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

Friday, December 20th, 2013

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.

Dipole Derivative, Polarizability Derivative, And Vibrational Polarizability Contribution Output From Gaussian09 With IOp(7/33)

Thursday, August 30th, 2012

For those itching for polarizability derivative orientation information and wondering where it is when you ask for it… what’s included below is a combination of a few points in one, specifically pointing out that the IOp options are not just “another part” of the Gaussian input file (with the IOp Overlays currently linked HERE).

The problem I realized after an email from Gaussian HQ was that, as was the case for the KMLYP density functional call discussed in previous posts about [18]-annulene, “opt” and “freq” keyword combinations are seen as two distinct runs in Gaussian that don’t pass the IOp information along (and, admittedly, I should have remembered that). Specifically, the additional print-out for the polarizability info is called by IOp(7/33=3).

What I provide below is a two-in-one input file that saves you from having to run double-duty input files in the checkpoint file. This also serves as a template for those looking for examples of combining multi-step input files that include mixed basis sets (as many of the problems I’ve been emailed stem from carriage return issues more than anything else). Note that the input file is set to run Raman intensities and produce higher-precision (hpmodes) eigenvectors (so, if you just want to test this, remove the “raman”).

%chk=C4H5Cl_B3LYP_631Gdp_LanL2DZ_IR_Raman.chk
#p scf=tight opt=tight b3lyp/GEN pseudo=read

C4H5Cl_B3LYP_631Gdp_LanL2DZ_IR_Raman Opt

0 1
 C                 -1.74671095   -0.64168298    0.00000000
 H                 -1.53944096   -1.69141587    0.00000000
 C                 -0.73010315    0.25446188    0.00000000
 H                 -0.93737314    1.30419477    0.00000000
 C                  0.73010315   -0.25446188    0.00000000
 H                  0.93737314   -1.30419477    0.00000000
 C                  1.74671095    0.64168298    0.00000000
 H                  1.53944096    1.69141587    0.00000000
 H                 -3.73526840    0.03531673    0.00000000
 Cl                 3.73526840   -0.03531673    0.00000000

C H 0
6-31G(d,p)
****
Cl
Lanl2DZ
****

Cl
Lanl2DZ

--Link1--
%chk=C4H5Cl_B3LYP_631Gdp_LanL2DZ_IR_Raman.chk
#p Geom=Check Guess=Read freq(raman,hpmodes) iop(7/33=3)
 
C4H5Cl_B3LYP_631Gdp_LanL2DZ_IR_Raman Freq
     
0 1

Note the carriage return after the second “0 1″.

For the demo molecule above, additional print-out below.

 Dipole derivatives wrt mode   1:  3.96988D-14 -1.15747D-14 -1.96904D-01
 Polarizability derivatives wrt mode          1
                 1             2             3 
      1   0.000000D+00  0.000000D+00  0.206435D+00
      2   0.000000D+00  0.000000D+00  0.143916D-01
      3   0.206435D+00  0.143916D-01  0.000000D+00
 Vibrational polarizability contributions from mode   1       0.0000000       0.0000000       0.0257731
 IFr=  0 A012= 0.23D-23 0.77D+00 0.13D+00 Act= 0.90D+00 DepolP= 0.75D+00 DepolU= 0.86D+00

Alternately, keep track of the checkpoint file.

Bond Alternation In Infinite Periodic Polyacetylene: Dynamical Treatment Of The Anharmonic Potential

Sunday, August 5th, 2012

In press (DOI:10.1016/j.molstruc.2012.07.051) in the Journal Of Molecular Structure. May go down in history as a hardest-fought paper acceptance. In a similar line of research as the [18]-annulene study, but exploring the infinite limit of geometry and bond length alternation energy barrier for this infinite case. If the numbers are correct, the infinite polyene chains (polyacetylene) do not exhibit bond length alternation because the Peierls’ barrier between the single-double and double-single bond alternate minima is below the vibrational zero-point level. Plenty of ramifications.

Bruce S. Hudson and Damian G. Allis

Abstract. The potential energy of the infinite periodic chain model of polyacetylene (pPA) is symmetric with two equivalent minima separated by the Peierls’ stabilization barrier. In this work it is shown how an energy scale and vibrational energy levels for this highly anharmonic Peierls’ degree of freedom can be estimated. Attention is given to the potential energy increase for large deformations. The Born-Kármán treatment of translational symmetry is applied. Two empirical methods and a direct periodic boundary condition (PBC) density functional theory (DFT) calculations are in semi-quantitative agreement, each leading to the conclusion that pPA has a zero-point level that is above the Peierls’ barrier. The argument does not depend critically on the barrier height or the other parameters of the model or the computation method. It is concluded that pPA will not exhibit bond alternation and that the zero-point average geometry does not preclude possible conductivity.

The Structure Of [18]-Annulene: Computed Raman Spectra, Zero-Point Level And Proton NMR Chemical Shifts

Saturday, August 4th, 2012

In press (DOI:10.1016/j.molstruc.2012.05.016) in the Journal Of Molecular Structure (Volume 1023, 12 September 2012, Pages 212–215) in the special issue: MOLECULAR VIBRATIONS AND STRUCTURES: THEORY AND EXPERIMENT — A collection of papers dedicated to Professor Jaan Laane on the occasion of his 70th birthday.

This paper on the “actual” geometry of [18]-annulene is part of several larger stories addressing a larger polyene (or larger-polyene) issue. First among these is the meaning of experimental results obtained by various spectroscopic methods (in this case, using previous X-ray, Raman (with the C2 (blue) and D6h (red) simulated spectra shown in the image above), IR, and NMR data that produce different results within the limitations of the methods to study the single molecule). Second is the quality of the theoretical method for reproducing certain types of spectroscopic data. In the case of the [N]-annulene series, the ever-present B3LYP density functional is found to produce the time-average geometry of [18]-annulene found in X-ray data, but another density functional (in this case, KMLYP), finds that bond-alternate minima exist. Third is the importance of the zero-point level in the treatment of systems for which bond-alternate geometries exist with transition-state barriers calculated to be below the zero-point level in the classical approximation of nuclear positions (the Born-Oppenheimer Approximation).

NOTE 1: The KMYLP density functional is called in Gaussian with the following keyword set:

BLYP iop(3/76=1000005570) iop(3/77=0000004430) iop(3/78=0448010000)

NOTE 2: Optimization and Frequency calculations must be performed as TWO SEPARATE CALCULATIONS. The iop-called density functional does not carry itself over between opt + freq (or other properties) in the same input file. If you opt + freq in the same input file, you will Opt with KMLYP but freq with BLYP. This will be obvious by the number of imaginary modes.

Bruce S. Hudson and Damian G. Allis

Abstract. [18]-annulene has been of great interest from the structural point of view of its bond alternation. High-level calculations based on structures selected for agreement with NMR spectra lead to a bond-alternate C2 form over a non-alternating planar D6h structure deduced from diffraction, infrared (IR) and electronic spectral studies. Here it is shown that computed Raman spectra for the D6h and C2 forms are expected to be very different. However, two equivalent non-D6h bond-alternate minima of D3h or C2 geometries are separated by only a small barrier along a motion that involves CC stretching and compression. It is shown here that the zero-point level is above the barrier for this species. In light of that fact, the NMR calculations are reconsidered with inclusion of zero-point level averaging.

CCSD(T) and MP4 Z-Matrix Coordinate Oddity In Gaussian: When In Doubt, Change Your Format

Sunday, April 29th, 2012

This post was instigated by Syracuse University Professor of Chemistry and well-known non-blogger Tim Korter concerning efforts to, I believe, generate proper Møller–Plesset Perturbation Theory Of The 4th Order (MP4, and also testing coupled cluster CCSD(T) calculations) intermolecular potentials for improving terms for Grimme dispersion-corrected density functional theory (DFT) calculations with the Gaussian09 package (a program for which many people grumble about various issues but which is, by nearly all metrics, a fantastic set of quantum chemical programs). The examples below, using water only, are just for ease-of-testing, which produce the following results based on the form of the input of the molecular coordinates. For those wondering why, z-matrices are the preferred format for performing SCAN or other automated trajectory calculations (an absolutely useless format, in my opinion, now that we have computers that can handle more than five atoms).

1. Molecular coordinates defined in the z-matrix (obviously in z-matrix format) and “z-matrix” called in the opt keyword…

#p scf=tight opt(tight,z-matrix) MP4/aug-cc-pVTZ
 
h2o test 1
 
0 1
O              
H                  1    0.96000000
H                  1    0.96000000    2  109.50000032

… produces:

 ************************************************
 ** ERROR IN INITNF. NUMBER OF VARIABLES (  0) **
 **   INCORRECT (SHOULD BE BETWEEN 1 AND 50)   **
 ************************************************

2. Molecular coordinates defined in the z-matrix (obviously in z-matrix format) and “z-matrix” NOT called in the opt keyword…

#p scf=tight opt=tight MP4/aug-cc-pVTZ
 
h2o test 2
 
0 1
O              
H                  1    0.96000000
H                  1    0.96000000    2  109.50000032

… produces:

 ************************************************
 ** ERROR IN INITNF. NUMBER OF VARIABLES (  0) **
 **   INCORRECT (SHOULD BE BETWEEN 1 AND 50)   **
 ************************************************

3. Molecular coordinates defined by variables in the z-matrix (obviously in z-matrix format) and “z-matrix” called in the opt keyword…

#p scf=tight opt(tight,z-matrix) CCS(D)/aug-cc-pVTZ
 
h2o test 3
 
0 1
O              
H                  1    B1
H                  1    B1     2  A1 

B1 0.96000000    
A1 109.50000032

… produces:

Normal termination of Gaussian 09 at Fri Apr 27 11:28:33 2012.

4. Molecular coordinates defined by variables in the z-matrix (obviously in z-matrix format) and “z-matrix” NOT called in the opt keyword…

#p scf=tight opt=tight MP4/aug-cc-pVTZ
 
h2o test 4
 
0 1
O              
H                  1    B1
H                  1    B1     2  A1 

B1 0.96000000    
A1 109.50000032

… produces:

Normal termination of Gaussian 09 at Fri Apr 27 11:28:33 2012.

So, a solution, for when the dreaded…

 NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-
 NUMERICAL EIGENVECTOR FOLLOWING MINIMUM SEARCH
 INITIALIZATION PASS


 ************************************************
 ** ERROR IN INITNF. NUMBER OF VARIABLES (  0) **
 **   INCORRECT (SHOULD BE BETWEEN 1 AND 50)   **
 ************************************************

… error appears, the simple solution is to re-define your system.

In the interest of wasting a few cycles, I ran a series of the same calculations with other post-Hartree-Fock methods [B3LYP, MP2, MP4, CCS(D), CCSD(T)] to see how pervasive the issue with coordinate definitions might be. It appears to be limited only to MP4 and CCSDT (CCS(D) worked but took an unbelievably long time for Option 3 above), meaning people generally running significant molecules likely have never come across the issue.

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