August 2008 Archives

Sun Aug 31 17:26:09 PDT 2008

Strange News About Molecules

For the last few days I have been posting links to news articles which mention the term molecule. If you take a look at the articles which make this list (I only keep the latest 100 on the page), you will invariably see some interesting stories. (See Molecules in the News).

Why are the stories interesting? Well, partly because molecules are interesting. Molecules are tiny. In general their existence needs to be inferred rather that directly appreciated. Molecules are hard to make, chemists need to carry out complex syntheses to put the atoms of a molecule into a specific configuration. Yet, despite these caveats, molecules are often in the news and molecular images are included in adverts for the latest pharmaceuticals.

The stories are also interesting because they present so many different points of view. There are stories about the cancer causing effects of moisturizing creams and suntan lotions, among other items. Stories like these are invariably alarmist and convolute the original scientific research from which they are based to achieve a degree of sensationalism. Why is that? Sensationalism makes for more interesting stories and more interesting stories make for more readers and more readers make for more advertising revenue.

Then there are the stories which contain interesting inaccuracies. Some of these are trivial, like calling 'radiation' 'irradiation' (see this article on irradiating food) and this article which says 'A molecule you can barely see...' (when, in reality, you cannot see a molecule because they are far too small).

So, there is some good news. Molecules are generally understood by the news article writers and the readers that they write for. There is some bad news too. Often the information is a little misleading and this spreads and perpetuates various falsehoods. Additionally, the news sound bite leaves little scope for an explanation of cause and effect, and statistical analysis, which would help reduce the more alarmist articles to an informational level.

However, all in and all, I have been very pleasantly surprised by how frequently articles mentioning molecules are published these days. Hopefully the trend will continue and, if so, there is a likelihood that the inaccuracies and missed opportunities for detailed explanations will decline with time. To examine the current state of molecules in the news, here is the appropriate link: (See Molecules in the News).

Posted by ZFS | Permanent link | File under: general

Sat Aug 30 14:15:13 PDT 2008

Need to Know the Structure of a Molecule?

If you ever need to know the structure of a given molecule, use the eMolecules ( site to obtain all the information that you need.

I have found this site extremely useful for obtaining chemical information rapidly. The site has a large database of chemical information, obtained from the suppliers of a range of chemicals and chemical intermediates. You can query the database using an effective Java sketching tool, by SMILES string, or by common names.

Once you have obtained your hit you will see the various suppliers of the compound, so if you are a chemist you will be able to buy the appropriate amount, you will also be able to obtain additional information on the compound. The additional information includes the SMILES string, and using the SMILES string you can obtain a chemical connectivity file (.mol file) from the InChi site:

So, if you are interested in the structure of Aspirin, for example, head over to eMolecules to obtain a SMILES string for Aspirin (e.g., CC(=O)Oc1ccccc1C(=O)O), then go to the InChi site, to obtain a .mol file. Then you can read the .mol file into PyMol, or your favorite molecular viewer, to see the structure of Aspirin.

These sites will give you a good idea of the structure of a range of molecules. The procedure above does not include a treatment of the lower energy confirmation of the shape of the molecule, and it does not include adding hydrogen atoms to the molecule. I will cover those steps in a future posting.

The Structure of Aspirin

Posted by ZFS | Permanent link | File under: general

Thu Aug 28 12:31:03 PDT 2008

Welcome to The Molecular Universe Blog!

Having restarted The Molecular Universe after a year or two off, I thought that now would be a good time to start up a blog as well!

Naturally, this involves an interesting search for suitable a suitable blogging engine, and after checking for a day or two on the various options, I selected 'NanoBlogger'.

NanoBlogger is a blogging engine written in the Bash scripting language. It produces a blog which is composed of simple html pages, so there is no database, or server side technology to maintain. The downside is that adding comments to the blog is not completely trivial - so for now, please email me at the address on the navigation panel if you have comments or questions.

One of the things that I was worried about was how the pages would look in a variety of browsers. So, I tested appearances with which uses a bank of web clients and screenshots of the results, to give a sense of how different browsers render the pages on a site. So far, the results are quite encouraging!

Posted by ZFS | Permanent link | File under: general


IPhone 3G First Impressions and Minor Concerns

My wife is now the proud owner of a new iPhone 3G. This is a unique experience for her, the convergence between the computer that she used to use for email and her trusted cell phone. So far, she could not be happier. Here are her initial impressions and a few concerns that have been detected in the first few days of ownership. Do not get the wrong impression, the positives significantly outweigh the concerns. For the first time, my wife can be seen playing with a high technology device, for many minutes at a time. And most of the time she is beaming happily - it has been a strange experience for everyone in the family.

When you bring your new iPhone 3G home after a minor amount of queuing in the mall, you find yourself the possessor of a black cardboard box, about the size of a house brick. The packaging is stylish, happily not the acrylic polymer bubble beloved of some cell phone manufacturers, and reassuringly minimalist. The iPhone itself is a heavy metal and glass monolith with its only outwardly mechanical protuberances one or two slight switches. The impression you are given is that there is little to go wrong from a mechanical perspective, no hinges, or sliders to wear out with repeated snapping. However, the weight and the apparently large amount of glass involved in the touch sensitive screen create the impression that a fall could be fatal. The sale of protective cases will, no doubt, be brisk.

After an initial charge you get to try your iPhone out for the first time. Actually you will have already had a chance to play with it in the store - my wife sent me a message from the store where the initial registration was done. But after its first real charge you get a chance to explore the capabilities that the device offers.

The first pleasant surprise is that the software is beautifully integrated. The black cardboard brick does not contain a manual. When you play with the applications that the iPhone comes with you soon realize that you probably will not need to use a manual, ever. Of course, this cannot be good news for the technical writing community. When software is beautifully engineered it is so intuitive that you can carry out complex operations without needing to try to guess how the programmers intended the programs would be used. The hardware is also nicely integrated with the software. There is a position sensor which tells the software which way up the iPhone is. When a rotation of the horizontal is required it happens in an animated way that keeps the user in the loop, rather than creating a confusing and sudden jump. The result is very intuitive. Similarly, the scrolling of images and the movement of screens are handled with style and finesse, which do not appear to unnecessarily waste the power of the underlying CPU (no unnecessary animations of the types favored by lesser software vendors) but do allow the user to understand what the software is doing and how the user's input is being interpreted by the device.

Back to initial impressions. Within a few seconds the telephone has been shown to work as a normal telephone, the email has been experimented with, and the user is beginning to marvel at the nicely constructed contacts database which combines a variety of different coordinates for each of your contacts in a seamless manner.

The most impressive application is the Map capability. This gives you an inbuilt GPS like capability. Not only is the GPS inbuilt, it is also beautifully integrated with the Google views of the world from satellite, and integrates with Google's driving directions as well. Clearly your iPhone will be a great help when next discussing the fastest, most scenic, most economical, etc. route from A to B with your spouse.

The iPhone comes with ATT internet service for a fixed monthly fee. So, to all intents and purposes, once you have signed away your life for the iPhone contract you really ought to use the device as much as possible. So an early question is, how is web browsing on this device? The short answer is surprisingly straightforward. The version of Safari supplied with the iPhone readily scales in various directions, intuitively and typing web addresses is straightforward with the keyboard widget that appears when you touch the address bar.

If YouTube is your web destination of choice, the iPhone comes with a YouTube application, complete with an ancient television image as its icon. Once you brave entry to the application through this forbidding icon you open a fascinating world of all the wonderful content that has been uploaded (rightly or wrongly) to YouTube. Perversely, as the iPhone device has a relatively low resolution display, the low resolution YouTube videos look fantastic and the iPhone YouTube interface has been designed to use as much of the screen as possible for the video image. As with many new technologies, it isn't immediately clear how YouTube will make money from this use of their content (no adverts are displayed) but now is not the time to worry about the guys at YouTube, now is the time to watch all of your favorite video artists on your iPhone, on the bus, on the way to work.

The final marvel my wife has discovered in her first few days with the iPhone 3G is the ability to easily email photographs to email contacts. This is nothing new for most cell phone users, but the level of integration and ease of use are exemplary with the iPhone and now a steady stream of iPhone taken photographs are coming from my wife's email account heading to different corners of the world.

Here are some of the things which we have not experimented with yet. Backing up to iTunes, storing and playing music on the iPhone, anything other than the supplied applications. We haven't tried them yet - but given experiences with the other programs that come with the iPhone our expectations are high.

I threatened some concerns and here they are. My wife's preferred email account in the past had been a Hotmail account. Naturally, Microsoft do not permit email clients to easily connect with Hotmail and so this does not work too well with the iPhone. The only solution has been for her to switch to a GMail account. The battery life does not seem to be stellar. The iPhone seems to be quite thirsty in power consumption. This raises the specter of battery replacement at some point in the future. Unlike the robust construction of typical cell phones, which permit user battery pod replacement, the iPhone gives the impression of requiring delicate surgery when the time for battery replacement comes. Finally, that touch screen is getting a lot of action, and is getting plenty of marks with all its use.

Don't let these niggles put you off, however. The iPhone is a wonderful combination of hardware and software brilliance. Get yourself one, and get its peripherals too, and you too will be smiling as you use them!

Posted by ZFS | Permanent link