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The Low-/Room-temperature Forms Of The Lithiated Salt Of 3,6-dihydroxy-2,5-dimethoxy-p-benzoquinone: A Combined Experimental And Dispersion-Corrected Density Functional Study

In press, in CrystEngComm (DOI:10.1039/C2CE26523). This is my first full paper completely internet-powered, in that I've not physically met any of the other co-authors (also in the internet-powered context, the recent paper on [18]-annulene was written and submitted without sharing a room with Dr. Bruce Hudson, but we're in the same building, so it doesn't quite count). Also, one of the few papers for which I had no image generation duties (a rare treat).

The discussion of the very interesting possibilities of molecular redox materials in lithium-ion batteries aside, this paper presents a very thorough example of the power of computational approaches to greatly improve the understanding of solid-state molecular materials by (specifically) 1: overcoming the hydrogen position identification problems inherent in X-ray diffraction methods, 2: reproducing the changes that come with temperature variations in molecular crystals and explaining the origins of those (possibly subtle) changes by way of dispersion-corrected density functional theory, and 3: demonstrating that the nature of intermolecular interactions (specifically hydrogen bonding) can be rigorously cataloged across varied materials using post-optimization tools (in this case, using Carlo Gatti's excellent TOPOND program).

2013dec20_crysengcommcover

Caption: Issue cover.

Gaëtan Bonnard, Anne-Lise Barrès, Olivier Mentré, Damian G. Allis, Carlo Gatti, Philippe Poizot and Christine Frayret*

Abstract

Following our first experimental and computational study of the room temperature (RT) form of the tetrahydrated 3,6-dihydroxy-2,5-dimethoxy-p-benzoquinone (LiM2DHDMQ·4H2O) compound, we have researched the occurrence of hydrogen ordering in a new polymorph at lower temperature. The study of polymorphism for the Li2DHDMQ·4H2O phase employs both experimental (single crystal X-ray diffraction) and theoretical approaches. While clues for disorder over one bridging water molecule were observed at RT (beta-form),a fully ordered model within a supercell has been evidenced at 100K (alpha-form) and is discussed in conjunction with the features characterizing the first polymorphic form reported previously. Density functional theory (DFT) calculations augmented with an empirical dispersion correction (DFT-D) were applied for the prediction of the structural and chemical bonding properties of the alpha and beta polymorphs of Li2DHDMQ·4H2O. The relative stability of the two polymorphic systems is evidenced. An insight into the interplay of hydrogen bonding, electrostatic and van der Waals (vdW) interactions in affecting the properties of the two polymorphs is gained. This study also shows how information from DFT-D calculations can be used to augment the information from the experimental crystal diffraction pattern and can so play an active role in crystal structure determination, especially by increasing the reliability and accuracy of H-positioning. These more accurate hydrogen coordinates allowed for a quantification of H-bonding strength through a topological analysis of the electron density (Atoms-in-molecules theory).

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UNAFold 3.8, MFold Utilities 4.5/4.6 And Additional Component Installation (Using XCode Tools 3 And Fink 0.29.21) For OSX 10.6.x

NOTE: The version numbers for everything are given specifically because aspects of the installation process may change with different versions and, in the event, I will not necessarily know the answer to subsequent problems if major version changes include major changes to the below (and that should clear up the "qualifications" section).

The UNAFold (UNified Nucleic Acid Fold(ing)) nucleic acid folding and hybridization prediction program set (here using version 3.8) can by itself be built with few (and not important) errors in OSX with Xcode Tools 3. The actual running of UNAFold.pl produces several errors that do not affect the run but do affect the amount/format of the output. It is my assumption that any OS running a less-than "kitchen sink" installation of Linux/Unix (Ubuntu, gentoo and Damn Small Linux come to mind) will have these errors and will require subsequent installations of programs/libraries that pieces of UNAFold rely on for processing output into, specifically, images and PDF files. OSX has the same issue that is easy to handle using Fink (and less so trying to install otherwise completely unrelated programs to make these "dependencies" (programs and libraries) available to UNAFold). Once Fink is installed, it is a few-step process to build UNAFold, move the Mfold Utilities contents to their proper folders (and there is a small trick here as well), and generate a UNAFold-complete install for all your DNA/RNA needs.

1. UNAFold 3.8 Installation

To begin, download (currently at mfold.rna.albany.edu/?q=DINAMelt/software), extract, open a terminal, cd into the unafold_3.8 directory (likely ~/Downloads/unafold_3.8), and run ./configure. 

[prompt]$ cd ~/Downloads/unafold_3.8
[prompt]$ ./configure

On my machine (MacBook Pro, 10.6.x OSX + XCode Tools 3), this produces the output found in the local file 2011june_unafold_configure_output.txt.

You will likely note two sets of errors in the ./configure output:

./configure: line 8579: sort: No such file or directory
./configure: line 8576: sed: No such file or directory

./configure: line 10077: sort: No such file or directory
./configure: line 10074: sed: No such file or directory

The 10077 and 10074 errors are a bit odd because there are only 10039 lines in the configure file.

Are these errors important? No, you can build UNAFold just fine. I have run into these two "sort" and "sed" problems with a few other build attempts in OSX but have no good answer as to how to get around them (in case you're wondering, sort and sed are most certainly installed on the machine. The "sort" error can be removed by specifying the path explicitly in the configure file (in line 8579, change "sort" the "/usr/bin/sort"), but the sed error persists in the few attempts I tried to work around it. It doesn't appear to be a simple PATH issue. I'm not yet interested enough in finding a proper solution but, if you know, please post a comment or send a message. Is it just a character issue as discussed at itmercenary.livejournal.com/1585.html?).

running "make" produces the output found in the local file 2011june_unafold_make_output.txt.

[prompt]$ make

No issues. To install UNAFold, which will default to putting components into /usr/local/bin and /usr/local/share/, run sudo make install, which produces the output found in the local file 2011june_unafold_sudo_make_install_output.txt.

[prompt]$ sudo make install

Again, no issues. You will now have a populated /usr/local/bin folder.

2. MFold Utilities 4.5 (and, currently, the source for 4.6)

The next (optional) step is the inclusion of the mfold_util-4.5-Mac binaries (currently available at mfold.rna.albany.edu/?q=mfold/download-mfold), which I've also placed into the /usr/local/bin folder by extracting the contents of this file, them performing a cp * /usr/local/bin from within the MacBin directory.

[prompt]$ cd ~/Downloads/MacBin/
[prompt]$ sudo cp * /usr/local/bin

The processing of the data into plots with these programs requires that a set of *.col files be placed in the folder /usr/local/shared/mfold_util. Furthermore, these *.col are NOT provided in the mfold_util-4.5-Mac binary package. To get these files, you need only download the mfold_util-4.6.tar.gz file (currently at mfold.rna.albany.edu/?q=mfold/download-mfold), cd your way into src, make the /usr/local/shared/mfold_util folder, and copy the *.col files to /usr/local/shared/mfold_util.

[prompt]$ sudo mkdir /usr/local/shared/mfold_util
[prompt]$ cd Downloads/mfold_util-4.6/src
[prompt]$ sudo cp *.col /usr/local/shared/mfold_util

3. Fink 0.29.21 Install From Scratch

The first indication that other work was required came from trying to run mutplot randomly, which produced the following error:

dyld: Library not loaded: /sw/lib/libpng12.0.dylib
  Referenced from: /usr/local/bin/mutplot
  Reason: image not found
Trace/BPT trap

As digging around for libraries is not as straightforward as it would be for a Linux distro, I chose instead to solve the many problems by installing dependencies through the Fink program (currently fink-0.29.21). As 10.6.x users will find that there is no available Fink binary, you must build this from the source (which, with Xcode Tools 3 installed, occurs without error. If you don't have Xcode Tools 3 installed, the new mechanism for buying a copy of XCode Tools 4 is less than ideal (to me, anyway. $4.99?) but now occurs through the App Store).

Download the fink source (fink 0.29.21), extract, cd into the fink-0.29.21 directory, and run bootstrap. Upon completion, you run pathsetup.sh, source your .profile, and update fink.

[prompt]$ cd ~/Downloads/fink-0.29.21
[prompt]$ ./bootstrap
[prompt]$ . /sw/bin/pathsetup.sh 
[prompt]$ cd ~/
[prompt]$ source .profile
[prompt]$ fink selfupdate-rsync
[prompt]$ fink update-all

The output for my installation can be found in 2011june_fink_install_output.txt. The rsync output can be found in 2011june_fink_selfupdate_rsync_output.txt. NOTE: You will be asked several questions about the installation process. Be prepared to blindly select the default settings with [enter], but don't just walk away from the screen.

This completes the UNAFold install, MacBin install, and Fink install, meaning now we can walk through the dependencies.

4. Installing UNAFold (well, MFold Utils) Dependencies

First dependency-free UNAFold.pl run attempt produces the following error:

[prompt]$ UNAFold.pl seqtest.txt 
Checking for boxplot_ng... dyld: Library not loaded: /sw/lib/libpng12.0.dylib
  Referenced from: /usr/local/bin/boxplot_ng
  Reason: image not found
found, supports Postscript
Checking for hybrid-plot-ng... found, supports Postscript
Checking for sir_graph_ng or sir_graph... dyld: Library not loaded: /sw/lib/libpng12.0.dylib
  Referenced from: /usr/local/bin/sir_graph
  Reason: image not found
found, supports Postscript
Checking for ps2pdfwr... not found
Calculating for seqtest.txt, t = 37

As the UNAFold install page states, you need glut, the GD library, and gnuplot installed (and all of the many libraries therein). 

[prompt]$ fink install libjpeg tetex gd2 gnuplot

For gnuplot, you will be required to make a few selections during the build process (blindly hitting the enter key at these questions will do, but this is not just a "type and go" install process. And it took about two hours on a MBP).

A final working error-free run looks as below, leaving you to process the data with the MFold Utilities as you like:

[prompt]$ UNAFold.pl seqtest.txt 
Checking for boxplot_ng... found, supports Postscript
Checking for hybrid-plot-ng... found, supports Postscript
Checking for sir_graph_ng or sir_graph... found, supports Postscript
Checking for ps2pdfwr... found
Calculating for seqtest.txt, t = 37