welcome to somewhereville (.com)
est. 2001, pop. 1 ~ Damian G. Allis Ph.D., residing
Title says it all (A&S Article | Local PDF). As to the "Resistance Is Futile" subheading, we can ponder the futility of a material trying to not manifest an intrinsic property under stimulus, but you’d get many more visits to your site debating the relevance of anthropomorphizing members of The Collective.
With thanks to Daniel Bernardi of the (and my) College of Arts and Sciences for the article and for keeping the science behind the original article understandable.
In press, in Chemistry of Materials (doi.org/10.1021/acs.chemmater.9b03644).
The theory that underlies the reason for this article is addressed in "Bond Alternation In Infinite Periodic Polyacetylene: Dynamical Treatment Of The Anharmonic Potential," then the history of the material is exhaustively reviewed in "Polyacetylene: Myth and Reality" (open access, so you've no excuse to not read it). The preparation of the starting material, di-iodo-butadiene, C4H4I2, in urea, is published in "Commensurate Urea Inclusion Crystals With The Guest (E,E)-1,4-Diiodo-1,3-Butadiene."
I'm also very happy to be able to officially acknowledge my use of the Syracuse University Academic Virtual Hosting Environment (AVHE) as part of this work, which was involved in everything from periodic DFT calculations and the anharmonic treatment of polyacetylene on the electronic structure side, to cleaning up crystal cells of the polyacetylene-urea complexes for the generation of images in VMD and UberPOV – why just make a picture when you can, at least, make a method-consistent one?
As an aside, this is also my first experience using GIMP for a production-quality graphic – in this case, in the form of a proposed journal cover image (below. We'll see if it gets accepted in the coming month or so).
This GIMP use was instigated by originally formatting my MPB post-repair to Case-sensitive APFS three years ago, for which Photoshop refused to install with a widely-posted but little-addressed "Case-sensitive drives not supported" error (for which the Adobe solution remains "don't do that"). After a small learning curve, I'm pleased to say that GIMP is a hell of a program, well worth the price, and is just as pleasant an experience in Ubuntu 18.04 as it is in OS X 10.15 – a tidy sum saved each year for the 0.2% of features actually needed in either program to do the above.
Steluta A. Dinca, Damian G. Allis, Michael D. Moskowitz, Michael B. Sponsler, Bruce S. Hudson
Abstract: We report a novel, highly effective strategy for controlling the synthesis of polyacetylene as a guest in an organic host crystal by monitoring in situ an elimination–condensation polymerization reaction. Specifically, in this process, the polymer material is forced to have its chains extended and aligned such that translational periodicity applies, producing a bond alternation potential that has a symmetric double minimum. The synthetic approach used is photochemical elimination of iodine from a conjugated diene, (E,E)-1,4-diiodo-1,3-butadiene, which forms a commensurate and fully ordered urea inclusion compound. Photochemical cleavage of the terminal C–I bonds results in elimination of iodine from the single crystal and formation of C–C bonds between adjacent radicals to produce the conjugated 1,8-diiodo-1,3,5,7-octatetraene and subsequent longer polyene species. The combination of in situ crystal mass-loss measurements and vibrational Raman spectroscopy demonstrates clearly the presence of new polyene chains and loss of iodine from the urea substructure. The first few product oligopolyenes exhibit very strong Raman scattering with the most intense vibrational features decreasing in frequency for longer chains approaching an asymptotic limiting frequency that mimics the behavior of conjugated polyenes of known lengths from previous vibrational Raman studies. With extensive irradiation, the mass loss approaches that anticipated from the crystal stoichiometry and, at the same time of irradiation, the Raman intensity largely disappears. These results demonstrate that the reaction reported here proceeds to completion, leading to a quasi-one-dimensional array of isolated polyacetylene chains that are constrained to be in a continuous extended, all-trans conformation within the tunnels formed by the urea crystal lattice.
And Happy Leap Day (a first after nearly 20 years of this domain existing).
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).
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:
...
Minotr: UHF open shell wavefunction.
Direct CPHF calculation.
Differentiating once with respect to electric field.
with respect to dipole field.
Electric field/nuclear overlap derivatives assumed to be zero.
Using symmetry in CPHF.
Requested convergence is 1.0D-08 RMS, and 1.0D-07 maximum.
Secondary convergence is 1.0D-12 RMS, and 1.0D-12 maximum.
NewPWx=F KeepS1=T KeepF1=T KeepIn=T MapXYZ=F SortEE=F KeepMc=T.
MDV= 3932153962 using IRadAn= 1.
Generate precomputed XC quadrature information.
Solving linear equations simultaneously, MaxMat= 72.
There are 3 degrees of freedom in the 1st order CPHF. IDoFFX=0 NUNeed= 3.
3 vectors produced by pass 0 Test12= 3.94D-11 3.33D-08 XBig12= 2.15D+05 2.71D+02.
AX will form 3 AO Fock derivatives at one time.
FoFJK: IHMeth= 1 ICntrl= 0 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F
IRaf= 160000000 NMat= 3 IRICut= 1 DoRegI=T DoRafI=F ISym2E=-1.
FoFCou: FMM=T IPFlag= 0 FMFlag= 100000 FMFlg1= 2001
NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T
wScrn= 0.000000 ICntrl= 0 IOpCl= 1 I1Cent= 0 NGrid= 0
NMat0= 3 NMatS0= 3 NMatT0= 0 NMatD0= 3 NMtDS0= 0 NMtDT0= 0
Petite list used in FoFCou.
FMM levels: 10 Number of levels for PrismC: 9
3 vectors produced by pass 1 Test12= 3.94D-11 3.33D-08 XBig12= 1.52D+04 3.94D+01.
3 vectors produced by pass 2 Test12= 3.94D-11 3.33D-08 XBig12= 1.29D+04 3.31D+01.
3 vectors produced by pass 3 Test12= 3.94D-11 3.33D-08 XBig12= 1.65D+06 4.27D+01.
3 vectors produced by pass 4 Test12= 3.94D-11 3.33D-08 XBig12= 1.92D+08 6.96D+02.
3 vectors produced by pass 5 Test12= 3.94D-11 3.33D-08 XBig12= 4.40D+10 7.74D+03.
3 vectors produced by pass 6 Test12= 3.94D-11 3.33D-08 XBig12= 4.42D+12 1.70D+05.
3 vectors produced by pass 7 Test12= 3.94D-11 3.33D-08 XBig12= 3.50D+14 1.14D+06.
3 vectors produced by pass 8 Test12= 3.94D-11 3.33D-08 XBig12= 3.13D+16 1.34D+07.
3 vectors produced by pass 9 Test12= 3.94D-11 3.33D-08 XBig12= 1.75D+18 4.02D+07.
3 vectors produced by pass 10 Test12= 3.94D-11 3.33D-08 XBig12= 1.28D+20 7.81D+08.
3 vectors produced by pass 11 Test12= 3.94D-11 3.33D-08 XBig12= 1.50D+22 7.70D+09.
3 vectors produced by pass 12 Test12= 3.94D-11 3.33D-08 XBig12= 1.12D+24 5.57D+10.
3 vectors produced by pass 13 Test12= 3.94D-11 3.33D-08 XBig12= 2.86D+25 5.87D+11.
OrtVc1: Ph=1 IOff= 0 IPass=20 DotMx1= 2.08D-06
OrtVc1: Ph=1 M= 1181528 NPass=20 Test1= 3.94D-11 Small= 1.18D-06 VSmall= 1.00D-12
OrtVc1 failed #1.
Error termination via Lnk1e in /opt/g09/l1002.exe at Sat Oct 11 01:10:22 2014.
What little there is available online for the "OrtVc1 failed #1." error (from CCL – here and here) is less than helpful in addressing the problem. The problem is also coordinate system-independent (Cartesian and z-matrix formats both provide the same error), but is sensitive to the choice of basis set (6-31G(d,p) would work fine through the Raman intensity predictions, 6-311G(2d,p) would fail at the stage above).
Directing the issue to Gaussian, the provided workaround is straightforward.
The prediction of Raman intensities requires using Coupled Perturbed Hartree-Fock (CPHF), for which a special sensitivity in the code (currently) exits when using both molecular symmetry and the fast multipole method, the use of which (FMM, that is) is governed by Gaussian09 based on the atom count.
The workaround, provided by Dr. Fernando Clemente at Gaussian, Inc., is to divide the calculation into two steps. My input for the first successful run is shown below. A few details:
1. The first stage contains no Raman keywords (just the plain "freq" call).
2. In the second stage, the cphf=rdfreq is reading an incident light frequency of 0 (cm-1 or nm) at the bottom of the input file ("0"). You can run the static or dynamic cases as you like at this stage.
3. Also in the second stage, FMM is turned off (nofmm).
4. Also still in the second stage, the option to calculate Raman intensities is turned on (polar=raman). This is, as it happens, a recommended way to perform Raman intensity calculations – run a typical normal mode analysis, then import the force constants (and geometry) from this calculation into a Link1 step while increasing the basis set size (for better intensity prediction).
%chk=checkpoint.chk %nprocshared=12 %mem=50000MB #p integral(grid=ultrafine) freq=hpmodes b3lyp/6-311++g(3df,3pd) scf=novaracc symm=loose Part 1 - just the frequency calculation 0 1 C 0.00000000 48.56668920 -0.34496298 C 0.00000000 47.35252242 0.35603740 ... H 0.00000000 -49.50718415 0.19804614 H -0.00000000 49.50718415 0.19804614 [blank line 1] [blank line 2] --link1-- %chk=checkpoint.chk %nprocshared=12 %mem=50000MB #p integral(grid=ultrafine) polar=raman cphf=rdfreq nofmm b3lyp/6-311++g(3df,3pd) geom=checkpoint Part 2 - Raman intensities 0 1 0 [blank line 1] [blank line 2]
In theory, your calculation should run just fine.
The next problem is GaussView-specific – one that only comes up when you've a system with dynamic polarizability (incredibly long polyenes being a prototypical example) or when you perform frequency-dependent Raman calculations and you slip near resonance.
When running a series of Raman intensity calculations with increasing incident light frequency (cphf=rdfreq, then an array of energies), Mode 17 of this particular molecule either has a really large activity (cannot be printed out) or we're approaching resonance (also a case of really large activity and it can't be printed out). This isn't a problem with the code, it's your molecule.
16 17 18
BG AG BG
Frequencies -- 218.8851 257.7857 266.9993
Red. masses -- 3.5318 5.1372 2.2022
Frc consts -- 0.0997 0.2011 0.0925
IR Inten -- 0.0000 0.0000 0.0000
Raman Activ -- 0.2046 0.7412 0.2871
Depolar (P) -- 0.7500 0.3044 0.7500
Depolar (U) -- 0.8571 0.4667 0.8571
RamAct Fr= 1-- 0.2046 0.7412 0.2871
Dep-P Fr= 1-- 0.7500 0.3044 0.7500
Dep-U Fr= 1-- 0.8571 0.4667 0.8571
...
RamAct Fr=12-- 90.1095 ************ 0.3406
Dep-P Fr=12-- 0.7500 0.3333 0.7500
Dep-U Fr=12-- 0.8571 0.4999 0.8571
This is all well-and-good if you only rely on the .log file. If you skip the .log file inspection and only ever use GaussView, the result of inspecting the Raman intensities is below.
Note that Mode 17 has the intensity of Mode 18, and Mode 18 has zero intensity. Something is afoot! If you know what to expect out of your system, the missing intensities should be obvious. If not, you're missing some very important information about your molecule.
The GaussView developers are aware of the problem. In the meantime, you can get around this problem by globally replacing all of the " ************ " (note the spaces on either side!) with a huge number (at which point the Raman intensity issue will become obvious – careful to preserve the spacing in the .log file).