ChemistryViews, Alchemist, espresso

ChemistryViews just launched, so here’s my first link to my stuff on there together with the regular Alchemist round-up and a surprising finding about espresso.

  • Small molecules for fighting cancer – My first short feature article in the all-new ChemistryViews magazine from Wiley covers research into tumor necrosis factor (TNF-alpha)
  • Alchemist news – This week, The Alchemist hears how chemists are helping deal with the major oil spill in the Gulf of Mexico, that mosquitoes could be evolving a way to ignore strong formula insect repellent, and what actually killed legendary racehorse Phar Lap. In electrochemistry, flexible plastic electrodes can be printed and a remedy for stressed out poplar trees may emerge from molecular biology. Finally, a major funding award could pave the way for thermopower devices that bring us powerful, but miniaturized batteries.
  • Chemistry is key to perfect espresso coffee – There are just three steps in the preparation of an espresso, and millions are made every day across the globe, but only chemistry can provide the answers to optimising the process.

Wheels within wheels – the scientific lifecycle

An oft-repeated message from scientists involved with the Large Hadron Collider (LHC), mapping the human genome, the search for extraterrestrial life and other vast scientific projects, such as supercomputing experiments is that the tera-bytes, peta-bytes, perhaps even the yotta-bytes of data generated by large-scale projects is hard to handle, to say the least.

Not only has there to be a way to manage the outpouring of data from the sensors, monitors, and arrays, but this data has to be channelled through the appropriate digital conduits, dumped into robust databases, processed in parallel, and finally interpreted by the scientists themselves. Only then can DNA be fully unravelled, ET phoned home about, and god in the particles revealed…

A team at the Federal University of Rio de Janeiro and the Fluminense Federal University in Brazil hope to one day help big science address this big problem by finding ways to manage the scientific workflow on large-scale experiments.

Computer scientist Marta Mattoso and colleagues explain that, ‘One of the main challenges of scientific experiments is to allow scientists to manage and exchange their scientific computational resources (data, programs, models, etc.).’ They add that effective management of such experiments requires experiment specification techniques, workflow derivation heuristics and provenance mechanisms. In other words, there has to be a way to characterise an experiment’s life cycle into three phases: composition, execution, and analysis. To be frank, the same scientific ethics apply to all experiments from the simplest kitchen science fair project to the LHC and beyond by way of a million laboratory benches.

However, while most scientists and students are familiar with this format of introduction, method, conclusion, the researchers point out that research into improving efficiency and efficacy in big science projects has largely focused on execution and analysis, the method and conclusion, rather than considering the scientific experiment as a whole. For example, Mattoso and colleagues point out that the myGrid project back in the early 2000s was one of the first works to define a scientific experiment life cycle and I worked with the myGrid team on information materials at the time. Their approach used six phases: construction, discovery, personalisation, execution and management. However, they stick to the execution and analysis aspects of the project. Others have focused on large-scale projects in a similarly limited way.

Mattoso and colleagues have proposed an approach for managing large-scale experiments based on provenance gathering during all phases of the life cycle. ‘We foresee that such approach may aid scientists to have more control on the trials of the scientific experiment,’ they say.

In their model, each phase – composition, execution and analysis – has an independent cycle within the lifecycle as a whole, wheels within wheels, one might say. Each independent cycle runs at distinct points in the experiment and is associated with its own explicit meta data.

‘The composition phase is responsible for structuring and setting up the whole experiment, establishing the logical sequence of activities, the type of input data and parameters that should be provided, and the type of output data that are generated,’ the team explains. This cycle has within it the conception sub-phase responsible for setting up the experiment and the reuse phase responsible for retrieving an existing protocol and adapting it to new ends. The execution phase is responsible for making the experiment happen and represents a solid workflow instance and within this cycle there are two sub-phases: distribution and monitoring. The third cycle within the whole is the analysis phase, which is responsible for studying the data generated. This phase might be carried out by query or by visualisation.

The ultimate output of this wheels-within-wheels lifecycle is one of two possibilities: (a) the result upholds the scientific hypothesis (b) the hypothesis is refuted by the results.

In both cases scientists will then need a new workflow lifecycle to either validate the results or devise a new hypothesis that takes into account the new findings. The former is the stuff of peer review and publication, the latter hopefully posits that most intriguing of scientific exclamations: ‘That’s funny!?‘

The raison d’etre for the Open Notebook Science movement is brought to mind by the team’s concluding remarks about reproducibility and validity encapsulated by a scientific lifecycle that lays bare the experimental provenance and entire history:

‘The authors believe that by supporting provenance throughout all phases of the experiment life cycle, the provenance data will help scientists not only to analyse results to verify if their hypothesis can be confirmed or refuted, but also may assist them to protect the integrity, confidentiality, and availability of the relevant and fundamental information to reproduce the large scale scientific experiment and share its results (i.e., the complete history of the experiment).’

Research Blogging Icon Mattoso, M., Werner, C., Travassos, G., Braganholo, V., Ogasawara, E., Oliveira, D., Cruz, S., Martinho, W., & Murta, L. (2010). Towards supporting the life cycle of large scale scientific experiments International Journal of Business Process Integration and Management, 5 (1) DOI: 10.1504/IJBPIM.2010.033176

Chemical structure drawing poll

Yesterday’s blog feature quoted my various contacts on Twitter, LinkedIn and elsewhere on what program they use to draw chemical structures. There were some interesting answers, including mentions of sites like ChemSpider and PubChem that are not drawing packages per se but do allow you to retrieve a vast array of molecular structures.

Today, I thought it would be interesting to run a more formal poll on the question. You can choose up to 2 programs. If you check “other”, please let us know which program you’re using in the comments. If I’ve missed any popular ones off the list, someone please let me know.

Interesting to see new-kid-on-the-block ChemDoodle riding high in the poll.

Draw chemical structures

Chemical structure drawing is of ongoing interest to chemists so we have a list of programs and reviews by users. Of course, with the likes of PubChem and ChemSpider now available one might wonder whether there is any need to draw one’s own structures from scratch, but plenty of chemists and others still do. Sciencebase polled a few contacts via Twitter and LinkedIn to find out what chemical structure packages people are using, what are the pros and cons.

The vast majority of users seem to side with ChemDraw, especially those in academia because of the liberal licensing, but they all gripes about compatibility and cutting & pasting. The likes fo ChemSketch fair well and others such as Pymol and Symyx seem to be used by specialists in particular areas.

Wozza told me that he uses ChemDraw, but hates how it’s broken on the Mac and lacks support for that platform, it’s also unfortunate that it has broken round trip editing, and poor cut&paste into other applications. Nevertheless, ChemDraw has good functionality, compatibility with colleagues, and produces “good looking drawings”.

davidperrey uses ChemDraw, as part of ChemBioOffice 2010, though says that he probably draws more structures using Java apps on ChemSpider/Reaxys/etc. “I use ChemDraw for preparing Powerpoint slides or report figures, but most of the time when I am drawing structures (using a computer at least) it is doing literature searches and/or looking up information on chemicals that I am interested in using,” Perrey explains. “ChemDraw is perfectly fine, though I have a pet peeve that when I type an atom in lower case ( say n or cl) it fails to recognize that as the element I am putting in.” As far as the java apps go: Reaxys is the browser-based replacement for Beilstein, so I use it a lot. I find it slow to get started, but once it is going, it is quite responsive and easy to use (except copy/pasting structures takes a while, sometimes easier to just redraw the product). Atom-mapping is useful, but the auto-mapping is occasionally awful — better to do manually.

[Chemaxon’s Alex Allerdyce commented: I think davidperrey was referring to Marvin when he mentioned Reaxys ‘…As far as the java apps go: Reaxys is the browser-based replacement for Beilstein, so I use it a lot…’. So far as I know Marvin is the native editor on Reaxys tho other sketchers (resident at the user — not delivered at the site) are supported.]

Perrey explains that with ChemSpider, “It seems like there are more steps to get down to drawing than there should be, but once you get there, the interface is functional but smooth. All the various rings are hidden away in “templates” but there is a lot to choose from, and simply drawing structures is easy. Atom changes are straightforward too, as you click on the element you want and then just click everywhere you want it.” Then there is eMolecules, which is “mostly for looking for available chemicals, it has a very bare-bones interface, with one panel of tools, but it does the job and has very little load-up time as the Java starts. Labelling atoms is easy, with a fixed list of the most common and a space to fill in your oddballs (it recognizes the elements too, though won’t let you type say zn for zinc, has to be Zn)

He adds that Chem ACX is another for looking for available chemicals, basically a ChemDraw type browser plugin, so similarities to that. Doesn’t like lower case atom labels either. Feels a bit slower and clunkier than the others above.

littleghoti says he uses ChemDraw (despite the price), when he has to because it does all he needs. “But, as a physical chemist, I am deeply suspicious of anything with more than 10 atoms.”

biochembelle also uses ChemDraw. “It’s pretty easy to figure out the basics, even for beginners,” she says, “but has many options available, like a TLC plate drawing tool, templates/clip art for conformers, glassware, complicated ring structures, and it’s easy to generate and modify figures quality and properties, save as multiple file types for publication. It also has the ability to convert chemical names to structures and vice versa. However, the disadvantages are the price but for those who can get an institutional site license. Also, structure and reaction cleanup options are not useful for aesthetics or minimizing space used.

But, chemical informatics expert Wendy Warr, tells me she uses Symyx Draw and its Structure Resolver too. “Symyx Draw is free for personal or academic use,” she adds. Steven Bachrach of Trinity University is also a Symyx Draw user because of the “nice looking drawings, good structure to name facility, can produce InChIs, easy to use, free to academics, front end into many database systems.”

Undergraduate detox29 has found ChemSketch to be adequate and gxusm told me that they use Symyx Draw user, mainly because that’s what we were taught to use at University. kjhaxton is also a Symyx Draw user, who occasionally uses ChemDraw or ChemSketch, and Accelyrs DC visualizer & Avogadro for the really pretty graphics!

jat45 uses Chem4Word, ChemDraw, Marvin, JChempaint, and a bit of JME. Jerome Baudry of the University of Tennessee/Oak Ridge National Laboratory, uses Isis Draw or MOE and translate to 2D for “really good looking” structures. Hans Johansson also mixes it up: “Marvin and JChem!” he exclains, adding that, “The ChemAxxon package is just great and works on most platforms, but
ChemDraw is just not worth money, unless you draw and analyze structures all the time.”

Robert Slinn uses ChemBioOffice 12.0 which includes ChemBioDraw which is excellent but not free except to academics. There are a number of free packages available including ACD/Labs ChemSketch and ISIS Draw.

xtaldave uses PyMol and CCP4m, while modernscientist and proteopedia also use Pymol with its Deep View for some structure alterations.

Wozza adds that he looked at Chemdoodle a few months ago and describes it as “very promising, especially with web features, but at the time lacked the functionality to use every day.”

hhhernandez uses ChemDraw as does jordancdarwin if it’s available, but MarvinDraw out of principle.

barneygrubbs laments the fact that all of his old files are in a particular format, therefore, “I sadly use ChemDraw (like @NeilWithers, a former Atoms user for solid state stuff),” he told me. Like others, Grubbs, of Stony Brook University, gave me a list of pros and cons for ChemDraw: Relatively easy to use (now that I’ve been using it for 13 years), exports to other formats reasonably well (.tiff, especially), and has decent layout tools (align, distribute, etc.). But on the down side: Native structures usually look bad when pasted directly into powerpoint, editing embedded figures in Word sometimes crashes ChemDraw, drawing polymers often requires stretching backbone bonds and using wider bond angles, but there doesn’t seem to be an easy way to do this repeatedly beyond eyeballing the structures. ChemDraw also still has a number of annoyances (cyclopentadiene rings cannot be drawn with a flat bottom bond, many keyboard shortcuts are different from other programs, C60 default structure looks bad, squiggly single bond is the only real option for generic polymer structures).

“I recently updated my ChemDraw and continue to use it,” Tony Addison, Professor of Chemistry at Drexel University says, “I tried using our free site subscription to ChemSketch (under VMWare Fusion), but the structures I got were of unpublishably poor quality. So I got ChemDraw at an ACS Expo for $90. One thing I find useful about it is the variety of file types to which you can save a diagram for later editing (e.g., in 雷竞技炉石传说 hop).”

Which package you use strongly depends on what you need to draw structures for, says Computational Chemist Richard Wood. “If I am doing docking calculations, then I’d probably “draw” the molecules in Sybyl, as we mostly use SurflexDock to do the docking. If I’m doing QM calculations, then I would probably use GaussView. I’ve occasionally drawn things in Avogadro, but that’s rare. I’ve used ChemDraw in the past, but I’ve noticed that sometimes the structures don’t convert correctly if you want to use them in other applications.” Michael Mayo also explains that he uses GaussView4 as well as generating coordinates with PVWave for Gaussian03 input.

For Drexel University open notebook pioneer Jean-Claude Bradley it’s ChemSketch all the way, although he recently came across a little issue: “SMILES generated from ChemSketch often don’t work on Daylight or ChemSpider but InChIs generated by Chemsketch work fine (except seem to draw the minor tautomer for all the amides I have been drawing,” he explains.

Like so many others, experienced analytical consultant Bruce Girton says he uses ChemSketch when the terms of the freeware license permit. “I think the drawing interface on ChemDraw is a lot more intuitive than that of ChemSketch, but it’s too expensive for the amount of drawing I do,” he says.

Teaching Fellow Matthew Colo of Harvard University compared the two packages he uses: CambridgeSoft ChemOffice/ChemDraw is powerful, fast, easy to use, has templates to incorporate into structures, and automatic nomenclature (and reverse nomenclature). In contrast, ACD/ChemSketch is free, almost as powerful as ChemOffice, and although it takes a bit longer to use, and there is less automation in drawing, it is still relatively easy to use, has templates to incorporate into structures, and automatic nomenclature (and reverse nomenclature).

Frederick Pruijn, a Senior Research Fellow at The University of Auckland, uses ChemDraw and ChemSketch but prefers the latter because it happens to be the front end for other ACD packages that he often uses. “Our chemists use ChemDraw as their workhorse,” he adds. “They also IsisDraw sometimes but I think that is a little clunky compared to the more “modern” packages.”

Brian Halden echoes the sentiment expressed by most respondents in that ChemDraw outshines the other applications but isn’t free. “I picked ChemDraw because that is all I have ever used,” he says. “I did try MarvinSketch for a while but I found it was still a ways off from being my choice of software. ChemDraw was great for drawing reaction schemes and pushing arrows. It even had some graphics for lab equipment that I had used it the lab so all-in-all, it was the preferred program.”

Jayshree Bhatt, Senior Associate at InnovarIP Consulting Group, adds, “I am a scientist and also draft patents where I draw chemical schemes. I have used both ChemDraw and Symyx Draw. ChemDraw is a good tool for scientists, so is ACD draw which gives predicted NMR values, bond lenghts etc, but both are paid software. For the ordinary task of simply drawing structures, Symys is fine as this can be freely downloaded and is compatible with most other software.”

Several correspondents mention checking out SourceForge on a regular basis for updates to the likes of JMol and for newly emerging chemical structure drawing packages and molecular viewers.

Programs mentioned in this post:

  • ChemDraw, Chem ACX
  • ChemSketch
  • Symyx, Isis Draw
  • Pymol
  • Reaxys
  • ChemSpider
  • Microsoft Chem4Word
  • Marvin
  • JChempaint
  • JME
  • Sybyl
  • GaussView
  • MOE
  • eMolecules
  • PubChem
  • JMol

The LinkedIn Q&A session is now open again, if you wish to contribute to this post or else you can leave a comment here or on Twitter.

Getting wood

Wood is the focus of new research into biofuels, while removing toxins from other crops is important for biofuels and food supply. Forest fires and phosphorus are analysed while the route discovered to taken by aluminium through the aquatic foodchain might quell some pollutant fears. This week’s column on SpectroscopyNOW.com:

  • What’s wood worth? – X-ray technique confirms the properties of catalysts used to make biofuels derived from a potentially sustainable woody source, lignocellulose.
  • Spectral statistics study on toxic crops – Some crops contain natural toxins that are usually removed during processing and cooking. Now a statistical analysis of visible and near-infrared (vis-NIR) spectroscopy has demonstrated how they can be quantified alongside oil and protein determination in cultivars of one of the most important crops, rapeseed.
  • Forest fire phosphorus – Phosphorus NMR spectroscopy has been used to investigate the effects on the chemistry of phosphorus in soil as an indicator of nutritional quality for vegetation and tree growth following a forest fire.
  • Aquatic aluminium all-clear – Spectroscopy was used to track the path of an aluminium contaminant in water as it travels through the food chain. The study indicates that the toxic metal accumulates only in the inedible parts of some shellfish.

Tellura, angiogenesis, favourites

Tellurium steroids, angiogenesis against cancer, favourite chemical things and more…

  • My name is tellura – Drugs based on tellurium catch the eye of Derek Lowe
  • Antiangiogenic "anticancer" foods – Can eating these foods help prevent pin-head sized cancers that grow in people from gaining the blood vessels they need to grow into something malignant? In other words, can we eat to starve cancer?
  • Spicing meat cuts cancer risk – They say variety is the spice of life, but spice has some hidden benefits in reducing the risk of absorbed cancer-causing chemicals from barbecued meat, apparently.
  • A few of my favorite (chemistry) things – One of the originals from the chemistry things meme to which I succumbed this week.
  • UK Geocoding – Want to know precisely where you are in the UK, just enter your postcode to get latitude and longitude.
  • Sunless tanning will not protect you – Fashionable (but generally ugly) spray tanning that gives caucasians a familiar orange glow do not protect them from UV skin damage caused by the sun

My favourite chemistry things

Sceptical Chymist tells me (via Twitter) that they were enjoying the favourite things about chemistry meme started by ChemJobber and continued by Azmanam (known to Sciencebase readers for his chemical spelling dictionary and the C+EN team. As is the wont of meme creators, you pay it forward and have to come up with your own “list” or whatever.

Skeptical Chymist had, “The smell of ethyl acetate (in the morning)”, Peter Atkins’ textbooks, the elements song, and freaky glassware and the prowess of glassblowers on their list of ten favourite things about chemistry. They then passed the baton on to the Chemistry World gang, Michelle Francl of Culture of Chemistry, their Boston- and Tokyo-based teammates Steve and Anne, and yours truly.

Now, I usually don’t bother with the generic memes (unless it’s one I’ve come up with myself) but how could a chemist resist a chemical meme? Unfortunately, several of the things I thought about putting on my list, like Tom Lehrer’s The Elements Song have already been listed by by meme predecessors. So, I thought I’d do something slightly different and list my favourite compounds in no particular order:

As with all of these kinds of memes, one has to pass it on, so I’m nominating ChemistPD, Jon Edwards, and Egon Willighagen

Submarine eruptions, hybrids, and quarks

The first three links are to my latest column on Intute, which is now online:

  • Scrubbing up knowledge of submarine volcanoes – Consider the simple pumice stone next time you're having a bathtime scrub…
  • Metallic liquid crystals – A new class of materials formed by combining liquid crystals and metal clusters glow intensely red and in the infra-red region of the electromagnetic spectrum when irradiated over a broad range of wavelengths
  • Quark, strangeness, and charm – US researchers have calculated, with a tiny margin of error, the mass of the three lightest and, therefore, most elusive quarks
  • Neanderthal genome sequenced – Did your great, great, great, great, great, great, great, great, great, great, great, great, grand-dad get it on with a Neanderthal? New evidence of interbreeding between humans and Neanderthals 50-100,000 years ago
  • Andrew Wakefield research fraud exposed: the MMR investigation – For any vaxophobes who still think that the MMR vaccine has anything to do with autism check out this tale.
  • Cleaning-chemicals industry takes on the final frontier… – Eradicating invisible stains…surely if they're invisible they're not stains, and who knows what invisible residues are left behind by cleaning fluids, anyway?
  • Cosmic comic book – Hiliarious rhyming comic book takes us on an explosive tour of the origins of the universe

I have a free high-resolution copy of the Cosmic comic book (PDF) to give away, just retweet this post or leave a comment and I’ll send you a link!

Metal, quantum dots, and life on earth

Latest science news with a spectral twist from my column on SpectroscopyNOW.com and more…

  • X-ray fuel – X-ray absorption spectroscopy, XAS, has been used to probe the metal centre of an important enzyme that can oxidise methane, natural gas, to methanol. Turns out the metal is copper not iron as previously thought and the discovery could open up a route to novel catalysts for converting "waste" methane (either from landfill or oil well flare-off) into useful liquid methanol for processing into fuel or other more valuable products.
  • Quantum boost for anticancer drugs – Quantum dots (QDs) have received significant attention in biological and biomedical fields. Now, UV-Vis spectroscopy and other techniques have been used to investigate their utility in enhancing the activity of the anticancer agent daunorubicin (DNR) in treating leukaemia cells.
  • MRI reporter – Researchers have developed an extracellular enzymatic gene-reporter system for magnetic resonance imaging (MRI). The system yields strong, reversible contrast changes in response to the expression of secreted alkaline phosphatase (SEAP). The products of SEAP activity can then be detected using an iron oxide based sensor.
  • Chemistry with bite – US chemists have constructed a molecule that bites its own tail and in so doing can trip other small molecules within the cavity that results. Fed a diet of zinc ions the "ouroborand", reported in Angewandte Chemie, will release its bite to let other smaller molecules into the central cavity. Remove the zinc ions and it loses its grip on the guest. Nuclear magnetic resonance spectroscopy was used to characterise the components and the process.
  • Microbial detection – Surface-enhanced Raman scattering (SERS) can be used in a new microarray approach to microbial detection that is label-free, according to researchers writing in the April issue of the journal Analytical Chemistry.
  • All about crystal Eve – Scientists have reported the discovery of what may be the "ancestral Eve" crystal that billions of years ago gave life on Earth its curious and exclusive preference for so-called left-handed amino acids. Fourier transform IR spectroscopy and powder X-ray diffraction provide the evidence. Molecules of aspartic acid of a sinister, or left-handed, orientation, could be the ancestral Eve of all amino acids, the building blocks of proteins, terrestrial life.
  • Interview with Michael Mueller aka @eurogene aka @nutrigenomics – The pros and cons of being a scientist
  • WolframTones ringtones with a scientific twist – Create your own mobile phone ringtones using Wolfram's audio perspective on the computational universe

April Alchemist Arrives

copper-alchemistThe Alchemist travels back billions of years to the dawn of life this week to learn how aspartic acid may be the crystal Eve, the mother of all chirality while heading back to the future also discovers how biology and nanotechnology might be fused to produce new metamaterials for a range of medical and analytical technologies. Banned scent compounds turn up in childrens toys, we hear while US chemists have built a molecule that bites its own tail to trap smaller molecules within. In environmental news, the recent volcanic activity that grounded thousands of travelers to and from Northern Europe may not have the environmental impact some observers have suggested. Finally, chemistry is the word as Microsoft launches a CML, chemical markup language, add-in for its well-known word processing application.

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