lot of built in waste from raft and tip cleaning fence material. Turning off rafts and supports does not save filament because these help ensure a successful print. If the print fails without rafts and supports, then you have still wasted a lot of filament.

So get those creative juices flowing, and comment on what you would use these tiny little fences for. Toys? Rear view mirror bling? Let me know.

## Corporate Research Funding in Uncertain Times

Some points that describe the current R&D funding climate:

• Continued uncertainty in corporate R&D hiring
US non-financial corporate cash holdings rose to \$1.24 trillion at the end of 2011 according to Moody’s. One reason among many is a reluctance to hire until the uncertainty surrounding benefits costs is reduced.
• Tightening of government funding of university R&D
The US government still funds a significant amount of chemical research, but competition for those funds is increasing greatly. The growing deficit must eventually have an impact on the availability of funds for chemical research.

As a physical chemist, I am partial to APPLIED chemistry research, and the interactions I have had with corporations and government contractors have been enjoyable and fruitful for both parties.

I have prepared this blog post and my new “Sponsors Page” on my university website to actively address the R&D needs of corporations and government contractors.  Many of these entities are under a hiring freeze, and yet, their chemistry-related problems continue unaddressed.

When I worked for a government contractor, I dealt with these issues:

• “I could solve this problem in 6 months, if I didn’t have to support production, also.”
• “I’d love to hire someone to research this and other issues but
1) we are under a hiring freeze,
2) we don’t have the budget for a whole person (1.0 FTE),
3) we can afford the salary but are reluctant to commit to an unknown fringe benefit committment,
4) we can afford a science temp, but we need a Ph.D. chemist.”
• “Maybe a university researcher could help, but there’s no telling what an Ivory Tower Pinhead is going to spend our money on.  And, what would we have to show for it?”

To quote a recent President, “I feel your pain.”  But not all residents of the Ivory Tower are Pinheads.  Here are the benefits of funding an APPLIED-SCIENCE-MINDED university professor and his students to address your problem.

• Academic salaries for Ph.D. chemists (\$70k, 2012 median) are 65% of that in Industry (\$107k, 2012 median) according to the ACS Employment Survey, so renting a brain is potentially cheaper than buying one.  Often these are 9-month salaries, but this annualizes to \$93k, which is \$14k less than the industry median 12-month salary.
• Academic chemists are able to spend 100% of their effort on your problem during the summer months.  If the median salary of \$70k is for 9-months, then funding this scientist for three full months in the summer is only \$23k.  Universities tack on varying amounts of overhead and fringe benefits costs to this number so the actual costs will be more like \$40k (\$85 / hr all-inclusive).  This is still a very reasonable amount for 3-months of a PhD chemist’s time.
• Academic institutions have an amazing array of instrumentation that your company could not justify purchasing.  The overhead costs tacked onto the academic chemist’s labor rate is the price of admission to the instrumentation lab or computational facility.  Our lab charges consumables costs on a per-day or per-sample basis in the range of \$20.  This may seem to add up, but so do the costs of solvents, vials, etc.
• Academic institutions are FULL of eager chemistry majors who LOVE to study research problems that are “real life”.  These students are also inexpensive when compared to hourly chemical technicians.  A typical student will have a fully-burdened (with overhead) rate of \$20 per hour all-inclusive.  These students will graduate with a working knowlege of your industry and will be excellent prospects for future hires.

The number-one factor to consider is the principal investigator (PI).  Does he or she understand your problem?  Have they done similar work in the past?  I have turned down funding because I did not think I could deliver value to the sponsor.  Find someone who understands your terms, your culture, your requirements, and the practical aspects of implementing the ideas proposed.

If your interests are in any of these areas, I’d love for you to contact me.

• Cleanliness verification, contact angle measurements, coupon tests
• Solvent properties, surface tension and hydrostatic densities, Hansen solubility parameters vs Hildebrand solubility parameters
• Solvent blending, solvent blend prediction, miscibility
• Solvent substitution, reduction of hazards, reactivity, ozone depletion potential, or global warming potential
• Material compatibility, polymer stress cracking, polymer swell, polymer processing solvents
• Recrystallization and crystal morphology control based upon non-solvent interactions
• High-explosive detection, solubility, modeling, spectroscopy, recrystallization, precipitation, and PBX production/processing
• Spectral assignments and predictions (FTIR, Raman, UVVIS, XPS)
• Computational chemistry, ab initio, density functional theory, quantitative structure property relationships (QSPR/QSAR)
• Six-Sigma Blackbelt – consulting services

There are ways to continue innovating in the current business climate.  I’d love to help if I can.

-Darren

Posted in D L Williams, Education, Physical Chemistry

## Potential Source of the Fukushima Daiichi 1 Explosion

Here is my personal analysis of the Fukushima Daiichi 1 explosion that occurred March 12, 2011. It is possible that the cooling water level in the spent fuel storage pool dropped enough to expose the fuel elements. This could generate hydrogen gas, and is a potential source of the explosion. Hat tip to the Nuclear Energy Institute for providing an image of the reactor design and secondary containment area.

I have created a Prezi to walk you through my thoughts.

Thanks for watching, and keep praying for the Japanese people as they continue to battle the after effects of this earthquake.

Posted in D L Williams, Education, Physical Chemistry

## This Week in Pchem – Energy Minimization Techniques

This week in pchem we are discussing the energy minimization techniques that are used in computational chemistry. The students will build a mock energy function that models the dihedral rotation of 1,2-dichloroethane. Then three methods (The Monte Carlo Method, Newton minimization, and Metropolis simulated annealing) will be employed to solve for the preferred (lowest energy) dihedral angle (a).

A performance plot will also be generated that shows the lowest energy and its root mean squared deviation RMSD from the known minimum structure (a = 180 degrees).  This plot clearly shows Newton’s propensity to get stuck in local minima.  It also clearly shows that the Monte Carlo method will always find the global minimum, but with increasing inefficiency.  And finally, the Metropolis simulated annealing technique is found to be flexible enough to accurately locate the minimum energy structure every time provided that the step size and temperatures are “tuned”.

Stay “tuned” for a planned video of the spreadsheet in action.

You can participate!  Download the Rosetta@home screen saver, and solve protein folding problems in your sleep.  (I have no official connection to the Rosetta at home folks, but their work is great! http://boinc.bakerlab.org/rosetta/)