VT-NMR Simulation Calculator

Enter Temperature (T) in Kelvin and the rate-constant (k) from the simulation (see H. Reich's WinDNMR).

Contstants: Gas (R), Boltzmann (kb) & Planck's (h) constants.

PhD Dissertation - The End is Near

I thought maybe it would beneficial to document some of the process of writing my dissertation since I went about it a bit nontraditionally (not just taking too long to do too little) using predominantly open-source software.

Disclaimer: Although writing a chemistry dissertation with open-source software is readily accomplished, it is probably unwise to make a switch from MS Windows after already starting your writing. It is recommended that you make the decision a year-ish early and write at least one hefty report to acclimate :)

Software Used

OpenOffice.org 3.1 Office Suite:

OOO3 Writer - Word Processor

OOO3 Draw - Drawing Program - I used this to prepare all of my Figures and Schemes saving each one separately with a unique alpha-numeric identifier for easy renumbering at the end.

OOO3 Calc - Spreadsheet - Used to generate tables and graphs


JabRef 4.2 - Java-Based Reference Manager - Fast and flexible, however there is a bit of a learning curve (maybe a few hours) associated with using the "style file," a template that formats your bibliography. I know there are several others out there, but JabRef was easy enough that I could get started with it right away and it is very robust. Documentation on their web site is good, and you will find there the critical plugin for syncing to OOO3.

SciFinder Scholar - Chemical and Biological Database Search Engine - SciFinder Scholar is sooo expensive that you shouldn't have to pay for it. Your institution will likely have a site-license (mine has one with only 3 seats or simultaneous users for a student body of 12000) and you need only download the Windows executable and obtain a copy of the site.prf file (a key granting you access) from the school (check with the library). Yes it is windows only, but again I found it to run nearly flawlessly in WINE for Linux.

BKChem 0.13.0 - Python-based 2D Chemical Structure Editor - BKChem is far from perfect, but for my thesis it worked great. This may in part be due to most of the chemistry I do is with flat polycyclic aromatic hydrocarbons, however anyone looking for open-source 2D structure editors should have good success with BKChem (also look at JChemPaint). The only major set back I had was in resizing objects as BKChem would crash. Otherwise very robust. Since BKChem exports a scalable vector graphic (SVG) to OOO2 .odg format I had no resolution trouble with resizing in OOO3 Draw.

Avogadro 1.0 - Powerful 3D Chemical Structure Builder and Force-Field Minimizer - I can't say enough good things about Avogadro. It is my front end to all of my computational chemistry. It is easier to use than GaussView (almost as intuitive as Spartan's Builder), offers beautiful, fast graphics, implements MMFF, UFF and Ghemical force-fields, reads loads of file-types including Gaussian Cube files, displays MOs, cross-platform (YES Mac and Windows too!) and it's bloody free!! (I don't know how but thanks to Marcus Hanwell and his faculty advisor Geoff Hutchison).

PyMOL - 3D Chemical Structure Viewer and Graphics Renderer - Although a little clunky, PyMol's greatest strength is producing very nice graphics which are saved in .png format. I know it has many additional uses, however, I only used it to prepare beautiful 3D molecular visualizations for my thesis. It is only missing a "ball-and-stick" display style (which is available in avogadro) but the "stick" style is clean and the images do come out much sharper and scale well.

WinDNMR in WINE - Dynamic NMR Line Shape Simulator - Although not available for Linux or Mac, WinDNMR worked without any trouble through WINE for Linux. The program is free-ware, but the author H. Reich requires e-mail registration in exchange for an activation code. This program requires adequate knowledge and skill for proper execution but the manual/tutorial is available and thorough.

MestReNOVA - Advanced NMR Workup Software - MestReNOVA is not free, but a 45 day trial is available for Windows/Mac/Linux, giving the average graduate student enough time (I got a 15 day extension) to do the final workup of all NMR FIDs.

pdftk - PDF merge/split Command Line Tool - This little gem came in real handy to manage my dissertation in 5 parts. Splitting up the OOO3 .odt files allows for faster save times and handling. I didn't learn how to start page numbering from a different number than 1 until after I merged my 3 chapters and appendix into the .odt file which was a little frustrating to manage the 155 page document for final minor edits. Still saving each part separate and exporting as a PDF worked well and pdftk seamlessly merges one printable document. Most likely pdftk is downloadable from your package manager (that's what I did with Ubuntu) and type pdftk --help for a list of command options.

Hurdles and Lessons for Writing a Dissertation/Thesis with this Software:

The OOO3 office suite is nearly as powerful as MS Office but there are some significant differences, some advantageous. There is no way I can give a complete overview of these differences, but there are a few helpful points I may make.

1. Page Numbering in OOO3 is tricky. It is a good idea to break your document up into sections as it saves time in the end. However, this is only true if you learn how to number starting with a different page than 1 well in advance. OOO-Writer uses page "styles" to manage this information. For example to number your preface with Roman Numerals and then start Chapter 1 with page 1 (as is usually the case), the preface pages must be designated a separate style "preface" than the rest of the document which will probably remain "default." It is imperative to sort this out early with some test pages. Consult the following website documentation: OOO3 Wiki, Taming OOO3, OOBlog. I'm sure there are lots of other sites with this information, but the first 2 alone basically got me up-and-running (although a bit late!).

2. Build a detailed and "Advisor Approved" outline for your entire thesis. Use the Outline Formatter in OOO3 (usually defaults as you build) for this and you'll be happy you did. My outline literally became my headings and subheadings for each section of my dissertation which I could easily reformat numerically after I was finished using the Bullets/Numbering toolbar.

3. Use a reference manager to keep your bibliography organized. I used JabRef with an OOO-plugin (see above) and it worked well for me. I did the best with my "style-file" for ACS formatting and left it alone until I was finished the document before a final format.

4. Organize your Tables, Figures, Schemes and Componds with a well designed alpha-numeric coding system so you can use "Find/Replace" tool in OOO3 at the end to provide a final number. I used "T" for Table, "F" for figure and so on, followed by a 1,2,3 for which chapter the table or figure was in, followed by Roman Numeral designation for which part within the chapter it was in, followed by a capital letter. The trouble I ran into was when substituting C2II (the "I-th" compound of part I Chapter 2) with the number 16, compounds C2IIA-C2IIZ (compounds in part II of Chapter 2) became 16A-16Z!!! So don't do that! Use a better system and you'll be golden.

5. Export and test as you go. Your advisor will probably want to use your well-crafted figs, schemes, tables in journal submissions later on (hopefully) so you should save each one individually with a good systematic archiving method and export them into a format that will be useful for collaboration purposes (MS Word 2003 / 2007). Also deal with your text. I found exporting to .rtf worked well for keeping my text formatting, but my figures/schemes/etc were botched. It is useful to figure out a system that you know will work early on so you're not "stuck like chuck... cuz chuck was stuck" -MM.

Writing my Dissertation: Linux or Windows?

I have noted previously that I am a Ph.D. student writing his dissertation. Recently I've been having some saving problems in MS Word and I've lost a couple paragraphs of writing twice. I have reconfigured my school desktop to dual-boot xp and ubuntu (jaunty) and I started to determine if I could accomplish writing my dissertation within linux. I already have about 40 pages of what should be around ~150 page document including over a dozen figures, schemes and tables. One of the likely culprits is Endnote, a powerful bibliography database manager which seamlessly manages your MS Office Word citations in any format you need. However, it may be inturrupting Word in some ways and causing it to flake out on me on save. And yet it is too useful to discard so I wondered if their was an alternative for Sun's OO-Writer.

There is and it is called JabRef. So far, JabRef seems just as useful as Endnote only perhaps not quite as powerful. It doesn't imbed a widget toolbar in Writer and if you delete a citation from your text it doesn't seem to omit it from the references section. (Although I still need to spend more time learning its capabilities.) [Update: JabRef works great. I imported my endnote database with ease, although I had to do some manual edits. Also, there is a "sync" button in the plugin that deals with any edits you make. The only downside (documented on Alver's site) is that you must only use the style-file downloaded directly from the web. You can edit it at will but I wouldn't even try to rename it or copy it in anyway or you are "stuck like chuck"] It can import from Endnote, SciFinder and numerous other databases with various formats. To get it to integrate with Writer a plugin (written by Morten Alver) must be added. Alver's site (see below or click here) details installation and includes a needed 'style-file' which tell JabRef how to format your citations.

When I installed JabRef from Synaptic, I found it was not the most up-to-date version. When I installed the .tar.bz2 from the JabRef site, it did not make available an icon in the menu which is a nice feature for commonly used programs (I don't mind command line, but I just like the clean feel of a menu icon to start-up). Although I had no idea how to fix this I found enough information in this ubuntu forum thread to get the job done. Very Nice!

In addition to JabRef, I will need a 2D chemical structure editor to generate structures for my figures and schemes. I love CambridgeSoft's ChemDraw and have used it freely (at school) for years. At home I had a copy of Isis Draw which was a free windows tool. In linux I am not fully satisfied here. I haven't found a single editor of nearly the capabilities as these programs. However, I did find a well written review on several available programs which can be found here. Possibly by using a few of these you can have the power of chemdraw. So far BKChem is the favorite by a small margin. Fortunately I mostly work with flat polycyclic hydrocarbons so I think BKChem will work for me.

In summary: Although it requires a little more work to install and configure and lacks marginally in functionality, at least for now, there appears to be a viable alternative for serious chemical thesis writing. I will probably make the effort to convert.

Links:

http://jabref.sourceforge.net/index.php

http://www.itk.ntnu.no/ansatte/Alver_Omholt_Morten/jabref/OOPlugin.html

http://groundstate.ca/chemdraw

http://ubuntuforums.org/showthread.php?t=225390

For an extensive list in chemical software written for linux see this link:

http://www.redbrick.dcu.ie/~noel/linux4chemistry/linux4chemistry.py

Introduction

The goal of this blog is mainly to keep myself on track with my life goals. Included in these are various projects which I will document here. May it also serve to provide some form of expression and the freedom to rant and rave as I see fit.

At the time of this writing, I am 28 years old, married to a lovely, caring, intelligent, passionate, driven woman named Elia who has given me 3 boys, the eldest Lucas (22 mos.) and the twins Ethan and Gavin.

I am currently in a state of slippage, redirection, and melancholly, quite possibly losing my mind, or at least changing it frequently. I am writing my Ph.D. dissertation on my work in physical organic chemistry. Although I have no working title, it's contents will enlighten the reader on the subject of polycyclic aromatic hydrocarbons (PAHs), specifically my work on the synthesis of a [4.4.4]Starphene as well as DFT calculations of large substituted acenes and a correlation of their HOMO-LUMO energy gap with their apparent photo-oxidative resistance (air-stability).

I used to be a musician; unafraid of expression, writing frequently, practicing often. I would like to restart the process: write, practice, record, learn.

I have a bit of a fancy for beer. I know, a bit 'cliche' whilst still in graduate school but I assure you I never completely went "off the deep end" by growing a full beard, touring breweries whenever possible just for free samples and turning my nose up at the award winning Pabst Blue Ribbon (their mommy put the blue ribbon ON THE CAN!)....okay I did that. Still, I have been lucky enough to acquire some great materials for homebrewing and better still, found some people who've shared my interest along the way. Again, I would love to "relax, have a homebrew" very soon. Did I mention the twins were born 3 months ago?

I used to ride a motorcycle. I've had my license since I was 18 and rode every year. My Dad pulled my first bike out of the dump, made it run (and pass inspection), slapped me on the back and said "don't kill yourself." It was a 1971 125 cc Honda Rebel and frankly I'm surprised I lived to tell about it. I remember cruising down the highway (litteraly down-hill) topping out at 80 mph just to push it (sorry Mom) and it was rattling so hard I thought the handlebars might come loose. I slowly upgraded from there: 1979 450cc Kawasaki rebuild; 1985 500cc Honda Magna V30; 2002 750cc Honda Shadow VT750. Last July my father-in-law lost his life on his Kawasaki. It's almost June this year and I've just registered mine and got it out of storage, it needs a chain and sprockets, I'm not sure if it will get them. I've got a lot of babies to look after.

So summer is here, I'm plugging away at my dissertation, looking for a job (hopefully a well-suited post-doc) and trying to find projects that will help maintain my sanity. I've been thinking for a while about trying a linux os at home and using it as a digital audio workstation. Why? Well it's a two-fer. I'll get to bang my head against the wall learning something that's not chemistry for a change. Linux is hard enough to get started in but I really want to compound it with the world of DAWs, sequencers, digital effects, samples, synths, VST plugins, etc. I sang bass in a college chamber choire. I played sax in the pep-band and guitar in the jazz band in high-school. I've been writing "singer-songwriter" crap for about 15 years (although a bit dried up for the past 5). I don't know much about any of that, but I don't know anything about digital composition and recording. Thus, this is the start of my blog.