The electronic structure of selected betaine dyes. A quantum chemical study

This thesis presents electronic absorption spectra, non linear optical properties and geometrical parameters of betaine dyes obtained by quantum chemical calculations.

Four betaines [4-(1-piridinium-phenolan), 3-(1-piridinium-phenolan), 2-(1-piridinium-phenolan) and 4-(1-piridinium-thiophenolan)] were selected for the study.

During the research various ab initio methods were applied. The Hartee-Fock method (HF) and the second order Møller-Plesset perturbation theory (MP2) were used to determine a geometrical and NLO properties. Moreover, the NLO were obtained using chosen variants of the coupled cluster metod (CC2, CCSD) and the geometry optimizations were perform using the Density Functional Theory (DFT/B3LYP) as well as complete active space methods (CASSCF and CASPT2). In the case of spectroscopic properties the CC and CASSCF/CASPT2 methods along with Time-Dependant DFT (with B3LYP, PBE0 and CAM-B3LYP functionals) and the Configuration Interaction with Singles (CIS and CIS(D)) were used.

Results obtained during the study indicate that the correct description of betaine dyes' electronic structure is an unusually demanding test for present quantum chemical methods. It is safe to say, that, for all of the investigated parameters, the electron correlation has to be take into account. It is also worth to notify that basis set selection is less important. However, diffuse and polarisation functions should be included in the case of spectroscopic and optical properties.

The presented computational result confirmed the very strong interaction between a betaine molecule and its environment. One of the outcome of this phenomena is a large difference between experimental results (usually obtained in condense phases) and theoretical data (calculated in vacuum). Another observation verified during project is the significant increase of the betaines' NLO by the conformational shifting. Finally, it is worth notify that the largest NLO response was obtained for 4-(1-piridinium-thiophenolan).

How you can quest I'm a doctor now! I defended my thesis (abstract above) 19th of June 2008 and my degree was confirmed by faculty of Chemistry board 26th of June. Thesis was written in Polish, so it isn't very useful for most of the world. However, there is the appendix with all available theoretical data of geometrical and spectroscopic parameters of betaine dyes. Additionally, some of results was published in following articles: JMM-11, JMM-13 and LETT-411 (I hope to write one, maybe more). PDF with thesis can be download here.

If I find some time I will might prepare English version of mentioned appendix, and of course, I will share my LaTeX, gnuplot, computational experience.

Introductions not only to Quantum Chemistry

Supercomputer Institute at University of Minnesota presents set of PDF files being nice introduction to resources available there. Most of them are related to Quantum Chemistry, but there is also CSD System and Material Studio. If you are interested please check the link.

Dalton problems 2: Too long input record (ERI)

Problem

My CC calculations stopped with the forrtl: severe (22): input record too long, unit 9, file /tmp/niewod/RhbCCS/betaccs_rhb631+gd/CCSD_IAJB error message.

Answer

I changed four things and the job finished properly.

• First I changed a machine, but both were Itanium.
• Next I lowered the print level from 3 to 2.
• In the original jobfile I requested a direct calculation in a CC part, in the new one I put .DIRECT keyword in a main part (for all calculations).
• Finally I requested more memory (1900mb).

I got the proper results but the calculations end with error 32. It means forrtl: severe (32): invalid logical unit number, unit -10001, file unknown I reran jobs with new commands at the first machine, and it worked. Next I upgraded print level to 3 and job finished with success. So the issue could be cause by small amount of requested memory or direct/non-direct calculation in a HF,MP2 or CC calculation.

Files

• betacssi-old.dal
• betacssi-new.dal
• rhb631+gd.mol
• betaccs_rhb631+gd.out
• RhbCCS.e127210
• RhbCCS.o127210
• betaccs_h2co.out

Dalton problems 1: Direct and NonDirect HF

Short introduction

Once, I tried to create a website with notes on my Dalton's problems. I have had not time to upgraded it because Quantum Chemistry (and Dalton) has become much less important for me. Recently, I've decided that the best way to save my notes would be to add them as entries in my English blog. So they are.

Problem

I found difference between direct and non-direct Hartree-Fock results. The direct calculation didn't converge when non-direct did (look into the files below).

Answer

The reason of my problems was a very sharp convergence criteria. The screening in the direct SCF gives round-off errors, which makes it impossible to converge to 1.0D-10. (The default screening is 1.0D-14, which is usually safe, unless users ask for very sharp convergence,as I did!) Disable screening in the direct SCF, resolve my problem. I had to add: **INTEGRALS *TWOINT .IFTHRS 20 When convergence was set to 1.0D-09 the difference between direct and non-direct results disappear and both calculations converged in 28 iterations, with (nearly) the same energy:

• direct_rhb631+gd.out: -551.031670938128
• nodirect_rhb631+gd.out: -551.031670938119

I would like thanks Kenneth Ruud and Hans Jorgen Aa. Jensen for help.

Files

• nodirect.dal
• direct.dal
• rhb631+gd.mol
• direct_rhb631+gd.out
• nodirect_rhb631+gd.out

PC GAMESS benchmarks

Alex Granovsky presented the results of the PC GAMESS (version of Gamess US designed to work better on x86 architecture) benchmarks on new AMD Opteron and Intel Core2 processors. You can find them here.

The most important observations are:

• Intel CPUs are much faster,
• but AMDs scale better with number of cores.

BTW. You can find other interesting benchmark in the Performance section of the PC GAMESS website.

Two chemical links

This time two links to websites related to chemistry.

• The Supercomputing Institute from University of Minnesota prepared kit of Tutorials for Computational Chemistry and Physics Sciences.
• Vitalii Vanovschi created the website with many important chemical informations.

Getting the Molcas CASPT2 exciation energy

This is the short bash/awk script printing an energy of excitation to a first excited stated obtain by CASPT2 method in Molcas6:

for i in *.log
do echo $i
grep "Total energy:" $i| gawk ' BEGIN {l=1} {if (l==1) {a=$3} else if (l==2) \
{b=$3; print 27.2097*(b-a)} l++} '
done

Geometries from Gaussian Scan

Reading geometries from Gaussian file storing information about Potential Energy Scan (PES) isn't easy. I was sure that there were some tools to do this, but I cannot find any yesterday, so I prepared my own. It is writing in python, of course ;). Right now have very basic features. It reads input file and created output xyz files (as many as stationary points was found). You are using it simply writing in command line:

scaner-0.1.py inputfile

Greping excitation energy from Gaussian output

I've already written about CIS energies, but my suggestion is more general. You can use that command also for TDDFT calculations. But if you need energies from perturbative correction of CIS method (CIS(D) method) you have to use this:

 grep "CIS(D) Exc\. E" *.log

Molekel 5.0 alpha

I wrote that Molekel was rebirth and version 4.6 was release. Recently, I found that the project has been moved and alpha version of Molekel 5.0 can be found hear. So, right now we have:

1. 4.3. It is very old version and the sources are close. [website]
2. 4.6. The whole project has been rewritten and it is alpha version, not all functions from 4.3 version are working [website]
3. 5.0 New, not ready yet version with open source (GPL). [website].

My dalton's problems

I created a website, where I share some info about my problems with Dalton. At the moment there is only one point (problems with HF direct convergence).

CCLib

The new version (0.5) of CCLib has been release. CCLib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. It currently parses output files from ADF, GAMESS (US), Gaussian, and PC GAMESS.

gaussfield.sh v0.1

It can be very useful to obtain value of some molecular properties in electric field. I.e. you can get dipole moment of excited states from energies in fields F and -F, hyperpolarizability from analytic polarizability etc. But it's quite annoying to create many very similar Gaussian input files, so I wrote short script to created this files:

#!/usr/bin/env bash
for i in $*
do
        name=`basename $i .com`
        sed -e '/^%/d; /^#/s/$/ Field=X-10/' $i > ${name}-x.com
        sed -e "/^%/d; /^#/s/$/ Field=X+10/" $i > ${name}+x.com
done

No CIS(D) in solvent [Gaussian]

I tried to calculate excitation energy with CIS(D) method in solvent (PCM method). I found that the CIS resalts from CIS and CIS(D) outout are different. I checked and CIS with Direct and without this option gave another results. I wrote to Gaussian Help and got replay: Yes, there are differences and the CIS=Direct results are correct.The non-direct methods, both CIS and CIS(D) use MO integrals where the solvent effects are not present and thus neither of them will give the correct results. Starting with G03 Rev. D the program correctly forces the use of CIS=Direct when combined with solvation. There is no option for doing CIS(D) with solvent and I don't expect this to change. Sorry for any confusion.

NLO in Gaussian 98/03

Sometime ago Damian Gregory published very nice article about NonLinear Optical (NLO) properties in Gaussian. Later he moved his website into wordress and forgot to transfer this article. Right now "Gaussian98/03 Nonlinear Optical (NLO) Response" is back. BTW. Damian's blog is very nice place for all interesting in so called NanoThechnology. His Nanotechnology Gallery is beautiful.

Molekel

I've just check the website of Molekel one of the most interesting program to visualization Quantum Chemistry date. An there are good news. Yes, they are working on the new version. And Yes, it is GPL program now!

Dipole moment in excited state [Gaussian]

To get values of dipole moment obtain with CIS method using Gaussian program you can use this bash command:

egrep "Tot*=|Population" *.log

From all of line you need only the line after Population analysis using the CI density. You can automate it. For example to get the total value of dipole moment use this script (you can write it in one line):

grep "Tot*=" *.log|
 gawk '  BEGIN { currline = 1 }
  {if (currline%3==0){print $9}
  currline = currline + 1}'

CESTC 2006

It's quite hard to find any info about Central European Symposium on Theoretical Chemistry 2006. So I'm adding link to the website: http://tiger.chem.uw.edu.pl/cestc/.

exit code 139 [Dalton & Bash]

After building dalton program, you should test it. If something is going wrong you'll get Exit Codes. Quite often it is code 139, what means Invalid memory reference (signal SIGSEGV 11 = 139- 128 ).

Orbiton - gallery of orbitals

I've just found Orbitron . It is a gallery of atomic orbitals and molecular orbitals on the WWW. The pictures are really nice, but animation of creating of molecular orbitals are great.