Archive for the ‘WATOC reports’ Category

WATOC 2025 report – extending the limits of computation (accuracy).

Wednesday, June 25th, 2025

This are just a few insights I have got from some of the talks I attended. As usual, this does not represent a report on the WATOC congress itself, but simply some aspects that caught my personal eye.

  1. Frank Neese talked about his Bubblepole approximation for large molecules.[1] And he was not kidding – large. Lets say a DFT calculation at the Def2-TZVPP basis set level (often the level used in this blog). Thus Crambin + 500H2O, which is 2142 atoms can not only be done at this basis set level (33,562 basis functions) but at the astonishing Def2-QZVPP level (rarely attempted here!) with 86,667 basis functions. But that is not the largest – he has also done unhydrated Crambin octamer (5132 atoms) with 116,904 basis functions using the Bubblepole method. Currently this method appears only in his ORCA code – and if I understood correctly they are still working on first and second derivatives. So it will be a little while longer before e.g. reaction transition states for such sizes appear, but probably not that long!
  2. Martin Head Gordon is responsible for the highly regarded ωB97 set of DFT functionals (again used throughout this blog). Until now, the most recent of these, ωB97M(2) from 2019[2] had represented a significant advance in accuracy (let’s say reaction barrier heights) over the previous generations, this having a mean error of ~0.9 kcal/mol compared to 2-3 kcal/mol for earlier generations. At the conference he introduced a “Carefully Optimised and Appropriately Constrained Hybrid” or COACH functional. He introduced 17 constraints or exact conditions that an ideal functional should have and explained that COACH satisfied 12 of these (another relatively recent functional, SCAN satisfies all 17[3]). Earlier functionals satisfy ~6 or less. For 7 selected properties, including barrier heights, the mean errors are around ½ to ⅓ of earlier functionals such as the veritable B3LYP+D4 dispersion. His concluding remarks suggested that DFT as such is nearing the ultimate limit of general purpose accuracy achievable by such procedures. I hope to be trying out e.g. COACH here in the next year or so.
  3. Fritz Schaefer “threw the kitchen sink” at the small tetra-atomic fulminic acid, or HCNO, to try to answer the simple question – is it bent or linear?[4] At the CBS (complete basis set) limit and the CCSDTQ(P) level of coupled cluster theory (wow!), the answer converges to the conclusion that it is linear! This level cannot be that far off an exact solution of the Schroedinger equation – and it agrees with experiment!
  4. Oh, a general observation, machine learning permeates the entire congress.

References

  1. F. Neese, P. Colinet, B. DeSouza, B. Helmich-Paris, F. Wennmohs, and U. Becker, "The “Bubblepole” (BUPO) Method for Linear-Scaling Coulomb Matrix Construction with or without Density Fitting", The Journal of Physical Chemistry A, vol. 129, pp. 2618-2637, 2025. https://doi.org/10.1021/acs.jpca.4c07415
  2. N. Mardirossian, and M. Head-Gordon, "Survival of the most transferable at the top of Jacob’s ladder: Defining and testing the <i>ω</i>B97M(2) double hybrid density functional", The Journal of Chemical Physics, vol. 148, 2018. https://doi.org/10.1063/1.5025226
  3. J.W. Furness, A.D. Kaplan, J. Ning, J.P. Perdew, and J. Sun, "Accurate and Numerically Efficient r<sup>2</sup>SCAN Meta-Generalized Gradient Approximation", The Journal of Physical Chemistry Letters, vol. 11, pp. 8208-8215, 2020. https://doi.org/10.1021/acs.jpclett.0c02405
  4. A.M. Allen, L.N. Olive Dornshuld, P.A. Gonzalez Franco, W.D. Allen, and H.F. Schaefer, "Tests of the DFT Ladder for the Fulminic Acid Challenge", Journal of the American Chemical Society, vol. 147, pp. 14088-14104, 2025. https://doi.org/10.1021/jacs.4c13823

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WATOC25 and its (Dr Who like) regeneration to Young WATOC25.

Saturday, June 21st, 2025

The WATOC congresses occur every three years. WATOC25, the 13th in a series which started in 1987  takes places tomorrow in Oslo, Norway, The day before the main event there is something new – a session just for early career researchers or “Young WATOC”. As an “old” WATOCer, I dropped into the opening session and was delighted to find a packed auditorium, with literally standing room only comprising mostly young researchers in their 20s.

Apparently in terms of presenters, the event was more than five times over-subscribed with >100 submissions, of which around 18 being selected for presentation.

The first talk was also really great, involving how to locate the equilibrium geometries of molecules and the transition states connecting their reactions. The standard methods used nowadays involve Taylor series expansions of the energy and it’s good to see new methods based on ML and image processing techniques being adapted for this.

It looks like the future of computational chemistry is in enthusiastic new hands! And, for the first time, this 13th Congress now has its own app containing speaker information, abstracts, the timetable and much more. All indexed and searchable!

The week ahead is packed with talks and I may report back here.

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A ROR Persistent Identifier for the WATOC organisation – helping to make scientific connections.

Thursday, March 9th, 2023

Science frequently works by people making connections between related (or even apparently unrelated) concepts or data. There are many ways of helping people make these connections – attending a conference or seminar, searching journals for published articles and nowadays also searching for data are just a few examples. For about 20 years now, one technology which has been helping to enable such discoveries is what are called “Persistent IDentifiers” or PIDs. These are unique labels which can be attached to a (scientific) object such as a journal article, a dataset or a researcher. The PIDs for the first two examples have become better known as DOIs (digital object identifier), the last is known as an ORCID. The PID is registered with a registration authority. Two of the oldest and  best known authorities are CrossRef for journal articles, funders (etc) and DataCite, who specialise in citable identifiers for data. The registration process includes creating and adding a metadata record to the PID, the record is then indexed and can then be used for searching for the objects. The terms of these metadata records are carefully controlled to use specified and standardised vocabularies to describe the objects (one current initiative in chemistry in this area is described here[1]).

The PID “ecosystem” is constantly expanding and a recent addition is the ROR registration authority. This issues PIDs for research organisations, so that one can then easily associate a scientific object with the organisation where the research was conducted. The initial focus for ROR PIDs was the traditional forms of organisation such as a university and company research labs. Here I tell about how a rather different type of organisation came to have its own ROR, the “World Association of Theoretical and Computational Chemists” or WATOC. The aims of WATOC are primarily to hold triennial congresses to promote scientific exchange and to help researchers make those connections through presentations, posters and numerous coffee breaks!

Last July, the proposal for creating a ROR for WATOC was accepted by its decision making body and can now be announced as https://ror.org/04rp40h82, where 04rp40h82 is the unique WATOC identifier. The prefix https://ror.org/ is called the “resolver”, which in turn allows access to the associated metadata record via an API. That record in turn includes a link to the organisation, similar to links to journal articles as specified by a DOI.

It is now time to show some examples of how the WATOC ROR can actually be used.

  1. One outcome of the last WATOC Congress held in 2022 in Vancouver is the production of a themed peer-reviewed issue of the Canadian journal of chemistry, created by inviting speakers to submit an article corresponding to their presentation. Armed with the WATOC ROR, the publisher was approached to ask if this identifier could be included in the metadata record for each accepted article. This was agreed and in due course will be added to the Crossref metadata record for each article in this special issue. When this happens, it can be searched using e.g. https://api.crossref.org/works?filter=ror-id:04rp40h82  Because creation of a metadata record is actually part of the complex journal production workflow, this will not occur until the journal has updated its procedures to do this, which may take a little while yet. Invoking that search would then allow all published articles associated with (at least in part) WATOC activities.
  2. The link https://api.crossref.org/works?filter=ror-id:04rp40h82 is actually part of the CrossRef API (application programmer interface) and so can now be used to construct complex programatic queries which include the WATOC ROR and for deployment in e.g. AI applications.[2] Although not derived from the CrossRef API, I can show here some similar uses of metadata for the construction of so-called Knowledge Graphs [2], which can be thought of as visual representation of connections between scientific objects, organisations and other types of entity to which a registered PID has been assigned.
    1. This knowledge graph was created using SciFinder by specifying a person (myself in this case) and any conferences they have been associated with. However, in the past the capture of conference attendance was a rather hit and miss process and so the record is very incomplete. It is the expectation that metadata associated with ROR PIDs will help make these records more complete and hence useful.  ROR is also fully open and hence its use is less restricted than the proprietary SciFinder system.
    2. I cannot resist also adding this one. The metadata record now contains named concepts, this one being “transition states” which I have been associated with in the past.
    3. As of today, the WATOC ROR has not propagated to any CrossRef metadata records and so I cannot yet show any knowledge graphs with nodes based on WATOC.

  3. The ROR PID can also be used for inclusion in metadata records describing datasets. This is one such search, now of the DataCite metadata store:
    https://commons.datacite.org/doi.org?query=((contributors.affiliation.affiliationIdentifier:*04rp40h82)+AND+(contributors.affiliation.affiliationIdentifierScheme:ROR))+OR+((creators.affiliation.affiliationIdentifier:*04rp40h82)+AND+(creators.affiliation.affiliationIdentifierScheme:ROR))
    Note the somewhat more complex logic being used, in part because a dataset can be “created” by a named person but also can be “contributed to” and one should really search for both possibilities.

  4. One can also combine two different identifiers, namely an organisational ROR and a researcher ORCID into a single query:
    https://commons.datacite.org/?query=((creators.affiliation.affiliationIdentifier:*04rp40h82)+OR+(contributors.affiliation.affiliationIdentifier:*04rp40h82))+AND+(contributors.nameIdentifiers.nameIdentifier:*0000-0002-8635-8390)
    There are many more combinations of searches that can be constructed using other types of identifiers.[3]

  5. Further in the future, one might expect that metadata records from e.g. both CrossRef and DataCite could be combined to create knowledge graphs by combining information based on both journal articles and published FAIR datasets. Currently, CrossRef does not identify PIDs for datasets that might be cited in an article bibliography as explicit data, but that too may be coming in the near future.[4]

Way back in January 1994, WATOC was one of the very first chemical-science based organisations to have its own web page. Now it is leading the way in acquiring and deploying its very own persistent identifier in the form of a ROR. One might hope that many more such organisations acquire one soon.

The DOI for this post is 10.14469/hpc/12363

References

  1. R.M. Hanson, D. Jeannerat, M. Archibald, I.J. Bruno, S.J. Chalk, A.N. Davies, R.J. Lancashire, J. Lang, and H.S. Rzepa, "IUPAC specification for the FAIR management of spectroscopic data in chemistry (IUPAC FAIRSpec) – guiding principles", Pure and Applied Chemistry, vol. 94, pp. 623-636, 2022. https://doi.org/10.1515/pac-2021-2009
  2. A. Hogan, E. Blomqvist, M. Cochez, C. D’amato, G.D. Melo, C. Gutierrez, S. Kirrane, J.E.L. Gayo, R. Navigli, S. Neumaier, A.N. Ngomo, A. Polleres, S.M. Rashid, A. Rula, L. Schmelzeisen, J. Sequeda, S. Staab, and A. Zimmermann, "Knowledge Graphs", ACM Computing Surveys, vol. 54, pp. 1-37, 2021. https://doi.org/10.1145/3447772
  3. H.S. Rzepa, and S. Kuhn, "A data‐oriented approach to making new molecules as a student experiment: artificial intelligence‐enabling FAIR publication of NMR data for organic esters", Magnetic Resonance in Chemistry, vol. 60, pp. 93-103, 2021. https://doi.org/10.1002/mrc.5186
  4. . , "NISO JATS4R Data Citations Recommendation v2.0", . https://doi.org/10.3789/niso-rp-36-2020

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Personal Impressions from WATOC 2020 – Dispersion and non Born-Oppenheimer models.

Monday, July 11th, 2022

WATOC 2020 was just held in 2022 in Vancouver Canada, over one week. With many lectures held in parallel, it is not possible for one person to cover anything like the topics presented, so this is a personal view of some of those talks that I attended. As happens with many such events, common themes gradually emerge and here I highlight just two that struck me as important for the future of computational chemistry.

  1. Dispersion. This goes back to Fritz London and his formula: Edisp = -(C6/R6), where where coefficient C6 depends on the expectation values of the instantaneous dipole moments and average atomic excitation energies. The nature of this formula suggests that it decays rapidly with the distance between any pair of nuclei, R. But an increasing body of evidence is suggesting that such simple approaches (implemented as a correction in many e.g. DFT methods and known as e.g. D3+BJ, or D4 etc) may be underestimating the long range dispersion attractions. One nice example is what is known as the exfoliation of layers of graphite, where the forces holding the layers together can be measured quite accurately and which emerge as a great deal greater than the simple formulae suggest. It appears we now have a renaissance in developing new more accurate dispersion energy methods which include various higher order terms and are being applied to a variety of discrete molecule and solid state systems. One space to look out for!
  2. .Non Born-Oppenheimer behaviour. It is a mainstay of most solutions of the Schroedinger equation where the nuclei are treated as classical point charge objects with fixed positions in an electronic field described by a wavefunction. But there is now considerable activity in developing methods that generate an extended Hessian (2nd derivative matrix) describing the forces that depends on both the classical nuclear coordinates of non-hydrogen atoms and the expectation values of quantum proton coordinates. This matrix is diagonalised to obtain the coupled vibrational frequencies which now naturally include the anharmonicity of the now quantum-treated protons and recovers the electron-proton correlation. It impacts most directly on so-called proton tunnelling and isotope effects, which can slice off 2-4 kcal/mol from barriers, but is now seen as a manifestation of electron-proton correlations in non-Born Oppenheimer potentials. The classical approach is to shave these energies off using eg Eckart potentials, but is now being replaced by e.g. a nuclear-electronic orbital method (NEO) which calculate the barriers from first principles. Typical types of reactions that are affected by non-BO behaviour are proton coupled electron transfers (PCET, see here for an example) which are increasingly seen as important in many biological processes.

I have tried to highlight just two themes that emerged from WATOC of personal interest to me; of course there was a great deal of new and exciting stuff that I have not mentioned. The next WATOC will be in Oslo in 2025, and no doubt new and exciting themes will emerge there as well!

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One more WATOC 2017 Report.

Thursday, August 31st, 2017

Conferences can be intense, and this one is no exception. After five days, saturation is in danger of setting in. But before it does, I include two more (very) brief things I have learnt.

  1. Sason Shaik introduced a theme he first investigated years ago, but for which no experiment had been devised for verification. He revived his theme when a journalist contacted him last year to report exactly such an observation, which I now recount. A Diels-Alder adduct was captured between a flat layer of gold atoms and the tip of a scanning-tunneling microscope. With the molecule exactly oriented, a strong external electric field (OEEF) was applied, in both senses of polarisation. This is exactly the model studied by Sason, who had argued thus. A Diels-Alder reaction can be modelled using VB theory as the avoided crossing of a covalent ground state with ionic excited states at the transition state. Depending on the polarisation of an applied external electric field and the orientation of the molecule, one of these ionic states can stabilized or destabilised by about 8 kcal/mol, thus either stabilising or destabilising the transition state itself by mixing with the covalent state.

    And so it was that the oriented molecule caught between a gold layer and an STM probe could be persuaded to undergo a retro-Diels-Alder far more easily than it would thermally. The technique can even be tuned to selecting between endo and exo isomers. Sason held out the prospect that the toolbox of the synthetic chemist, which already includes Δ, hν and ? (ultrasound) as reagents, might be extended using OEEF. He called this a smart reagent since it can be tuned to the reaction required (as of course can light). At the moment this technique can only be applied to one molecule at a time, but it might be just a matter of designing a suitable apparatus!

  2. Pavel Hobza talked about non-covalent interactions, an occasional theme on this blog. Amongst many interesting observations was that the DNA helix is not stabilised as such by the hydrogen bonding between the base pairs but by the π-π stacking between them. One of these examples caught my eye, the known weak “hydrogen bonded” weak complex between benzene and chloroform in the gas phase. The C-H hydrogen points directly to the ring centroid and the C-H vibrational wavenumber is blue shifted by 12 cm-1. At the time this (experimental) observation caused consternation, since all known hydrogen bonds (both strong and weak) were routinely characterised by the magnitude of their red shift (up to ~100 cm-1). In fact, as Pavel showed, this interaction is less electrostatic in nature and more like dispersion attraction. Accurate calculations including dispersion also predict a blue shift for this system. A question from the audience suggested that as many π-facial “hydrogen bonds” in the crystal state tend to point not to the ring centroid but to the ring edge, what would happen if the chloroform H were to slide across the surface of the ring until it reached the edge; would the CH shift invert to become red, implying a change from dispersion interaction to whatever is implied by a hydrogen bond?

Apologies to all those who gave fascinating talks which are unrecorded here. I hope some tiny and selective flavour nevertheless emerges of WATOC 17.

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(another) WATOC 2017 report.

Tuesday, August 29th, 2017

Another selection (based on my interests, I have to repeat) from WATOC 2017 in Munich.

  1. Odile Eisenstein gave a talk about predicted 13C chemical shifts in transition metal (and often transient) complexes, with the focus on metallacyclobutanes. These calculations include full spin-orbit/relativistic corrections, essential when the carbon is attached to an even slightly relativistic element. She noted that the 13C shifts of the carbons attached to the metal fall into two camps, those with δ ~+80 ppm and those with values around -8 ppm. These clusters are associated with quite different reactivities, and also seem to cluster according to the planarity or non-planarity of the 4-membered ring. There followed some very nice orbital explanations which I cannot reproduce here because my note taking was incomplete, including discussion of the anisotropy of the solid state spectra. A fascinating story, which I add to here in a minor aspect. Here is a plot of the geometries of the 52 metallacyclobutanes found in the Cambridge structure database. The 4-ring can be twisted by up to 60° around either of the C-C bonds in the ring, and rather less about the M-C bonds. There is a clear cluster (red spot) for entirely flat rings, and perhaps another at around 20° for bent ones, but of interest is that it does form something of a continuum. What is needed is to correlate these geometries with the observed 13C chemical shifts to see if the two sets of clusters match. I include this here because in part such a search can be done in “real-time” whilst the speaker is presenting, and can then be offered as part of the discussion afterwards. It did not happen here because I was chairing the meeting, and hence concentrating entirely on proceedings!

  2. Stefan Grimme introduced his tight binding DFT method, an ultra fast procedure for computing large molecules and in passing noted the arrival of his D4 procedure (almost everyone currently uses D3 methods for this, including many of the results reported on this blog) for correcting for dispersion energies in molecules based on computed charge dependencies using the TBDFT methods. Thus we see dispersion as a property which is based on the wavefunction of the molecule, but still fast enough to accurately correct dispersion energies. He followed this with his automated procedures based on the TBDFT methods for computing full spin-spin coupled 1H NMR spectra of organic molecules. The core of this method is to recognise conformational and rotational freedoms and to compute the NMR properties for all identified isomers. These parameters are then Boltzmann averaged prior to computation of the final spin-coupled simulated frequency domain spectrum (rather than inverting this procedure by computing spin-coupled spectra of all rotamers and conformations and then averaging the spectral envelopes). This should widely revolutionise the interpretation of 1H NMR spectra by synthetic chemists.
  3. Another automated tool for synthetic chemists was presented by Jan Jenson, and can be seen here. It used MOPAC PM3 semi-empirical theory to compute relative proton affinities for a series of regioisomers as a prelude to predicting the position of aromatic electrophilic substitutions in heteroaromatic molecules. Try it out by putting a SMILES string into the box provided (e.g. COC1=CC=CC=C1) waiting a bit and seeing what the prediction is (it should be p- for the preceding example). During Q&A, a question was asked about the canonical “purity” of the SMILES (the one used in this tool comes from the Chemdraw program, which might not be identical to a SMILES for the same molecule produced by a different program), and whether an InChI descriptor might be better (also produced by Chemdraw, but perhaps a bit more canonical). Also asked was whether the prediction for an electrophile rather larger than a proton might not give good predictions? This one perhaps could be tested by readers, who could report back here?
  4. Walter Thiel completes the semi-empirical theme when he reported the new ODM2 method, the D now including dispersion. This is a powerful program, which includes e.g. full CI (configuration interaction + gradients) capability and is especially good for excited states, for dynamic simulations, and for combining these into dynamic photochemical simulations. This was applied to the chromophore in the famous “nanocar” in studying the dynamics of the photochemical rotation of the motor of the car (the thermally induced rotation was not studied). At the time that the nanocar caught my attention, I wondered about how the four independent molecular motors synchronised their rotations to allow the car to drive in a straight line. No doubt the answer is known, and if anyone reading this knows, please tell! It is probably a dynamics problem on four rotors (Walter reported just on one!).

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WATOC 2017 report.

Tuesday, August 29th, 2017

The triennial conference is this year located in Munich. With 1500 participants and six parallel sessions, this report can give only a flavour of proceedings.

  1. Edward Valeev talked about the scaling problem in coupled cluster theories, the so-called gold standard for computing the energy and properties of small molecules. The problem is that the number of basis functions N describing the atomic basis set for the atoms scales from between N6 to N10 in terms of computer time, with similar behaviour for the memory required for the calculation. He described methods based on natural pair orbitals and localisation schemes which can achieve linear scaling, ie N1 for the energy, quite a break through! Using reasonable basis sets, CCSD(T)-like energies for molecules with 100s of atoms were reported. During the Q&A time afterwards (the tight schedules associated with so many speakers means questions are often limited to 1-2, with very short answers) a question was posed about the prospects for first and second derivatives for the method. This means that e.g. reaction mechanisms can then be probed with unprecedented energetic accuracy. The answer was non-committal, but if these derivatives do arrive, it will revolutionise our ability to understand mechanisms.
  2. Which brings me nicely to Jeremy Harvey, who talked about calculating accurate overall rate constants for complex mechanistic cycles. The rate equations are solved for the steady state condition and include concentrations of all species and the energies are obtained using CCSD(T)-F12 theory (a modification which allows better basis set scaling without increased computation time) as single point geometries. He described an example where the barrier associated with a postulated mechanism was about 6 kcal/mol higher than derived from the observed rate. This was sufficient to induce them to explore alternative mechanisms, which were indeed located with an appropriately lower barrier. I have used the value of ~10 kcal/mol as my mechanistic test on this blog, and it’s really nice to see this value being reduced further.
  3. Yet again this theme emerged with Yitzhak Apeloig, who asked about the mechanism for C=Si bond rotations in substituted systems recently made in his group. The energy of this rotation is low enough to be observed in NMR spectra. But when the energy of C=Si bond rotation is computed it comes out about 10 kcal/mol too high. Again alternative mechanisms were explored and it turns out that a 1,2 migration from R2C=SiR2 to form a carbylidene species, R-C-SiR3, rotation and then 1,2 again to reformulate the R2C=SiR2 system came up with the goods.
  4. Peter Scheiner talked about how attractions between molecules can be induced by dispersion. He described how Ph3C-CPh3 is an unknown molecule (dissociating into Ph3P• radicals) but when 4,6-di-tert-butyl groups are placed on all the phenyl rings, the dispersion attractions between them can account for ~60 kcal/mol (!), more than enough to stabilise the system. I have already described some of this work in a post here. The prospects are very exciting for more dispersion-stabilised molecules to emerge. During Q&A, a question was posed about what other atom pairs other than H…H might be brought into ultra-short contact by these attractive dispersion forces; we may expect further examples to emerge in the near future.
  5. Ken Houk gave a fascinating glimpse into the post-transition state world of reaction dynamics, as applied to Diels Alder cycloadditions and Cope rearrangements. The reactions are characterised by the residency times of the dynamic trajectories in the region of the transition state as short (~4 fs), medium (20-40fs) and long (80+fs), these times mapping on to what we used to call “synchronous”, “asynchronous” and “stepwise”. A good example is the so-called bis-pericyclic reaction of cyclopentadiene where the trajectories pass through a transition state but then bifurcate into two (in this case) equivalent pathways. He discussed other examples where the trajectories follow either a 2+4 cycloaddition pathway or a 4+6 alternative pathway and how the number of trajectories for each can be influenced by either solvent (water) or an enzyme. Ken described several 20-40fs trajectories as corresponding to “dynamic stepwise” reactions, which during Q&A was suggested are equivalent to the term “hidden intermediate” pathways coined by Dieter Cremer and as revealed in many posts here from the intrinsic reaction coordinates or IRCs. This is a clear growth area and expect many more examples of reaction dynamics to be applied to many exciting systems in the future.
  6. Leo Radom talked about very simple molecules, H3CX and the effects on the bond dissociation energy (BDE) of the C-H bonds if the group X is either strongly or weakly protonated (the latter via a hydrogen bond), or deprotonated (again strongly or weakly via a hydrogen bond from hydroxide anion). This is important in several enzymic pathways, where the CH bond might be activated in a similar manner by the enzyme. He also talked about similar effects on the ionisation potential. I noticed a connection between this theme and what might be called the electron affinity of H3CX. If you want to see what the connection is, go visit the Aachen bond Slam, about which I have previously blogged! 

I will stop with an observation that all the notes above were taken in real-time during the talks, which all emerged as Powerpoint slides, having an average residency time on the screen of perhaps 1-2 minutes each. References were invariably given as full journal citations (authors, journal, year, volume, pages) rather than as DOIs, and given the time constraints I did not try to capture them. Hence the lack of citations above to the presenters’ work. The slide displays are traditionally not made available to audiences‡ and photography of the screen or recording is considered very bad form. Conferences are not really about FAIR data, which I have described often on this blog.

I hope these six examples give one flavour of what is happening at WATOC 2017. If another interesting collection emerges, I may describe it here.

‡But see e.g. doi: b9r9 for an Aachen talk.

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WATOC2014 Conference report. Emergent themes.

Thursday, October 9th, 2014

This second report highlights two “themes”, or common ideas that seem to emerge spontaneously from diversely different talks. Most conferences do have them.

The first is “embedding“, which in this context means treating different parts of a probably complex molecular system at different levels of theory. Thus Emily Carter in her plenary described how a periodic crystal treated by density functional theory, or DFT could have an embedded component in which the electronic structures are described instead by multi-reference correlated wave functions (CAS-PT2). She illustrated this by discussing what happens when a triplet state oxygen molecule approaches the surface of an aluminium crystal, and (mostly) dissociates into surface bound oxygen atoms with Al-O bonds. The spin state of the oxygen changes smoothly to an overall singlet, with a rapid transfer of charge at the saddle point in the potential energy surface. The numbered of embedded Al atoms had to be at least a cluster of 14 to reproduce the observed reaction barriers (DFT on its own gets a zero barrier!). This sort of study is important in understanding the details of what is happening in metal surface catalysis.

Arieh Warshel then addressed the same theme with his own talk entitled Multiscale Modeling of Complex Biological Systems and Processes. Here you got quantum embedding in a mechanical force field description of some very large molecules. This was a broad brush talk, but what I did get out of it was the concept of asymmetry in molecular systems. Whereas an organic chemist thinks of asymmetry as often relating to just a single chiral carbon centre in a molecule, nature operates on vaster scales. Thus the enzyme ATPase has a molecular axle or spindle, which rotates to assemble the phosphate groups one at a time. This spindle rotates asymmetrically, i.e. always in a specific direction, and Warshel attempts to describe the origins of this rotational asymmetry at a molecular level. Well, this is Nobel prize winning stuff! He followed this up with filaments that “walk” along surfaces in one (asymmetric) direction, first lifting up one point of attachment, and then re-attaching at a different point such that the filament develops a clear sense of direction in its walk. This of course is all done with molecular dynamics, and (I think) has its origins in subtle electrostatics.

Stefan Grimme in his plenary also described dynamic processes, this time those that happen in a mass spectrometer when a molecule is ionised by electron impact. Removal of an electron produces a complex set of ionised states, in which many different single bonds may be weakened due to this ionisation. He developed simplified  DFT (sDFT) methods that can be applied to molecular dynamics, and assembled a “black box” which predicts the expected fragmentations over a time scale of a ps or so. By sampling the trajectories, he estimated the intensities of the various positively charged species and overlaid this on the observed EI-MS. The agreement was often spectacular. A particularly interesting example was the fragmentation of taxol. Here, no molecular ion is found, only much lighter ions. The molecular dynamics shows that rather than consecutive single-bond fragmentations, you instead get multiple bonds more or less all fragmenting at the same time. Tougher was to reproduce rearrangements, such as the McLafferty. Here, the semi-empirical method OM2 was more successful. His work means you can just “dial-a-mass-spectrum” and he speculates whether getting a good fit with the observed spectrum could tell you subtle aspects of the gas-phase molecular species, what its tautomeric state might be or perhaps even its conformation. He also described large-scale (800+) atom simulations of electronic circular dichroism (ECD) spectra of organometallic systems. Octahedral complexes can be prepared in chiral form, and this theoretical ECD treatment allows determination of absolute configuration of these often non-crystalline systems. Here you often need to compute 1000 or more electronic states, and if you have ever tried such ECD simulations, you will know that this is a lot of states!

We had been expecting Stefan to talk about dispersion effects in molecules, another emerging theme. Instead lots of other people mentioned them. In my talk I showed how including a D3-dispersion correction could dramatically change the predicted enantioselectivity of a chiral aldol condensation.[1]

The above observations of course cannot be in the least representative; typical of a modern conference there are five parallel sessions and 400+ posters, and so it represents a highly personal and selective snapshot.

References

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