Publishing can be kind of annoying. In particular if journals outsource
the last quanta of work required to convert a manuscript
prepared with latex into a journal article in PDF format to the authors.
JPC
recently decided to require the authors to provide references in manuscript with
article titles in title case as well as some other changes. To save at least some authors from the pain
of doing this by hand or searching the internet for the tools, here
they are:
1) Install the achemso package and use:
\bibliographystyle{achemso}
\AtBeginDocument{\nocite{achemso-control}}
2) Add these (hopefully self-explanatory) lines in the referenced .bib file:
@Control{achemso-control,
ctrl-Article-Title = "yes",
ctrl-etal-number = "10",
ctrl-max-authors = "10",
}
3) Use the perl script provided and described here:
http://www.stat.berkeley.edu/~paciorek/computingTips/Change_case_your_journal_ti.html
to change all the articles titles in the .bib file to title case.
4) Write an angry mail to ACS and complain.
So long!
Freitag, 9. Januar 2015
Donnerstag, 8. Januar 2015
Happy New Years!
Apparently, the past few months it was pretty quiet here. The reason was that I was completely occupied writing up a paper on the central project of my Ph.D. project followed by my thesis. Furthermore, there were the formalities of handing it in and organizing the defence, which I definitely underestimated.
After all, I got everything aligned and there will probably more activity in the next time. To begin with, I present to you my take on Theoretical Chemistry, which constitutes the foreword of my thesis.
In the next posts, as soon as I figure out a comfortable way of translating Tex code into HTML, I will publish my take on the Hartree-Fock self-consistent field method, Configuration-Interaction for ground and excited states, Perturbation Theory applied to HF as well as to CI, yielding the Intermediate-State Representation for the description of correlated excited-states.
After all, I got everything aligned and there will probably more activity in the next time. To begin with, I present to you my take on Theoretical Chemistry, which constitutes the foreword of my thesis.
In the next posts, as soon as I figure out a comfortable way of translating Tex code into HTML, I will publish my take on the Hartree-Fock self-consistent field method, Configuration-Interaction for ground and excited states, Perturbation Theory applied to HF as well as to CI, yielding the Intermediate-State Representation for the description of correlated excited-states.
So long.
On Theoretical Chemistry
Chemistry is defined as the science of the interaction and interconversion of complex atomic systems called molecules, including metals and salts. Since molecules are the subunits of any common matter, chemistry is ubiquitous and has a long history as scientific discipline. In the early 20th century, it was discovered that atoms themselves are not indivisible as their Greek-descending name (a-tomos, in-divisible) suggests, but are composed of protons, neutrons and electrons. Nowadays, only the latter are still seen as indivisible, or in other words fundamental with respect to the standard model of particle physics. Protons and neutrons, in contrast consist of even smaller subunits: so-called up and down quarks.
These quarks, which are again fundamental particles, carry fractions of the elementary charge of either plus two thirds (up quarks) or minus one third (down quarks). Protons consist of two up quarks and one down quark and thus carry one positive elementary charge, while for neutrons the charges of one up quark and two down quarks cancel out. The very number of quarks that constitute each proton and neutron does, in combination with their fractional charge, lead to an important coincidence: any atomic nucleus consisting of an arbitrary number of protons and neutrons will carry an exact multiple of the elementary charge and can in turn be neutralized by adding the respective number of electrons. Formally, this process yields the neutral atoms that constitute the periodic table of the elements.
Due to the huge binding energy of quarks, which is the result of the so-called strong interaction between them, they can only be observed in groups. Similarly, with the exception of hydrogen, neutrons and protons are fused together in the atomic core, where they are held in place by the very same short-ranged forces of the strong interaction. Despite the 10^5 times smaller size compared to the atom including the electrons, the nucleus contains virtually the complete mass of an atom. The biggest part of this mass is due to the huge binding energy according to Einstein's equation m = Ec^(-2), whereas the resting mass contributes less than 1%.
Ultimately, atoms may be rationalized as the frozen interaction energy of their elementary building blocks carrying a positive charge, which incidentally is a multiple of the elementary charge. Moreover, this charge exclusively determines which chemical element a nucleus belongs to, and gives rise to the Coulomb potential that attracts the much lighter, negatively charged electrons. It is the delicate interplay of many electrons in the field of complex nuclear arrangements which guides the nuclear motion and in turn the whole of chemistry with its vast number of stable molecules and reactions. Following this line of thought, chemistry could formally be categorized as the sub-field of particle physics concerned with the quantum mechanics of the electromagnetic interaction in complex systems composed of electrons and nuclei.
However, such a categorization would neither reflect the vast number of thinkable and/or stable molecules emerging from the interplay of electrons in the field of the nuclei, nor the great relevance this discipline had long before the connections to the underlying physical equations were discovered. The sheer infinite possibilities to combine atoms to molecules, investigate their properties in creative ways and find empirical solutions to chemical problems (e.g. acid-base models, Lewis-structures gave rise to an independent scientific discipline. Nevertheless, the utilization of the laws of quantum-mechanics to establish a first-principles approach for chemical problems is and has been very promising ever since these connections were first discovered at the beginning of the 20th century, as evident from the following quote:
"The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble. It therefore becomes desirable that approximate practical methods of applying quantum mechanics should be developed, which can lead to an explanation of the main features of complex atomic systems without too much computation."
These quarks, which are again fundamental particles, carry fractions of the elementary charge of either plus two thirds (up quarks) or minus one third (down quarks). Protons consist of two up quarks and one down quark and thus carry one positive elementary charge, while for neutrons the charges of one up quark and two down quarks cancel out. The very number of quarks that constitute each proton and neutron does, in combination with their fractional charge, lead to an important coincidence: any atomic nucleus consisting of an arbitrary number of protons and neutrons will carry an exact multiple of the elementary charge and can in turn be neutralized by adding the respective number of electrons. Formally, this process yields the neutral atoms that constitute the periodic table of the elements.
Due to the huge binding energy of quarks, which is the result of the so-called strong interaction between them, they can only be observed in groups. Similarly, with the exception of hydrogen, neutrons and protons are fused together in the atomic core, where they are held in place by the very same short-ranged forces of the strong interaction. Despite the 10^5 times smaller size compared to the atom including the electrons, the nucleus contains virtually the complete mass of an atom. The biggest part of this mass is due to the huge binding energy according to Einstein's equation m = Ec^(-2), whereas the resting mass contributes less than 1%.
Ultimately, atoms may be rationalized as the frozen interaction energy of their elementary building blocks carrying a positive charge, which incidentally is a multiple of the elementary charge. Moreover, this charge exclusively determines which chemical element a nucleus belongs to, and gives rise to the Coulomb potential that attracts the much lighter, negatively charged electrons. It is the delicate interplay of many electrons in the field of complex nuclear arrangements which guides the nuclear motion and in turn the whole of chemistry with its vast number of stable molecules and reactions. Following this line of thought, chemistry could formally be categorized as the sub-field of particle physics concerned with the quantum mechanics of the electromagnetic interaction in complex systems composed of electrons and nuclei.
However, such a categorization would neither reflect the vast number of thinkable and/or stable molecules emerging from the interplay of electrons in the field of the nuclei, nor the great relevance this discipline had long before the connections to the underlying physical equations were discovered. The sheer infinite possibilities to combine atoms to molecules, investigate their properties in creative ways and find empirical solutions to chemical problems (e.g. acid-base models, Lewis-structures gave rise to an independent scientific discipline. Nevertheless, the utilization of the laws of quantum-mechanics to establish a first-principles approach for chemical problems is and has been very promising ever since these connections were first discovered at the beginning of the 20th century, as evident from the following quote:
"The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble. It therefore becomes desirable that approximate practical methods of applying quantum mechanics should be developed, which can lead to an explanation of the main features of complex atomic systems without too much computation."
Paul A. M. Dirac, 1929
In the past decades ever faster computers in combination with powerful algorithms and wisely chosen approximations made it possible to solve these insoluble equations on a regular basis. Eventually, the empirical top-down models developed by chemists over hundreds of years could for the first time be challenged by a first-principles bottom-up approach providing a new quality of insights into the elementary steps of chemical reactions such electron transfer as well as into the electronic structure of matter. This first-principles approach is what characterizes the field of theoretical chemistry, which emerged from a fruitful collaboration of chemists, physicists, mathematicians and computer scientists over the past hundred years.
Samstag, 17. Mai 2014
looking at molecules 1
this is the first part of an upcoming multi-post guide, in which I want to describe how to address photochemical questions about a certain molecule or class of molecules. Therefore, I think it is a good approach to first line out the process of the quantum chemical investigation in a step-like structure and then go into details of each step in future posts. So lets start from the beginning:
For starters, I want to get an overview about the molecules inner (electronic) structure and reactivity. But before I turn on the electric heating of the server room I thoroughly consult existing literature and any available scientists about reactivity and photochemical behaviour of the molecule(s). This helps to avoid getting lost in the vast amount of information that the quantum-chemical machinery can provide you with.
Secondly, on the basis of the literature and my experience I hypothesize about the electronic structure of the molecule and only afterwards start my calculations. At this point, you inevitably face the choice of the methodology. Depending on the size of the system, I usually start off with some solid double-zeta (SVP) ab-initio treatment (if doable CCSD, otherwise SCS/MOS-MP2) and double-hybrid functional (B2-PLYP). At this point, the calculations are limited to ground state geometry of the molecule and I try to get familiar with the MOs. To assure reliability, it is always a good idea to compare the outcome various methods and learn from the differences in the predictions. This way you can e.g. identify highly correlated states whose energy changes a lot when going from second- to third-order methods or charge-transfer states when using TDDFT.
The third part of my guide will be concerned with the identification of the relevant coordinates of the system under investigation. Since most photochemical processes involve multi-state degeneracies (e.g. conical intersections and/or intersystem crossing), a key step in any quantum-chemical investigations is to learn along which geometrical parameters the involves states exhibit a different run and intersect. This can be intra-molecular coordinates such as bond length and angles or an inter-molecular distance coordinate along which a charge-transfer state of a molecular complex intersects with locally excited state.
The fourth and last section is about getting the numbers right. While in the first three parts we were satisfied with an approximate treatment of our system, we now want to get as quantitative as possible. Therefore, you should have some experimental numbers at hand to compare-to and a thorough insight into the electronic structure in the system as well as the experiments.
Now that I laid out the tasks, the next posts will be dealing with the first of those steps.
Cheers,
Jan
For starters, I want to get an overview about the molecules inner (electronic) structure and reactivity. But before I turn on the electric heating of the server room I thoroughly consult existing literature and any available scientists about reactivity and photochemical behaviour of the molecule(s). This helps to avoid getting lost in the vast amount of information that the quantum-chemical machinery can provide you with.
Secondly, on the basis of the literature and my experience I hypothesize about the electronic structure of the molecule and only afterwards start my calculations. At this point, you inevitably face the choice of the methodology. Depending on the size of the system, I usually start off with some solid double-zeta (SVP) ab-initio treatment (if doable CCSD, otherwise SCS/MOS-MP2) and double-hybrid functional (B2-PLYP). At this point, the calculations are limited to ground state geometry of the molecule and I try to get familiar with the MOs. To assure reliability, it is always a good idea to compare the outcome various methods and learn from the differences in the predictions. This way you can e.g. identify highly correlated states whose energy changes a lot when going from second- to third-order methods or charge-transfer states when using TDDFT.
The third part of my guide will be concerned with the identification of the relevant coordinates of the system under investigation. Since most photochemical processes involve multi-state degeneracies (e.g. conical intersections and/or intersystem crossing), a key step in any quantum-chemical investigations is to learn along which geometrical parameters the involves states exhibit a different run and intersect. This can be intra-molecular coordinates such as bond length and angles or an inter-molecular distance coordinate along which a charge-transfer state of a molecular complex intersects with locally excited state.
The fourth and last section is about getting the numbers right. While in the first three parts we were satisfied with an approximate treatment of our system, we now want to get as quantitative as possible. Therefore, you should have some experimental numbers at hand to compare-to and a thorough insight into the electronic structure in the system as well as the experiments.
Now that I laid out the tasks, the next posts will be dealing with the first of those steps.
Cheers,
Jan
On the molecular mechanism of non-radiative decay in nitrobenzene and the unforseen molecular challenges this small molecule holds for electronic structure theory
This lengthy title is from our recently published paper that had been mentioned earlier in this blog. Amongst with some other things, this paper or rather the work that went into it also was the reason for the long pause since the last post. Now that it finally completed the process of publication, I will continue with a tutorial on how I look at molecules with the tools of a theoretical chemist.
There will be multiple posts on this topic in the upcoming weeks, but first, here is the link:
http://pubs.rsc.org/en/content/articlelanding/2014/cp/c4cp01232a
So long!
There will be multiple posts on this topic in the upcoming weeks, but first, here is the link:
http://pubs.rsc.org/en/content/articlelanding/2014/cp/c4cp01232a
So long!
Mittwoch, 22. Januar 2014
Shiny Pictures
Today, Felix introduced me to his new density analysis code and how he translates the resulting .cube-files into shiny 3D-pictures.
His density analysis stuff comes in really handy for the characterization and interpretation of excited-states. There will be a paper out very soon, which you should definitely read (and cite)!
   |
| Transition densities of the bright 2 A1 (top), 1 B1 (middle), and lowest 1 A2 singlet excited states of nitrobenzene at the ADC2/ cc-pVDZ level of theory |
What impressed me even more coming in even handier was the degree of automation he established for turning the .cube-files into pictures via VMD. He wrote a post about that some time ago and since then I guess I could have saved 2 or 3 days of work if I read and used it ever since. If you belong to the group of people using VMD to render MOs the manual way, you should really look into this his post or continue reading here.
After he showed me his work today, I basically stole his bash script, added options to render either two or three isosurfaces instead of just one and then spent the whole day adjusting the surface properties to make the pictures as shiny and informative as possible. If you like the results shown on the right side (using 3 isosurfaces with the standard isovalues of our script (0.0128, 0.0032, 0.0008), you might want to read on and learn how the script works:
If executed in a folder, it iterates over all .cube files present to write out 4 files:
load_all_plt.vmd
plot_all.vmd
convert.bash
vmd_plots.html.
Next, the user reads the geometry (e.g. from any xyz file) into vmd (vmd file.xyz), which needs to have the same orientation as in the job that created the cube files.
Afterwards, the vmd option "load visualization state" is used to read in the "load_all_plt.vmd" file. This script basically tells VMD to load all the .cube files and sets the options for the surfaces. At this point, the user can adapt the visualization and orientation of the molecule according to his wishes.
After selecting a reasonable orientation for the molecule in the usual way (with the mouse), the "plot_all.vmd" file is loaded, causing VMD to successively render all .cube files found in the folder yielding a bunch of .tga picture files.
Now, the convert.bash script is executed from the terminal to turn all those .tga files into .png files, which can be viewed in a very convenient way - by just opening the .html file with any browser. - DONE
Again, many thanks to Felix for this script! Thank him by (using his analysis tools and) citing is work!
And here is the script:
#!/bin/bash
# 0. $pointval mo 65-74 (Turbomole), plots (QChem), ...
# 1. call this script
# 2. open the molecular structure file in VMD
# 3. load the .plt/.cube files and some settings
# - "Load state" load_all_plt.vmd
# - click "Apply" in "Graphical Representations"
# 4. adjust perspective
# 5. "Load state" plot_all.vmd
###
ifmt=cube
ofmt=tga
out=load_all_plt.vmd
plot=plot_all.vmd
conv=convert.bash
html=vmd_plots.html
ncol=4
###
echo 'USAGE: $0 [<2 or 3 surfaces, STD = 3 >] [<highest iso, STD(2/3) = (0.1/0.128)>]'
isotemp=$2
if [ $1 -eq 2 ]
then
isov=${isotemp:=0.01}
isov2=`echo $isov'/8' | bc -l`
isov3=0.99
#!/bin/bash
# 0. $pointval mo 65-74 (Turbomole), plots (QChem), ...
# 1. call this script
# 2. open the molecular structure file in VMD
# 3. load the .plt/.cube files and some settings
# - "Load state" load_all_plt.vmd
# - click "Apply" in "Graphical Representations"
# 4. adjust perspective
# 5. "Load state" plot_all.vmd
###
ifmt=cube
ofmt=tga
out=load_all_plt.vmd
plot=plot_all.vmd
conv=convert.bash
html=vmd_plots.html
ncol=4
###
echo 'USAGE: $0 [<2 or 3 surfaces, STD = 3 >] [<highest iso, STD(2/3) = (0.1/0.128)>]'
isotemp=$2
if [ $1 -eq 2 ]
then
isov=${isotemp:=0.01}
isov2=`echo $isov'/8' | bc -l`
isov3=0.99
#isovalue of 0.99 will produce no surface
echo 'Using 2 surfaces for isovalues:'
echo $isov $isov2
echo "material change opacity Glass3 0.150000" > $out
echo "material change diffuse Glass3 0.10000" >> $out
elif [ $1 -eq 3 ]
then
isov=${isotemp:=0.0128}
isov2=`echo $isov'/4' | bc -l`
isov3=`echo $isov'/16' | bc -l`
echo 'Using 3 surfaces for isovalues:'
echo $isov $isov2 $isov3
echo "material change opacity Glass3 0.400000" > $out
else
echo "Please enter 2 or 3 for # of surfaces!"
echo "Falling back to 3 surfaces with standard values"
isov=0.0128
isov2=0.0032
isov3=0.0008
echo "Using standard isovalues: "
echo "Values: "$isov $isov2 $isov3
echo "material change opacity Glass3 0.400000" > $out
fi
echo "axes location Off" >> $out
echo "display projection Orthographic" >> $out
echo "display rendermode GLSL" >> $out
echo "display depthcue off" >> $out
echo "color Display Background white" >> $out
echo "menu graphics on" >> $out
echo "material change diffuse Ghost 0.000000" >> $out
echo "material change ambient Ghost 0.300000" >> $out
echo "material change opacity Ghost 0.100000" >> $out
echo "material change shininess Ghost 0.000000" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol modmaterial 1 0 Opaque" >> $out
echo "mol modmaterial 2 0 Opaque" >> $out
echo "mol modmaterial 3 0 Glass3" >> $out
echo "mol modmaterial 4 0 Glass3" >> $out
echo "mol modmaterial 5 0 Ghost" >> $out
echo "mol modmaterial 6 0 Ghost" >> $out
echo "mol modstyle 1 0 Isosurface $isov 0 0 0 1 1" >> $out
echo "mol modstyle 2 0 Isosurface -$isov 0 0 0 1 1" >> $out
echo "mol modstyle 3 0 Isosurface $isov2 0 0 0 1 1" >> $out
echo "mol modstyle 4 0 Isosurface -$isov2 0 0 0 1 1" >> $out
echo "mol modstyle 5 0 Isosurface $isov3 0 0 0 1 1" >> $out
echo "mol modstyle 6 0 Isosurface -$isov3 0 0 0 1 1" >> $out
echo "mol modcolor 1 0 ColorID 0" >> $out
echo "mol modcolor 2 0 ColorID 1" >> $out
echo "mol modcolor 3 0 ColorID 0" >> $out
echo "mol modcolor 4 0 ColorID 1" >> $out
echo "mol modcolor 5 0 ColorID 0" >> $out
echo "mol modcolor 6 0 ColorID 1" >> $out
echo "" > $plot
echo "#!/bin/bash" > $conv
chmod +x $conv
echo -e "<html>\n<head></head>\n<body>" > $html
echo -e "<table>\n<tr>" >> $html
N=0
for I in *$ifmt
do
echo "mol addfile $I" >> $out
echo "mol modstyle 1 0 Isosurface $isov $N 0 0 1 1" >> $plot
echo "mol modstyle 2 0 Isosurface -$isov $N 0 0 1 1" >> $plot
echo "mol modstyle 3 0 Isosurface $isov2 $N 0 0 1 1" >> $plot
echo "mol modstyle 4 0 Isosurface -$isov2 $N 0 0 1 1" >> $plot
echo "mol modstyle 5 0 Isosurface $isov3 $N 0 0 1 1" >> $plot
echo "mol modstyle 6 0 Isosurface -$isov3 $N 0 0 1 1" >> $plot
echo "render TachyonInternal $I.$ofmt" >> $plot
echo "convert $I.$ofmt $I.png" >> $conv
echo "rm $I.$ofmt" >> $conv
echo "<td><img src=\"$I.png\" border=\"1\" width=\"400\">" >> $html
echo "$I<br></td>" >> $html
N=$(($N+1))
if [ $((N%$ncol)) -eq 0 ]; then
echo "</tr><tr>" >> $html
fi
done
echo -e "</tr></table>" >> $html
echo -e "</body>\n</html>" >> $html
echo "... finished."
echo 'Using 2 surfaces for isovalues:'
echo $isov $isov2
echo "material change opacity Glass3 0.150000" > $out
echo "material change diffuse Glass3 0.10000" >> $out
elif [ $1 -eq 3 ]
then
isov=${isotemp:=0.0128}
isov2=`echo $isov'/4' | bc -l`
isov3=`echo $isov'/16' | bc -l`
echo 'Using 3 surfaces for isovalues:'
echo $isov $isov2 $isov3
echo "material change opacity Glass3 0.400000" > $out
else
echo "Please enter 2 or 3 for # of surfaces!"
echo "Falling back to 3 surfaces with standard values"
isov=0.0128
isov2=0.0032
isov3=0.0008
echo "Using standard isovalues: "
echo "Values: "$isov $isov2 $isov3
echo "material change opacity Glass3 0.400000" > $out
fi
echo "axes location Off" >> $out
echo "display projection Orthographic" >> $out
echo "display rendermode GLSL" >> $out
echo "display depthcue off" >> $out
echo "color Display Background white" >> $out
echo "menu graphics on" >> $out
echo "material change diffuse Ghost 0.000000" >> $out
echo "material change ambient Ghost 0.300000" >> $out
echo "material change opacity Ghost 0.100000" >> $out
echo "material change shininess Ghost 0.000000" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol modmaterial 1 0 Opaque" >> $out
echo "mol modmaterial 2 0 Opaque" >> $out
echo "mol modmaterial 3 0 Glass3" >> $out
echo "mol modmaterial 4 0 Glass3" >> $out
echo "mol modmaterial 5 0 Ghost" >> $out
echo "mol modmaterial 6 0 Ghost" >> $out
echo "mol modstyle 1 0 Isosurface $isov 0 0 0 1 1" >> $out
echo "mol modstyle 2 0 Isosurface -$isov 0 0 0 1 1" >> $out
echo "mol modstyle 3 0 Isosurface $isov2 0 0 0 1 1" >> $out
echo "mol modstyle 4 0 Isosurface -$isov2 0 0 0 1 1" >> $out
echo "mol modstyle 5 0 Isosurface $isov3 0 0 0 1 1" >> $out
echo "mol modstyle 6 0 Isosurface -$isov3 0 0 0 1 1" >> $out
echo "mol modcolor 1 0 ColorID 0" >> $out
echo "mol modcolor 2 0 ColorID 1" >> $out
echo "mol modcolor 3 0 ColorID 0" >> $out
echo "mol modcolor 4 0 ColorID 1" >> $out
echo "mol modcolor 5 0 ColorID 0" >> $out
echo "mol modcolor 6 0 ColorID 1" >> $out
echo "" > $plot
echo "#!/bin/bash" > $conv
chmod +x $conv
echo -e "<html>\n<head></head>\n<body>" > $html
echo -e "<table>\n<tr>" >> $html
N=0
for I in *$ifmt
do
echo "mol addfile $I" >> $out
echo "mol modstyle 1 0 Isosurface $isov $N 0 0 1 1" >> $plot
echo "mol modstyle 2 0 Isosurface -$isov $N 0 0 1 1" >> $plot
echo "mol modstyle 3 0 Isosurface $isov2 $N 0 0 1 1" >> $plot
echo "mol modstyle 4 0 Isosurface -$isov2 $N 0 0 1 1" >> $plot
echo "mol modstyle 5 0 Isosurface $isov3 $N 0 0 1 1" >> $plot
echo "mol modstyle 6 0 Isosurface -$isov3 $N 0 0 1 1" >> $plot
echo "render TachyonInternal $I.$ofmt" >> $plot
echo "convert $I.$ofmt $I.png" >> $conv
echo "rm $I.$ofmt" >> $conv
echo "<td><img src=\"$I.png\" border=\"1\" width=\"400\">" >> $html
echo "$I<br></td>" >> $html
N=$(($N+1))
if [ $((N%$ncol)) -eq 0 ]; then
echo "</tr><tr>" >> $html
fi
done
echo -e "</tr></table>" >> $html
echo -e "</body>\n</html>" >> $html
echo "... finished."
Montag, 20. Januar 2014
finishing the story of dratted nitrobenzene
A few days ago I finally finished writing the manuscript for the paper on nitrobenzene photochemistry. I will post a link here as soon as it is published and I dont want to spoil to much. However, a few of the most remarkable outcomes I want to share:
- If you are planning on doing quantum chemical calculations on molecules including a nitro-group, don't use CC2 for obtaining ground state geometries, it will give you very poor results. I think in general, one should not use CC2 for the ground-state just because it is a coupled cluster approach. Obviously, MP2 is cheaper and seemingly also better/more stable. Even some of the developers of CC2 think so! In my experience, B2PLYP is even better, in particular in complicated electronic situations at pretty much the same or less cost than MP2 (The KS-SCF usually converges much faster and more stable than HF-SCF, which is true in particular for triplet states). For all singly excited-states of nitrobenzene, the excitation energies of TDA-B2PLYP are throughout very close to those obtained with ADC3. Eventually, I am really impressed by the performance of this double-hybrid functional, which it delivers at essentially no cost compared to the expensive ADC3.
- After doing A LOT of calculations with every theoretical methods I could get my hands on, I think I finally understood what the problem of nitrobenzene is: According to MOM-CCSD(T)/cc-pVTZ, the second lowest excited singlet state of nitrobenzene (1 B1, npi>pi*) has large double excitation character of 50 % according to the ADC3 state composition. Since this state is closely related to the lowest triplet state for which the problems persist, its still unclear which is the lowest triplet state of nitrobenzene. All I can say after doing all these calculations (ADC3, MOM-CCSD(T), EOM-CCSD, DFT-MRCI, CAS-NEVPT2(14/11), TDA-B2PLYP) is that the lowest two triplet states (one n>pi* and one npi>pi*) are very close together regarding their vertical excitation energies (n>pi ~ 0.2 eV above npi>pi) and if geometrical relaxation is considered, they become virtually degenerate (dE < 0.05 eV).
- I found an experimental spectrum of nitrobenzene vapor published in 1964 [S. Nagakura, M. Kojima, Y. Maruyama, J. Mol. Spec. 13 p. 174], which shows a peak exactly at the excitation energy of 4.4 eV predicted by MOM-CCSD(T) for the doubly excited npi>pi* singlet state. On the basis of a comparison to benzene, Nagakura et Al assigned this peak to an other state. According to my calculations (ADC3 and EOM-CCSD), however, this other state (2 B1) neither has any oscillator strength (~ 0.0002) nor does the energy fit (4.7 eV instead of 4.4 eV). Furthermore is the vibrational splitting of this peak in bare benzene 930 /cm just in the same ballpark compared to the 860 /cm they found for this peak in the spectrum of nitrobenzene. So I calculated the vibrational splitting for the doubly excited 1 B1 state and voi-la: 864 /cm (B2PLYP), which fits much better. After all, I'm pretty sure the first visible peak in the spectrum of nitrobenzene vapor is due to a doubly excited state, which is really unexpected, I guess.
Donnerstag, 5. Dezember 2013
continuing the story of dratted nitrobenzene
ω(r[NO])
I finished investigating the influence of the NO bond length (symmetric stretch) onto excitation energies at ADC(3)/SVP level of theory! The result is as expected: due to the population of the π* orbital at the nitro group (see first post concerning nitrobenzene) in all lower excited-states, the influence of this bond length is quite large in the following way: along the symmetric NO stretching mode, the energy of the ground state largely increases, while the absolute energies of the excited states decrease (see Figure 1).
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| Figure 1) Run of the absolute ground- and excited state energies along symmetric NO-stretching coordinate starting from the CCSD/def2-TZVP optimized structure. The scan was a rigid one, i.e. without reoptimizing the structural paramaters for each r(NO) but keeping them at the value of the original geometry. |
For the vertical excitation energies (ω) these effects add up and the ω of all states drop
rapidly by about 0.1 eV/pm (Figure 2), which explains for the large difference
between CC2 geometry with 125 pm NO-bonds and the CCSD geometry with 120
pm NO-bonds.
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| Figure 2) Run of the vertical excitation energies along the symmetric NO-stretching coordinate. The gradient is about 0.1 eV/pm. The equilibrium value for the NO distance is 120 pm at the CCSD/def2-TZVP level of theory (compare Figure 1). One can clearly distinguish between the local excited state of the nitro group and the valence excited states, since the latter have a slightly smaller gradient. |
Now I know why and how strong excitation energies depend on the NO bond length, but one very important question remains: Why is the ADC(3) result for the excitation energy of the lowest excited singlet state (almost 4.1 eV) so far off from the experiment (3.65 eV)? From a third order method like ADC(3) one would expect 0.1-0.3 eV deviation at max, in particular for singly excited states. Maybe the reason is lying in the dynamics of the molecule, cause in the experiment, this bond vibrates like any other bond. I will have a look into this using born-oppenheimer ab-initio molecular dynamic in the next post.
so long!
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