{"id":12978,"date":"2014-10-09T11:21:43","date_gmt":"2014-10-09T10:21:43","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=12978"},"modified":"2017-09-01T07:24:52","modified_gmt":"2017-09-01T06:24:52","slug":"watoc2014-conference-report-emergent-themes","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12978","title":{"rendered":"WATOC2014 Conference report. Emergent themes."},"content":{"rendered":"
\n

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

The first is “embedding<\/em>“, 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.<\/p>\n

Arieh Warshel then addressed the same theme with his own talk entitled Multiscale Modeling of Complex Biological Systems and Processes<\/em>. 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.<\/p>\n

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\u00a0 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.\u00a0By sampling the trajectories, he estimated the intensities<\/em> 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\u00a0taxol. 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<\/em>” 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\u00a0non-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!<\/p>\n

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<\/a> I showed how including a D3-dispersion correction could dramatically change the predicted enantioselectivity of a chiral aldol condensation.[1]<\/a><\/span><\/p>\n

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.<\/p>\n

References<\/h2>\n
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The study reports a molecular knot with the remarkable number of eight crossings. The DOI for the 3D model is 10.5517\/CCDC.CSD.CC1M85Y0\u00a0(or click on the image above). Such\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/01\/085-1021x1024.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":8,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8","url_meta":{"origin":12978,"position":5},"title":"Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog","author":"Henry Rzepa","date":"April 12, 2008","format":false,"excerpt":"Click on the static image to get an active model. 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