More On The Virtues Of VirtualBox – ACID (or AICD) Under Ubuntu 14.04 (By Way Of OpenSuse 11.2)

“Stop that!” – George Carlin

If you’ve obtained source code from an academic lab that was last developed some time ago and you spent a whole day installing libraries and symbolic links and redefining variables in your .bashrc and downgrading libraries and redefining paths and have 20 tabs open in your browser that all go to 20 different obscure error discussions on Stack Overflow and it’s late and you’re tired and you think you might not need the program after all if you do a bunch of other workaround things instead – what’s below is for you.

Academics have been developing small code for (nearly) millions of years to make their lives easier – and we all benefit when that code is made available to others (esp. when it helps in data analysis). When that code is a series of perl or python scripts, there’s generally little reason why you should have any run issues. When they call on external libraries or specific tools, generally that information is available in the README somewhere. Generally speaking, there’s no reason why a code shouldn’t work in a straightforward manner when the developer doesn’t make it known that something else needs be installed to make it work.

So, why doesn’t code A work on your linux box? A few possibilities.

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“OrtVc1 failed #1.” Workaround In Gaussian09; Warning About (Pre-)Resonance Raman Spectra In GaussView 4/5

And Happy New Year.

Two issues (one easily addressable, one only by external workaround) related to the prediction of Raman intensities in Gaussian09 – for which there’s next-to-nothing online to address either of them (likely because they don’t come up that often).

OrtVc1 failed #1.

In simulating the Raman spectra of very long (> C60) polyenes as a continuance of work related to the infinite polyacetylene case (see this post for details: Bond Alternation In Infinite Periodic Polyacetylene: Dynamical Treatment Of The Anharmonic Potential), I reached a length and basis set for which Gaussian provides the following output and error:

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The EMSL Basis Set Exchange 6-31G, 6-31G(d), And 6-31G(d,p) Gaussian-Type Basis Set For CRYSTAL88/92/95/98/03/06/09/14/etc. – Conversion, Validation With Gaussian09, And Discussion

Jump to the basis sets and downloadable files here: files, 6-31G, 6-31Gd, 6-31Gdp.

If you use these results: Please drop me a line (damian@somewhereville.com), just to keep track of where this does some good. That said, you should most certainly cite the EMSL and Basis Set references at the bottom of this page.

It’s a fair bet that Sir John Pople would be the world’s most cited researcher by leaps and bounds if people properly cited their use of the basis sets he helped develop.

The full 6-31G, 6-31G(d), and 6-31G(d,p) series (yes, adding 6-31G(d) is a bit of a cheat in this list) from the EMSL Basis Set Exchange is presented here in the interest of giving the general CRYSTALXX (that’s CRYSTAL88, CRYSTAL92, CRYSTAL95, CRYSTAL98, CRYSTAL03, CRYSTAL06, CRYSTAL09, now CRYSTAL14 – providing the names here for those who might be searching by version) user a “standard set” of basis sets that are, for the most part, the same sets one does / could employ in other quantum chemistry codes (with my specific interest being the use and comparison of Gaussian and GAMESS-US in their “molecular” (non-solid-state) implementations). Members of the CRYSTAL developer team provide a number of basis sets for use with the software. While this is good, I will admit that I cannot explain why the developers chose not to include three of the four most famous basis sets in all of (all of) computational chemistry – 3-21G (upcoming), 6-31G(d,p) (presented here), and 6-311G(d,p) (also upcoming).

Continue reading “The EMSL Basis Set Exchange 6-31G, 6-31G(d), And 6-31G(d,p) Gaussian-Type Basis Set For CRYSTAL88/92/95/98/03/06/09/14/etc. – Conversion, Validation With Gaussian09, And Discussion”

For The Windows-Specific: Sed For Windows And A .bat File To Get Gaussian09 Files Working With aClimax

Provided you’ve installed Sed For Windows and know its proper path, the .bat file below should make all the modifications you need to your Gaussian09 .out files (in differently-named files at that) to get them properly loading in aClimax (see the previous post for all the details). A few simple steps:

1. Download and install Sed for Windows. Currently available at: gnuwin32.sourceforge.net/packages/sed.htm

2. Find its location on your machine. Under XP (where I’m using aClimax), this should be C:\Program Files\GnuWin32\bin

Continue reading “For The Windows-Specific: Sed For Windows And A .bat File To Get Gaussian09 Files Working With aClimax”

Generating Molecular Orbitals (And Visualizing Assorted Properties) With The Gaussian09 cubegen Utility

To begin, this post owes its existence to the efforts of Dr. Douglas Fox at Gaussian, Inc., who provided me with an alternative explanation of how the cubegen utility works. After much wailing and gnashing of teeth, I intend on taking Dr. Fox’s advice and asking Gaussian Support for assistance earlier in my endeavors. What follows below, I hope, will save you some significant frustration (and, given how little there is online that really describes the extra workings of cubegen in a clear and example’ed way, it is my expectation that this page appeared early in your search list).

What I wanted out of cubegen that I couldn’t figure out how to get:

The situation was simple. I wanted my molecule centered and bound within an arbitrarily-sized box (X,Z,Y) for making images and doing additional post-processing. Specifically, I wanted to be able to take many different molecules (from hydrogen gas to big biomolecules) defined within the same-sized box for layering and presentation (different boxes for each, but all the same size).

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Compiling And Running GAMESS-US (1 May 2013(R1)) On 64-bit Ubuntu 12.X/13.X In SMP Mode

Author’s Note 1: It is my standard policy to put too much info into guides so that those who are searching for specific problems they come across will find the offending text in their searches. With luck, your “build error” search sent you here.

Author’s Note 2: It’s not as bad as it looks (I’ve included lots of output and error messages for easy searching)!

Author’s Note 3: I won’t be much help for you in diagnosing your errors, but am happy to tweak the text below if something is unclear.

Conventions: I include both the commands you type in your Terminal and some of the output from these commands, the output being where most of the errors appear that I work on in the discussion.

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Experimental And Theoretical Studies Of Tetramethoxy-p-benzoquinone: Infrared Spectra, Structural And Lithium Insertion Properties

Published earlier this year in RSC Advances (RSC Adv., 2013, 3, 19081-19096), a follow-up (for my part) to the study 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 CrystEngComm last year. The theoretical section for this paper is a tour-de-force of Crystal09 solid-state optimizations, density functional and dispersion-correction dependence, and post-processing using Carlo Gotti’s TOPOND software. In brief, the combination of vibrational spectra, electochemical measurements, and solid-state density functional theory tests are used to predict the structure of the previously unknown lithiated tetramethoxy-p-benzoquinone structure based on the good-to-excellent agreement with two known TMQ crystal structures (the testing of density functionals and dispersion corrections being a very good survey of the pros and cons of the varied methods. If you were pondering an approach to follow to perform the same kind of theoretical analysis, the procedure set up by Gaëtan and Christine in this paper is fully worth your consideration).

2013dec20_rscadvances

Gaëtan Bonnard, Anne-Lise Barrès, Yann Danten, Damian G. Allis, Olivier Mentré, Daniele Tomerini, Carlo Gatti, Ekaterina I. Izgorodina, Philippe Poizot and Christine Frayret*

In the search for low-polluting electrode materials for batteries, the use of redox-active organic compounds represents a promising alternative to conventional metal-based systems. In this article we report a combined experimental and theoretical study of tetramethoxy-p-benzoquinone (TMQ). In carbonate-based electrolytes, electrochemical behaviour of this compound is characterized by a reversible insertion process located at approximately 2.85 V vs. Li+/Li0. This relatively high potential reactivity, coupled with our effort to develop computational methodologies in the field of organic electrode materials, prompted us to complement these experimental data with theoretical studies performed using density functional theory (DFT). Single crystals of TMQ were synthesized and thoroughly characterized showing that this quinonic species crystallised in the P21/n space group. The experimental crystal structure of TMQ was then used to assess various DFT methods. The structural features and vibrational spectra were thus predicted by using as a whole five common density functionals (PBE, LDA, revPBE, PBEsol, B3PW91) with and without a semi-empirical correction to account for the van der Waals interactions using either Grimme’s (DFT-D2) or Tkatchenko–Scheffler (TS) scheme. The most reliable combination of the DFT functional and the explicit dispersion correction was chosen to study the Li-intercalated molecular crystal (LiTMQ) with the view of indentifying Li insertion sites. A very close agreement with the experiment was found for the average voltage by using the most stable relaxed hypothetical LiTMQ structure. Additionally, a comparison of vibrational spectra gained either for TMQ molecule and its dimer in gas phase or through periodic calculation was undertaken with respect to the experimentally measured infrared spectra. The topological features of the bonds were also investigated in conjunction with estimates of net atomic charges to gain insight into the effect of chemical bonding and intermolecular interaction on Li intercalation. Finally, π-electron delocalization of both quinone and alkali salts of p-semiquinone were determined using the Harmonic Oscillator model of Aromaticity (HOMA) or aromatic fluctuation index (FLU) calculations.

Commensurate Urea Inclusion Crystals With The Guest (E,E)‐1,4-Diiodo-1,3-Butadiene

Published in Crystal Growth & Design (Cryst. Growth Des., 2013, 13 (9), pp. 3852–3855) earlier this year. The theory work is less impressive than the successful crystal growth, with initial solid-state efforts in Crystal09 only very recently now producing good results (leaving the molecular calculations to Gaussian09 in this paper). The procedure leading to the observed crystal structure of this inclusion complex is a significant step in the direction of testing the theory proposed in Bond Alternation In Infinite Periodic Polyacetylene: Dynamical Treatment Of The Anharmonic Potential published earlier this year in J. Mol. Struct.

2013dec20_DIBD_UIC

Caption: Two views along the ba and ca crystal axes of the (E,E)‐1,4-Diiodo-1,3-Butadiene : Urea Inclusion Complex.

Amanda F. Lashua, Tiffany M. Smith, Hegui Hu, Lihui Wei, Damian G. Allis, Michael B. Sponsler, and Bruce S. Hudson

Abstract: The urea inclusion compound (UIC) with (E,E)-1,4-diiodo-1,3-butadiene (DIBD) as a guest (DIBD:UIC) has been prepared and crystallographically characterized at 90 and 298 K as a rare example of a commensurate, fully ordered UIC. The crystal shows nearly hexagonal channels in the monoclinic space group P21/n. The DIBD guest molecules are arranged end-to-end with the nonbonding iodine atoms in the van der Waals contact. The guest structure is compared with that for DIBD at 90 K and with computations for the periodic UIC and isolated DIBD molecule.

Isotopically-Labeled Solid-State Vibrational Mode Energies And Intensities In Crystal09 – A Simple How-To

The generation of isotopically-substituted molecular crystal spectra has become a point of interest, which means blog post. To be clear, this is for cases where isotopic substitution does not affect the crystal geometry – the crystal cell does not change significantly upon deuteration (and for those who believe isotopic substitution never leads to significant changes in the solid, I refer you Zhou, Kye, and Harbison’s article on Isotopomeric Polymprphism and their work on 4-methylpyridine pentachlorophenol, which changes dramatically upon deuteration. I beat on this point because blindly assuming of the crystal cell geometry in such cases will produce spectra noticeably different than measured. It’s NOT the calculation’s fault!).

The generation of isotopically-substituted spectra and intensities in Crystal09 is trivial provided that you KEEP THE FREQINFO.DAT FILE. In fact, you need keep ONLY the FREQINFO.DAT to generate these spectra, which greatly reduces file transfer loads and allows for the scripted calculation of new vibrational spectra and thermodynamic data post-frequency calculation.

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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).