tag:blogger.com,1999:blog-35997221776798601312024-03-20T05:22:04.198+01:00Chemical Quantum Images- Molecular Graphics and Theoretical Chemistry -
<br><br><i>If you have a question or if you like it, feel free to leave a message ...</i>Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.comBlogger252125tag:blogger.com,1999:blog-3599722177679860131.post-13242066372501648262023-11-16T12:46:00.000+01:002023-11-16T12:46:01.236+01:00Post-Doc Position on the Dynamics of High-Energy Materials at Loughborough University, UK<p>Applications are invited for a postdoctoral research associate
position in computational chemistry at Loughborough University. This is a
DSTL funded position to work with Dr Kenny Jolley and Dr Felix Plasser
(Chemistry, Loughborough University) on predicting the crystal
structure, dynamics and physical properties of energetic materials.</p>
<p>The successful applicant will conduct molecular dynamics (MD) and
accelerated MD simulations on energetic compounds. Bulk physical
properties, stability to shock and heat, and reaction pathways will be
modelled and compared to experimental data. In a later stage, we will
perform time-resolved simulations of explosion processes.</p>
<p>This position is ideally suited for an ambitious early career
researcher with a background in computational chemistry and materials
modelling. The successful candidate will be highly motivated with a
strong research track record and a desire to pursue multidisciplinary
research.</p>
<p>Feel free to contact me or <a href="https://www.lboro.ac.uk/departments/chemistry/staff/kenny-jolley" rel="noreferrer noopener" target="_blank">Dr Kenny Jolley</a> for informal equiries.</p>
<p>Closing date for applications is 24/11/2023, please follow this <a href="https://vacancies.lboro.ac.uk/jobdesc/REQ231362.PDF" rel="noreferrer noopener" target="_blank">link for further info</a>.</p>Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0Loughborough LE12, Vereinigtes Königreich52.772099 -1.20616624.461865163821152 -36.362416 81.082332836178836 33.950084tag:blogger.com,1999:blog-3599722177679860131.post-11713337518735713492022-04-27T15:14:00.003+01:002022-04-27T16:10:51.393+01:00Invasions<p style="font-family: Calibri; font-size: 11pt; margin: 0in;">George Bush's
invasion in Iraq is, by many measures, already quite a low starting point. But
something that was never on the table was the idea the that the USA was going
to annex part of Iraq's territory. No, annexing other people's territory is no
longer part of the game plan (as for example <a href="https://www.samharris.org/podcasts/making-sense-episodes/276-defending-the-global-order" target="_blank">Y. N. Harari argues</a>). It's
something that hasn't happened since WWII. So, then, what is Putin's goal? Is it about ousting a supposedly Nazi
(albeit Jewish) regime or is it about annexing Ukraine's territory? Well, it is
a question that we don't even have to ask. Russia has already annexed part of
Ukraine's territory.</p>
<p style="font-family: Calibri; font-size: 11pt; margin: 0in;"> </p>
<p style="font-family: Calibri; font-size: 11pt; margin: 0in;">Every country has its grievances. For example, Austria lost Trentino (= Southern Tyrol) after
WWII. German's are probably unhappy about giving Alsace and Lorraine to France.
The Ireland conflict is obviously still big. And here we are not even talking about
all the African countries with their neatly straight lines drawn in French and
British boardrooms, not reflecting any natural borders at all. Ever since
recorded history, these kinds of conflicts were resolved by war. But,
amazingly, no such territorial war has happened since WWII. So, what is at
stake with Russia's invasion and attempted annexation of Ukraine? Our whole
world structure assured by territorial integrity, putting peace and prosperity before pride and vanity.<br /></p>
<p style="font-family: Calibri; font-size: 11pt; margin: 0in;"> </p>
<p style="font-family: Calibri; font-size: 11pt; margin: 0in;">In summary, even if
all the pictures of bombed apartment buildings are fakes (which there is no
reason to believe), even if Zelensky is an oppressive Nazi (which is even more
absurd), even if one is unaware of the growing number of refugees, even then there is no way to compare Russia's invasion in Ukraine with
the US invasion in Iraq (which is already quite a low starting point). Much
more is at stake here.</p>
Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-35939355468563980302022-04-02T13:33:00.002+01:002022-04-02T13:33:41.260+01:00Covidiots and Covidians<p> The world is divided between <a href="https://zdoggmd.com/covidiots/" target="_blank">Covidiots and Covidians</a>. Covidiots, who think it is all overblown (or never a thing in the first place), that all major governments and global organisations got it wrong (and only they got it right), and who could not be swayed by any amount of evidence. Covidians, who would not leave the house without at least two face masks on and want everyone jabbed at least weekly. Obviously, there is a third route, the person who processes all the evidence without preconceived judgements and adjusts their actions according to the most recent data. Can we all say that we are truly in the third camp?</p><p>To a large part the divide aligns with the political spectrum (using some general ideas from <a href="https://scholar.harvard.edu/sandel/justice" target="_blank">Michal J. Sandel</a>). Libertarians on the one hand would say: "I would not force you to wear a face mask even if not doing so were to put me in danger (and hence I am not wearing one myself)." Community focussed people would say: "I would wear a face mask for you even on the off-chance that it provides any benefit at all (and hence I expect you to do so, too)." Both of those are clearly noble sentiments (if phrased like this). But, critically, neither of them actually needs to look at the data to make this judgement. And I think this is the real problem: We have already made up our minds about what is the right course of action. And then we retrofit the data to match our convictions placing us straight into the Covidiot/Covidian camps.<br /></p>Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-39595310451361863692022-03-21T15:10:00.004+01:002022-03-21T15:12:49.510+01:00Academic positions at Loughborough<p>Loughborough University is planning to fill up to three academic positions in the Chemistry Department.</p><p>Short summary:</p><ul style="text-align: left;"><li>High-quality research</li><li>Ability to teach Physical Chemistry or Biochemistry</li><li>Closing date: 3rd April 2022</li></ul><p>Full information here</p><p><a href="https://www.lboro.ac.uk/join-us/outstanding/science/">https://www.lboro.ac.uk/join-us/outstanding/science/</a></p><p>This is a great chance for anyone aiming to take their career to the next level. Hiring is at any level. Anyone between ~3 years postdoc experience and full professor can apply.<br /></p>Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-2412540387797877242022-03-15T17:03:00.002+01:002022-03-15T17:03:51.221+01:00Peace<p>This is just a small blog, not generally devoted to politics. But maybe in a world, where big outlets can be silenced, we need the small voices.</p><p>The conflict in Ukraine has to stop. I don't know who is behind this war. Is it just the mania of one man? Is it a well-organised tightly knit group of power-hungry individuals? Is there popular support?</p><p>If anyone reads this who is in favour of these attacks, I would ask you to think about the few facts that no one can deny. Russia's leader has been in power for more than two decades, obtaining an ever tighter grip. As a former KGB officer, Putin does not only provide continuity to the Soviet Union, he represents its most feared part. Ukraine was invaded; and even if the pictures from all the bombed apartment blocks do not make it to Russia, there is no denying that a sovereign country was attacked without provocation. </p>Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-41790826921335971792021-01-25T12:52:00.003+01:002021-01-25T12:57:21.824+01:00Chemical shielding tensors<div class="separator" style="clear: both; text-align: center;"></div><p>How do you visualise a tensor field? A 3x3 tensor as a function of the 3 spatial coordinates makes a 12-dimensonal object. How do we visualise a 12-dimensional object using a 2-dimensional screen? This is the problem we encountered trying to visualise the chemical shielding tensor, which is a common aromaticity criterion. The solution: we compute the principal axes of the tensor and represent those using little dumb-bells at different points in space providing us at least a coarse-grained description.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQ5NQa35pJlFoaE_12AbCf_wzCHpjUehkJQJ41EvbI_8uYRZLD888frUJrPgNRJSZ_ujTiEsWuLQTmF37TJqhwfzGQBkuHmVLPu_YFqnqCI3tMtoqLdmZExXISONjGAOhwzCJfyuevFeg/s1261/VIST_TOC.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="627" data-original-width="1261" height="199" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQ5NQa35pJlFoaE_12AbCf_wzCHpjUehkJQJ41EvbI_8uYRZLD888frUJrPgNRJSZ_ujTiEsWuLQTmF37TJqhwfzGQBkuHmVLPu_YFqnqCI3tMtoqLdmZExXISONjGAOhwzCJfyuevFeg/w400-h199/VIST_TOC.png" width="400" /> </a></div><p> To get the full story, check out our preprint “<a href="https://dx.doi.org/10.26434/chemrxiv.13580885" rel="noreferrer noopener" target="_blank">3D Visualisation of chemical shielding tensors to elucidate aromaticity and antiaromaticity</a>” available on ChemRxiv or this <a href="https://fplasser.sci-public.lboro.ac.uk/2021/01/20/3d-visualisation-of-chemical-shielding-tensors/" target="_blank">blog post</a>.</p><p>Here, I just wanted to show a few more computer graphics. This, for example, are the in-plane shielding tensors shown with our new VIST method in connection with the <a href="https://dx.doi.org/10.1021/acs.jpca.6b03950" target="_blank">ACID isosurface</a> as computed via <a href="https://github.com/qmcurrents/gimic" target="_blank">GIMIC</a>. <br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi0lIKf0hIRdg3pZfwxdqkZOeUPjf-UvlKax_P1Mtyx2UrJQ3iyVer0ecgt0JXzatr13GqMGJHw5yH6xWJgbpzeGsy-JHlawS6KS_Kq7GtSsPEmKTdysvHAty2a37LNZObayzTzIrx5_x4/s1238/NICS0_ACID003c80.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="721" data-original-width="1238" height="233" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi0lIKf0hIRdg3pZfwxdqkZOeUPjf-UvlKax_P1Mtyx2UrJQ3iyVer0ecgt0JXzatr13GqMGJHw5yH6xWJgbpzeGsy-JHlawS6KS_Kq7GtSsPEmKTdysvHAty2a37LNZObayzTzIrx5_x4/w400-h233/NICS0_ACID003c80.png" width="400" /></a></div>For comparison, the NICS(1) tensors along with the magnetically induced current densities also computed using <a href="https://github.com/qmcurrents/gimic" target="_blank">GIMIC</a>. Diatropic currents, giving rise to positive shielding are shown in blue; paratropic currents in red. Diatropic currents dominate, hence we see positive (blue) shielding.<br /><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQIC1dXxP8SP3wDycDMgwaq2SBKMwxL-dn6oo3bHfw_Srx5AHra9-BHqdS70tmAsT4llB_M3sHLqt1rpeuLEDfxesvAyqpXwlNHq9sQOU-uRwwIwjiuzD_WIRhVBEJhzwUiohJjDWWCUc/s1226/NICS1_curr09.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="728" data-original-width="1226" height="238" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQIC1dXxP8SP3wDycDMgwaq2SBKMwxL-dn6oo3bHfw_Srx5AHra9-BHqdS70tmAsT4llB_M3sHLqt1rpeuLEDfxesvAyqpXwlNHq9sQOU-uRwwIwjiuzD_WIRhVBEJhzwUiohJjDWWCUc/w400-h238/NICS1_curr09.png" width="400" /></a></div><p>The code will be released through <a href="https://theodore-qc.sourceforge.io/" target="_blank">TheoDORE</a> once I have the time to make it reasonbly well documented and user friendly.<br /></p><div class="separator" style="clear: both; text-align: center;"></div><p></p>Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-39274174993354243982020-06-26T14:33:00.000+01:002020-06-26T14:33:51.062+01:00Virtual Open Day with JmolI prepared some interactive Jmol molecular models for our Department's Virtual Open Day <a href="https://www.lboro.ac.uk/departments/chemistry/undergraduate/welcome/researchshowcase/">research showcase</a>. There are some bits with <a href="https://www.lboro.ac.uk/departments/chemistry/news-events/computational-chemistry-meeting-19/interactivemolecularmodels/bdt/">molecular orbitals</a> and <a href="https://www.lboro.ac.uk/departments/chemistry/news-events/computational-chemistry-meeting-19/interactivemolecularmodels/solarenergy/">molecular vibrations</a>, which look quite nice I think. I am not quite sure if any of our prospective undergrads went there or if they liked it. Anyway, my 5-year old son likes it - but he already had a pre-existing appreciation of molecules ;)Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-58730224573189125342020-06-07T19:50:00.000+01:002020-06-07T19:50:55.556+01:00Full economic costAccording to the official numbers from our Research Office the full economic cost of one hour of my time comes out at about 75 pounds. 75 pounds for every hour of research, 75 pounds for every hour of teaching, 75 pounds for every hour of debugging code, 75 pounds for every seminar visit, 75 pounds for every hour of target tracking, 75 pounds for every hour of shuffling around Excel sheets, and 75 pounds for every hour of filling out forms to claim back 75 pounds. I am not saying that this is what I am paid but it is the full cost of having me sit in my office including the heating, cleaning the halls, mowing the lawn outside, and keeping up the flower bed at the main entrance.<br />
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Obviously, this averaged and linear view does not tell the whole story, neither of the costs nor of productivity, but it is still a bit disturbing to think about all this cost involved. I am not quite sure what the moral of the story is but I guess it is that we should be a bit more careful regarding our colleagues' time and that institutions might be a bit more generous in terms of allocating funds.<br />
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I am in charge of organising the seminars here. Would all 26 full-time equivalents of academics show up to our seminar, this would be a bill of 2k pounds. Adding in all the PhD students and postdocs would move us well above 5k, almost three times the yearly seminar budget! As much as I believe in the importance of seminars, this is why I am not too pushy in making people come.<br />
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Another interesting factoid: If I had to pay myself with my own startup budget, then I could finance about 26 hours of my work time. I would be out of money on Thursday at 11am of the first week of the financial year!Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-2676545282580747872020-05-02T20:21:00.000+01:002020-05-02T20:21:33.140+01:00De-excitationsIf the electronic ground state of a molecule has double-excitation character and the excited state only single-excitation character, then you can view the molecule as being "de-excited." Electrons are taken from a higher lying orbital and moved into a lower lying orbital. A <a href="http://dx.doi.org/10.1039/D0CP00369G">recent paper</a> tries to formalise this idea by computing an expectation value of the particle-hole permutation operator. We take the two-body exciton wavefunction, switch the electron and hole and see how much it resembles the original wavefunction. If the hole resides purely in the occupied orbitals and the electron purely in the virtual orbitals, this has to yield zero. But with a correlated ground state it does not vanish.<br />
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The striking thing is that this expectation value of the particle-hole permutation operator seems to agree between TDDFT and wavefunction based methods in, both, magnitude and sign. This means that de-excitations are a "real thing" rather than just an artifact of TDDFT - not physically observable but a well-defined property of the wavefunction. For more on this, see <a href="http://dx.doi.org/10.1039/D0CP00369G">PCCP <b>2020</b>, <i>22</i>, 6058</a>.Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-1761703256030604122020-03-05T21:26:00.000+01:002020-03-05T21:26:44.772+01:00From eV to kJ/molWhat is the conversion factor from eV to kJ/mol? To go from eV to J, you have to multiply with the unit charge (formally speaking you insert the <i>e</i> into eV). To go to J/mol you multiply with Avogadro's number. What is the product of the unit charge and Avogadro's number - the <a href="https://en.wikipedia.org/wiki/Faraday_constant">Faraday constant</a>. And if you were treated to Chemistry Olympiad at school then, hopefully, you are still able to blurt out its value even when woken up in the middle of the night: 96 485 C/mol. If we divide this by 1000, we get the desired result 1 eV is 96.485 kJ/mol. Or more broadly speaking, you just have to multiply with a factor of 100 if you want to go from eV to kJ/mol. I have never realised that connection before.Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-19962430475880665602020-01-26T21:16:00.000+01:002020-01-27T10:24:56.605+01:00Negative singlet-triplet gapsA question that I was wondering about for a while: Are there molecules where the first excited singlet state lies below the first triplet? Apparently there are, as this <a href="https://dx.doi.org/10.1021/acs.jpclett.9b02333">recent paper in JPCL</a> shows.<br />
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In the single-electron picture this is not possible. Singlet and triplet excited states can access the same configuration space and the only difference between singlet and triplet energies is a repulsive exchange term (see my recent <a href="https://chemical-quantum-images.blogspot.com/2020/01/understanding-excitation-energies.html">post</a> and <a href="https://doi.org/10.26434/chemrxiv.11559819">preprint</a>). This exchange term is always positive and, thus, always pushes up the singlet above the triplet with the same orbital transition. But the situation changes when double excitations come into play. The reason is that only singlets can form the type of double excitations where two electrons are placed in the same orbital and, hence, singlets and triplets have a different accessible configuration space. If a doubly excited state is close enough in energy, it can push the S<sub>1</sub> down enough to be lower than T<sub>1</sub>. This is apparently the case for the cyclazine molecule at its ground-state equilibrium geometry (see <a href="https://dx.doi.org/10.1021/acs.jpclett.9b02333">DOI: 10.1021/acs.jpclett.9b02333</a>).Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-64195756864757214142020-01-22T16:04:00.000+01:002020-01-26T21:22:19.657+01:00Understanding excitation energies beyond the MO pictureIs it possible to get an intuitive understanding of electronic excitation energies that truly goes beyond the MO picture? This is what we are discussing in our newest preprint: <a href="https://doi.org/10.26434/chemrxiv.11559819">Toward an Understanding of Electronic Excitation Energies Beyond the Molecular Orbital Picture</a>. This is basically a sequel to my previous post <a href="https://chemical-quantum-images.blogspot.com/2013/06/why-is-homo-lumo-gap-not-good-guess-of.html">HOMO-LUMO gaps and excitation energies</a>, which seems to consistently attract visitors to this blog. In fact the paper started out as a short sequel and then it turned into 19 dense pages. Well, I hope it is worth the effort.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgeIDNbE-1dE1D6ddkV_zQ0R4LN-E0L56JcM6F0-fcSje_U9Kt-NirDQjgrystSSd8bMCsHbtbhw1lOa7RfcHnqw7xVMOPyXGnuHXiGboK4EMb7X6ZF-dhfG8PGbZ97IXUZC_NTp1R1WCA/s1600/TOC.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="302" data-original-width="475" height="253" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgeIDNbE-1dE1D6ddkV_zQ0R4LN-E0L56JcM6F0-fcSje_U9Kt-NirDQjgrystSSd8bMCsHbtbhw1lOa7RfcHnqw7xVMOPyXGnuHXiGboK4EMb7X6ZF-dhfG8PGbZ97IXUZC_NTp1R1WCA/s400/TOC.png" width="400" /></a></div>
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The TOC shows a diagrammatic representation of the exchange repulsion, which is responsible for the difference in energies between singlet and triplet states. The red and blue lines refer to the hole and electron, respectively. The dotted green line is the Coulomb interaction. The diagram is read in the following way: The hole and electron come together on the bra (bottom) and ket (top) side forming the transition density. They interact with each other via the Coulomb interaction. The resulting term can be interpreted as the Coulomb repulsion of the transition density with respect to itself. To represent this, we show the transition density and its electrostatic potential (ESP). The exchange repulsion is now simply an overlap between density and ESP.<br />
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The state shown is the first ππ* state of uracil. A closer look at the transition density (upper left) shows the expected π contributions. But why are there also σ contributions? It turns out that the pure ππ* state would have an excessively high exchange repulsion. That is why σ contributions are mixed in to lower the energy. These σ contributions lower the transition moment (shown in green) and, thus, have a direct experimentally observable consequence. They also mean that any description of the state in terms of only n and π orbitals is insufficient, which explains the problems of CASSCF in describing these sorts of states - called ionic states in the valence-bond description.Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-14474663518089548352019-09-18T10:59:00.000+01:002019-09-18T11:02:41.185+01:00A view at the ESP at varying distance from the nucleusJust a few more images from my little pymol wrapper <a href="https://github.com/felixplasser/qc_pymol">qc_pymol</a>. These images show the electrostatic potential (ESP) of the ground state of uracil mapped onto the density using different isovalues. We start out close to the nuclei where the ESP is highly positive (purple). When we move away it becomes less positive (blue). And finally, we have a negative (orange) ESP at the oxygens and positive (blue) around the remaining molecule. <br />
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Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-82938119284069170262019-09-13T15:34:00.000+01:002019-09-13T15:34:17.136+01:00Plotting the electrostatic potential with PyMOLIt has always been my aim to automatise the plotting of densities and orbitals. You can see my previous efforts in the context of <a href="http://chemical-quantum-images.blogspot.com/2011/10/automatic-plotting-of-orbitals.html">VMD</a> and <a href="http://chemical-quantum-images.blogspot.com/2011/10/orbitals-in-jmol.html">Jmol</a> in some previous posts, and you can find the associated scripts in the <a href="http://theodore-qc.sourceforge.net/">TheoDORE</a> distribution. Let's turn to PyMOL now. The nice thing about PyMOL is that it can be scripted with python, which means that it is easy to add functionality in an integrated way. I started creating a toolbox for using PyMOL with quantum chemistry programs: qc_pymol, which you can <a href="https://github.com/felixplasser/qc_pymol">find on github</a>.<br />
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Let's say we have a cube file called <code>es_1_diff.cube</code> and we want to draw isosurface at isovalues of -0.01 and 0.01, then using <a href="https://github.com/felixplasser/qc_pymol">qc_pymol</a> we just type into the pymol console:<br />
<blockquote class="tr_bq">
show_dens es_1_diff.cube, -0.01 0.01, cyan orange</blockquote>
And we get the following picture of the density. In this case, this is the difference density of an nπ* state with respect to the ground state (cyan is where the density is taken away, orange where it is added).<br />
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We can also map the electrostatic potential (ESP) onto the density if we have both as cube files. In this case, the command is<br />
<blockquote class="tr_bq">
map_esp es_1_dens.cube, es_1_dens_esp.cube</blockquote>
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Here, you can see that we have positive (blue) potential at the oxygen where the electron is taken away, and negative (yellow) potential at the other oxygen and at the carbon atom where electron density is added above.<br />
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We can do the same thing for the next three states and get the following combinations of difference densities and ESPs. We get the same trends as before depletion (cyan) in the difference density corresponds to positive ESP (blue), and addition (orange) corresponds to negative ESP (orange).<br />
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<br />Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com2tag:blogger.com,1999:blog-3599722177679860131.post-49522806615849264872019-06-17T14:18:00.000+01:002019-06-17T14:19:11.530+01:00Visualising electron correlation (2)Just a quick follow-up on <a href="http://chemical-quantum-images.blogspot.com/2019/06/visualising-electron-correlation.html">last post</a>. Here are some more pictures of conditional electron/hole densities taken from the computations performed in the original <a href="https://doi.org/10.1002/cptc.201900014">ChemPhotoChem paper</a> but with some extra rendering. To get a better overview, you can check my <a href="https://fplasser.sci-public.lboro.ac.uk/2019/06/17/talk-excited-states-of-transition-metal-complexes/">a newest talk</a> (starting at slide 32). What we are doing here is that we are pulling the hole through the system from left to right and we are observing how the electron behaves. For the S<sub>1</sub> state, the adjustment is rather small.<br />
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<br />
<a name='more'></a>For S<sub>2</sub>, the localisation is quite a bit stronger and the electron is always localised on only one half of the molecule.<br />
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<br />Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-34748772777105215322019-06-11T17:04:00.002+01:002019-06-12T09:55:14.516+01:00Visualising electron correlationHow do you visualise the correlation between two particles? One option is to fix one of them at a specific region of space and look at the distribution of the other one. This is the principle behind a new method for visualising excitonic correlation just presented in a paper in ChemPhotoChem: <a href="https://doi.org/10.1002/cptc.201900014">Visualisation of Electronic Excited‐State Correlation in Real Space</a>, and released within the <a href="https://fplasser.sci-public.lboro.ac.uk/2019/05/08/release-of-theodore-2-0-beta/">TheoDORE 2.0 code</a>. First, we have to interpret the excited state within the electron-hole picture as <a href="http://dx.doi.org/10.1103/PhysRevA.90.052521">explained previously</a> and compute the two-body electron-hole distribution. Then, we can fix one of the quasi-particles in space and observe the distribution of the other one.<br />
<br />
Below, I am showing what this analysis looks like for a simple PPV oligomer. I am fixing the hole either at the terminal phenyl, the vinyl or the central phenyl and plot the corresponding electron distribution. In the case of the S<sub>1</sub> state, the electron does not really care about the hole. The electron comfortably rests in the LUMO no matter what the hole does:<br />
<br />
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But for the S<sub>2</sub> state things look completely differently. The electron now tries to actively avoid the hole as it moves through the system.<br />
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S<sub>3</sub>, for comparison, has a much more localised structure where the electron is always focussed on the centre.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEglccy6-0sUcrAQVNul5DXrsyJNO3mk7AsBFqcgFl5a_SvhNqffDXS-8zfG7z-3H0-VITd1iTKm0sJlcw2OKUWYu4EG4p5pPbgXGIsOlfi-wqJzNnfcniKg49ZRMyvGTBaZ3nGVoZuB_xk/s1600/S3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="303" data-original-width="1600" height="75" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEglccy6-0sUcrAQVNul5DXrsyJNO3mk7AsBFqcgFl5a_SvhNqffDXS-8zfG7z-3H0-VITd1iTKm0sJlcw2OKUWYu4EG4p5pPbgXGIsOlfi-wqJzNnfcniKg49ZRMyvGTBaZ3nGVoZuB_xk/s400/S3.png" width="400" /></a></div>
S<sub>4</sub> has a somewhat more complicated structure:<br />
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<br />
By the way, I realised that the same type of analysis has been <a href="https://doi.org/10.1103/PhysRevB.97.241114">recently performed for periodic computations</a> as well. The difference is that in a periodic system every atom (or symmetry unit) will produce the same picture. In a finite system the picture also changes with the position of the probe.Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com2tag:blogger.com,1999:blog-3599722177679860131.post-28647774099972874642019-03-11T13:23:00.000+01:002019-03-11T13:25:19.170+01:00Creating fill-in-the-blanks handouts with LaTeX beamerFor some of my lectures I wanted to create handouts with blanks to fill in for the students. latex/beamer allows you to do this in a very convenient way. But it took me a while to figure out how to do this. This is why I just wanted to write a little memo in this blog post.<br />
<br />
The preamble looks like this
<br />
<blockquote class="tr_bq">
<pre>\documentclass[compress,transparent,10pt
,handout
]{beamer}
% toggle print-out to the handout for fill-in-the-blanks part
%\newcommand{\ho}{}
\newcommand{\ho}{|handout:0}</pre>
</blockquote>
With the initial handout tag I can toggle between handout mode and normal mode in latex. With the \ho tag I can decide whether the handouts are filled in or not.<br />
<br />
Let's look at the following code<br />
<blockquote class="tr_bq">
<pre>\begin{frame}
\frametitle{Energy and waves}
\begin{block}{Planck law}
\onslide<2-\ho>{\[ E = h\nu \]}
\end{block}
\begin{block}{Speed of light}
\onslide<3-\ho>{\[ c = \nu\lambda \]}
\end{block}
\begin{description}
\item[$E$] Energy
\item[$h$] Planck constant, $h=6.626\times 10^{-34}Js$
\item[$c$] Speed of light, $c=2.997\times 10^8 m/s$
\item[$\lambda$] Wavelength of light
\end{description}
\end{frame}</3-></2-></pre>
</blockquote>
This can be compiled in three different ways. For the initial student printout I am using the commands as shown above to obtain:<br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcoXNEsccZgBVOuaP_wCYCketsSrKS0BASfiXgrm-MI_UsnLQOdGnTKqbEqo9Le_58jnRqY5zcv5y07WQ8pt1IyLkPq87tmdNX8kBM5vaPc7iORK0Gs22w9v4sIQw1_Zm-mQqe4OPUC0M/s1600/Print-out.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1131" data-original-width="1600" height="282" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcoXNEsccZgBVOuaP_wCYCketsSrKS0BASfiXgrm-MI_UsnLQOdGnTKqbEqo9Le_58jnRqY5zcv5y07WQ8pt1IyLkPq87tmdNX8kBM5vaPc7iORK0Gs22w9v4sIQw1_Zm-mQqe4OPUC0M/s400/Print-out.png" width="400" /></a></div>
If I want to fill in the blanks, I just change the following:<br />
<br />
<blockquote class="tr_bq">
<pre>% toggle print-out to the handout for fill-in-the-blanks part
\newcommand{\ho}{}
%\newcommand{\ho}{|handout:0}</pre>
</blockquote>
to get<br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxQoFqoQuFI4YHhPX5QCOQ3HWJIr_nYyy0yAHStgIejYEmjjsoAJuV0yGu_sLQ0YIVqDoI0_si9oFpQCajkS0BisQFnwO2euOZTTY4VQp-WcUovdmcfgJ7cypTn9rKcmyrQnLLXXQAzdA/s1600/Filled-in.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1131" data-original-width="1600" height="282" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxQoFqoQuFI4YHhPX5QCOQ3HWJIr_nYyy0yAHStgIejYEmjjsoAJuV0yGu_sLQ0YIVqDoI0_si9oFpQCajkS0BisQFnwO2euOZTTY4VQp-WcUovdmcfgJ7cypTn9rKcmyrQnLLXXQAzdA/s400/Filled-in.png" width="400" /></a></div>
And for my lecture I uncomment the "handout" part to get three separate slides where the equations appear on click:<br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhJ0UhXNZJ50vRN4GuXib7Wu-3Dq3IJjq93vLgJ4ewz369eS2L_s3oN8vG8b-tPrP_ghYnQ6KG7By9CoPci8s7q4mHWG4nPNcGduTtvB0gfZW3rxANRvXTiu_4jnt0a91NVNTlg5iU4OzE/s1600/Screenshot+2019-03-11+at+12.16.54.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1079" data-original-width="477" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhJ0UhXNZJ50vRN4GuXib7Wu-3Dq3IJjq93vLgJ4ewz369eS2L_s3oN8vG8b-tPrP_ghYnQ6KG7By9CoPci8s7q4mHWG4nPNcGduTtvB0gfZW3rxANRvXTiu_4jnt0a91NVNTlg5iU4OzE/s640/Screenshot+2019-03-11+at+12.16.54.png" width="281" /></a></div>
<br />Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-87519041215603308692018-12-21T21:02:00.001+01:002018-12-21T21:02:30.383+01:00Benzene excimer<div class="separator" style="clear: both; text-align: left;">
I created this picture to illustrate excimer formation in the benzene dimer after light irradiation. We start with a slip-stacked geometry shown on the upper left and irradiate this with light. Then, as the molecules align during the first few hundred femtoseconds, the coupling increases and we get an energy transfer from the lower to the upper benzene. As the coupling increases, an excimer is formed. In our dynamics, this excimer decays later on as there is no way to dissipate the excess energy.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHEptduhtn23t6-WjoE2r4hTrjg357nXwFfNLTFyibRCjoCI63PmjTY7sslTlLCXj4zjSWyeFOCdHdqnoxaaF6ZuGMwKyHW2tzDe6pvr-WGwi4KFzl_UpILSSIx-m5E3-fK1SI6ExPPCQ/s1600/slide6.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1183" data-original-width="1600" height="295" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHEptduhtn23t6-WjoE2r4hTrjg357nXwFfNLTFyibRCjoCI63PmjTY7sslTlLCXj4zjSWyeFOCdHdqnoxaaF6ZuGMwKyHW2tzDe6pvr-WGwi4KFzl_UpILSSIx-m5E3-fK1SI6ExPPCQ/s400/slide6.jpg" width="400" /></a></div>
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The corresponding paper just appeared in PCCP (<a href="http://dx.doi.org/10.1039/c8cp06354k">DOI: 10.1039/c8cp06354k</a>) and we are trying to send a slightly adapted version of the above picture as a front cover to PCCP.</div>
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The pictures shown were created with <a href="https://pymol.org/">PyMOL</a> after creating cube files with <a href="https://www.q-chem.com/">Q-Chem</a>. As a memo to myself and anyone who might want to try this out, these are the main commands for PyMOL:</div>
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1. Load all the coordinate and cube files. If you set it up in a way that all the coordinate and cube files have the same names, then everything is loaded into different frames of the same object in pymol, which is needed for step 4.</div>
<blockquote class="tr_bq">
<div style="font-family: Menlo; font-size: 11px; font-stretch: normal; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures;">pymol S_*/plots/coord.mol S_*/plots/singlet_A_1_elec.cube</span></div>
</blockquote>
2. Create an isosurface for the density<br />
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<div style="font-family: Menlo; font-size: 11px; font-stretch: normal; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures;">isosurface elec, singlet_A_1_elec, 0.0015</span></div>
</blockquote>
3. Change the color of the isosurface, and for some reason it seems you have to write the command from 2. again afterwards.<br />
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4. To create the pictures of the different frames, you can use the integrated movie functionality of PyMOL<br />
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<div style="font-family: Menlo; font-size: 11px; font-stretch: normal; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures;">set ray_trace_frames=1</span></div>
<div style="font-family: Menlo; font-size: 11px; font-stretch: normal; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures;">set cache_frames=0</span></div>
<div style="font-family: Menlo; font-size: 11px; font-stretch: normal; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures;">mclear</span></div>
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<span style="font-variant-ligatures: no-common-ligatures;">mpng fig</span></div>
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That's it!<br />
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I was previously talking about how to <a href="http://chemical-quantum-images.blogspot.com/2011/10/automatic-plotting-of-orbitals.html">create surfaces automatically in VMD</a> and even created a <a href="https://sourceforge.net/p/theodore-qc/wiki/Utility%20scripts/#vmd_plotspy">script for that</a>. But actually, I am quite impressed by how well this works in the current PyMOL version. And the nice thing about PyMOL is that you can have a transparent background for the structures, which adds flexibility for creating the final image.Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-65316048933325674372018-12-17T16:36:00.000+01:002018-12-17T16:45:55.152+01:00PhD studentship at Loughborough UniversityA fully funded PhD studentship starting in October 2019 will be opening in my group at Loughborough University. If you are just finishing your Master's in chemistry, are interested in quantum chemistry and ambitious about learning new things, then go for it and apply!<br />
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<i>The official announcement is shown here:</i><br />
<h2>
Unravelling the electronic structure properties of functional molecular materials
</h2>
<blockquote class="tr_bq">
Functional molecular materials play an important role in modern science with applications in solar energy conversion, lighting, and data processing. Nowadays, computer simulations are an indispensable component in the study of these systems due to constant improvements in computer power. However, these computations have become so complicated that it is often a major challenge to make full sense of the results. To overcome this problem, a versatile computational analysis toolkit has been developed by Dr Plasser and co-workers, and it is the goal of this project to apply and further develop these tools. The student working on this project will develop skills in terms of applying modern quantum chemistry methods to various molecules of current scientific interest and will be given the opportunity to turn recently developed methods into high-impact scientific publications. In addition, programming skills will be developed, and the student will have the chance to work in an interdisciplinary setting with inputs from chemistry, physics and computer science.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEied7Hl6bfGQibQ0IvN3rivAwLkK0d7g1sB96bwuooEqn3Lyc34OX7vNqX_Jt2Rbh0ThnuDT6rMklyAzJjTPXtTe5Cs7HvsomnEhqZe7Zl2RWto_qVzSbZ9792g8t55dKIde3hBXP2ED08/s1600/6T_proposal.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="417" data-original-width="1600" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEied7Hl6bfGQibQ0IvN3rivAwLkK0d7g1sB96bwuooEqn3Lyc34OX7vNqX_Jt2Rbh0ThnuDT6rMklyAzJjTPXtTe5Cs7HvsomnEhqZe7Zl2RWto_qVzSbZ9792g8t55dKIde3hBXP2ED08/s400/6T_proposal.jpg" width="400" /></a></blockquote>
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The pictures shown pertain to a new method for visualising electron correlation in the excited state. Here, the <i>excitation hole</i> (red) is moved through the system and one observes how the <i>excited electron</i> (blue) adjusts to the position of the <i>hole</i> for the different excited states. I will talk about this idea some more once the underlying paper is published.</div>
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The tasks to be carried out during the project revolve around the topic of excited-state wavefunction analysis. First, we would be applying some of the recently developed tools, available within <a href="http://theodore-qc.sourceforge.net/">TheoDORE</a>, <a href="https://www.q-chem.com/">Q-Chem</a>, and <a href="http://www.molcas.org/">Molcas</a>. This work would be similar to <a href="http://chemical-quantum-images.blogspot.com/2015/12/conjugated-polymers.html">this post</a> or <a href="http://chemical-quantum-images.blogspot.com/2017/03/tddft-for-large-conjugated-systems.html">this post</a>. Subsequent work will be a combination of programming and/or scripting tasks together with applications.<br />
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You can find the official announcement and guidelines <a href="https://www.lboro.ac.uk/science/study/postgraduate-research/studentships/">here</a>. I guess the main point to realise is that we can only pay a stipend to UK/EU graduates. Others would just get their non-UK/EU tuition fee covered and not obtain a stipend on top of that.<br />
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If you are interested, go ahead and check out my <a href="https://fplasser.sci-public.lboro.ac.uk/">new group's homepage</a>. Feel free to contact me if you have any specific questions about the work to be done.Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-15097728406389602762018-11-12T17:48:00.000+01:002018-11-12T17:49:14.654+01:00Electron donating and withdrawing groupsAside from the fact that I do not believe in the existence of HOMOs and LUMOs, it is sometimes good to know how they work. In particular, I can never remember how electron-donating and withdrawing groups work. Here is how I understand it:<br />
<br />
<ul>
<li>An electron-<b>donating</b> group adds more electrons to the system and thus increases electron-electron repulsion (or decreases the effective nuclear charge). As a consequence the HOMO and LUMO energies <b>increase</b>.</li>
<li>An electron-<b>withdrawing</b> group removes electrons and, thus <b>decreases</b> the HOMO and LUMO energies.</li>
<li>An electron-<b>donating</b> group usually acts through an occupied non-bonding orbital. This is energetically close to the HOMO. Therefore, it has a <b>stronger effect on the HOMO</b> than on the LUMO (at least in organic molecules).</li>
<li>An electron-<b>withdrawing</b> group acts through a virtual orbital, which interacts <b>more strongly with the LUMO</b>.</li>
<li>As a consequence, electron-donating and withdrawing groups are <b>both</b> expected to <b>lower the HOMO-LUMO gap</b> in organic molecules.</li>
<li>Things are different for transition metal complexes. For example an electron-<b>withdrawing</b> fluorine group still <b>lowers</b> orbital energies. But it can affect the HOMO more strongly and increase the overall gap in fluorinated iridium complexes, see <a href="https://doi.org/10.1039/B512081K">this Ref</a>.</li>
</ul>
Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com3tag:blogger.com,1999:blog-3599722177679860131.post-67212458358909609672018-10-10T17:34:00.000+01:002018-10-10T17:35:23.242+01:00Cheap nonadiabatic dynamics simulations IIStaying true to the topic of cheap nonadiabatic dynamics simulations, here is another paper by us: <a href="https://dx.doi.org/10.1021/acs.jctc.8b00763">Surface hopping within an exciton picture - An electrostatic embedding scheme</a> that just appeared in JCTC. The idea in this case was to speed up the efficiency of photodynamics simulations by doing computations on individual chromophores and combining the results through a Frenkel exciton model.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgqXShctKdsIIbKW0ugVBmDC1hg0T3Wxjr3byrsXFB-6rD4KN8EYIyznQ-rwruq2jjE_lGDFvAxnlX4Lc0jE0Rh-8F1xJUDMZOFiQy68M3NkqU8q4nh40x-9bl2hKkC9RrRN3J-mS2NoeA/s1600/TOC.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="99" data-original-width="252" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgqXShctKdsIIbKW0ugVBmDC1hg0T3Wxjr3byrsXFB-6rD4KN8EYIyznQ-rwruq2jjE_lGDFvAxnlX4Lc0jE0Rh-8F1xJUDMZOFiQy68M3NkqU8q4nh40x-9bl2hKkC9RrRN3J-mS2NoeA/s1600/TOC.png" /></a></div>
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<span style="background-color: white; font-family: "trebuchet ms" , "arial" , "helvetica" , sans-serif; font-size: 13px;"><br /></span>Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-44420795813823745332018-10-05T12:49:00.001+01:002018-10-05T12:49:48.384+01:00Cheap nonadiabatic dynamics simulationsWhat is the cheapest way to run nonadiabatic dynamics simulations and get results that are at least better than a random number generator? How about parameterising a linear vibronic coupling Hamiltonian using only a single excited-state computation and running surface hopping dynamics with it. This is what we tried in our new paper "<a href="http://dx.doi.org/10.1039/c8cp05662e">Highly efficient surface hopping dynamics using a linear vibronic coupling model</a>" that just appeared in PCCP. And to our surprise, the results were actually a lot better than a random number generator. We could reproduce the main physics of the dynamics of intersystem crossing in SO<sub>2</sub>, the presence/absence of ultrafast internal conversion in adenine/2-aminopurine, as well as ultrafast intersystem crossing in 2-thiocytosine. Only for 5-azacytosine we were somewhat off the mark.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyfJ9lHvrYBSm1ukWwh8a4tq92B6dyDetz3AF6Bd_jzz6bIpMLuv0DaqPpgSsaLZ-YxoM7M2mAQJIActfhXxpPXcpzUGCKCSmoddOiKEe3zPzo0HSVjfZVrAWVoHFL8VAwYHWx_1zSAqY/s1600/toc_inkscape.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="516" data-original-width="538" height="306" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyfJ9lHvrYBSm1ukWwh8a4tq92B6dyDetz3AF6Bd_jzz6bIpMLuv0DaqPpgSsaLZ-YxoM7M2mAQJIActfhXxpPXcpzUGCKCSmoddOiKEe3zPzo0HSVjfZVrAWVoHFL8VAwYHWx_1zSAqY/s320/toc_inkscape.png" width="320" /></a></div>
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Some of the referees were a little bit "not amused" because it almost seems like kind of an unfair trick to run dynamics using such a simple setup. But if it works and if it gives you relevant information about the real world, why should you not do it?Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-48601183056905402882018-10-04T09:06:00.001+01:002018-10-04T09:06:42.649+01:00Bound vs BoundedIt's always good to start the day with an arbitrary rant. Here is the one for today (since a lot of people seem to get this wrong). There are two similar words in the English language: bind and bound. <a href="https://www.thesaurus.com/browse/bind">"Bind" means "to connect"</a> - and this is what we usually use in chemistry. <a href="https://www.thesaurus.com/browse/bound?s=t">"Bound" means "to restrict"</a> - and this does not really have a use in chemistry. Now, the tricky bit is that "bound" is also the past tense and past participle of "bind".<br />
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This is how you should use it:<br />
<br />
<ul>
<li>A strongly <i>binds</i> to B.</li>
<li>A strongly <i>bound</i> to B, yesterday.</li>
<li>A and B are strongly <i>bound</i>.</li>
<li>But A and B are not strongly <i>bounded</i> (unless you mean that they are restricted).</li>
</ul>
<div>
If you do want to use "bounded", then use it in a mathematical context:</div>
<div>
<ul>
<li>The function f(x)=x<sup>2</sup> is <i>bounded</i> from below.</li>
</ul>
<div>
You are allowed to say that.</div>
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<div>
By the way, if you want to avoid this whole dilemma, use bond/bonded/bonded.</div>
Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-11625275310591590552018-02-08T15:34:00.003+01:002018-06-14T13:46:50.464+01:00Move to LoughboroughI just relocated to Loughborough, UK, to work as a lecturer at the <a href="http://www.lboro.ac.uk/departments/chemistry/">Department of Chemistry</a>. It is a busy time but very exciting :)<br />
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You can check out my new homepage <a href="https://fplasser.sci-public.lboro.ac.uk/">here</a>. I will move the more "professional" announcements of papers and similar things to my new <a href="https://fplasser.sci-public.lboro.ac.uk/blog/">newsfeed</a>, and I will probably reserve this blog for more personal posts.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiF_4hK7LU0Sjg9O_syLeNslULYb_f4DHvZtbNMwjWX5F8yxG8GPXGAymVWOpLDmlMPqCTulDi2m5zFBRRVmBeLbM4IJt3AyX3cjZCnFAtpW-69WEAY32Rs6Uln3hktgIugoN3s33EifJI/s1600/lboro825.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="207" data-original-width="825" height="80" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiF_4hK7LU0Sjg9O_syLeNslULYb_f4DHvZtbNMwjWX5F8yxG8GPXGAymVWOpLDmlMPqCTulDi2m5zFBRRVmBeLbM4IJt3AyX3cjZCnFAtpW-69WEAY32Rs6Uln3hktgIugoN3s33EifJI/s320/lboro825.png" width="320" /></a></div>
<br />Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0tag:blogger.com,1999:blog-3599722177679860131.post-65532213193648548562017-12-13T20:50:00.002+01:002017-12-13T20:53:50.529+01:00Nonadiabatic photodynamics of large systems using the TD-DFTB methodThere is a new interface between the <a href="http://newtonx.org/">Newton-X</a> and <a href="https://www.dftbplus.org/">DFTB+</a> packages that allows performing nonadiabatic photodynamics of large systems in a highly efficient manner. This is described in a new paper "<a href="http://dx.doi.org/10.1021/acs.jctc.7b01000">Nonadiabatic Dynamics of Cycloparaphenylenes with TD-DFTB Surface Hopping</a>" that just appeared in J. Chem. Theory Comput. Check it out.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhl-Ul5hTX3gp2Jk8KtgNt6QQvYxrCt8u-iRz63CowqIFnRlra7sBkl2TSyR3AMHAWQYAAY43NVZ52LPySZgqLKyzM6slYdg6xGCIInjifihRUCfwAFct_qeevTc1lkXGKOyxSZjF220l8/s1600/ct.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="189" data-original-width="500" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhl-Ul5hTX3gp2Jk8KtgNt6QQvYxrCt8u-iRz63CowqIFnRlra7sBkl2TSyR3AMHAWQYAAY43NVZ52LPySZgqLKyzM6slYdg6xGCIInjifihRUCfwAFct_qeevTc1lkXGKOyxSZjF220l8/s400/ct.png" width="400" /></a></div>
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You can check <a href="https://barbatti.org/2017/12/02/surface-hopping-with-td-dftb/">Mario Barbatti's blog</a> for some more information.Felixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.com0