Posts Tagged ‘Physics’
Friday, April 13th, 2018
In several posts a year or so ago I considered various suggestions for the most polar neutral molecules, as measured by the dipole moment. A record had been claimed[1] for a synthesized molecule of ~14.1±0.7D. I pushed this to a calculated 21.7D for an admittedly hypothetical and unsynthesized molecule. Here I propose a new family of compounds which have the potential to extend the dipole moment for a formally neutral molecule up still further.

These molecules derive from a well-known class of molecule known as ortho-quinomethides. If the methide part is substituted with an electron donating substituent such as an amino group in 3, a push-pull opportunity now arises, which is strongly driven by aromatisation of the quinomethide ring. This allows one to design “neutral” molecules such as 1 and 2, which now contain respectively two and three rings that will be aromatised by the process. The aromatisation stabilization energy is balanced of course by an opposing increase in energy resulting from charge separation. You can observe that partially aromatising three independent rings as in 2 can drive a great deal of charge separation. One may indeed wonder how much charge separation can be sustained before a triplet instability occurs, driving the molecule back to being neutral. In the case of 2, the wavefunction is in fact stable to such an open shell state, but higher homologues may not be. An aspect worth investing!
Molecule 1 does have some precedent in 3[2] but this system exists as a phenol, having abstracted a proton from an acid and leaving behind the acid anion, as per below for 1. Any attempts to deprotonate this phenol with a superstrong base were unreported.

Unsurprisingly therefore, molecules such as 1 and 2 could be regarded as even more highly potent bases than 3, driven again by further aromatisation. The properties of such a potential superbase will be investigated in the next post.
References
- J. Wudarczyk, G. Papamokos, V. Margaritis, D. Schollmeyer, F. Hinkel, M. Baumgarten, G. Floudas, and K. Müllen, "Hexasubstituted Benzenes with Ultrastrong Dipole Moments", Angewandte Chemie International Edition, vol. 55, pp. 3220-3223, 2016. https://doi.org/10.1002/anie.201508249
- N.R. Candeias, L.F. Veiros, C.A.M. Afonso, and P.M.P. Gois, "Water: A Suitable Medium for the Petasis Borono‐Mannich Reaction", European Journal of Organic Chemistry, vol. 2009, pp. 1859-1863, 2009. https://doi.org/10.1002/ejoc.200900056
Tags:aromatisation stabilization energy, Chemical polarity, chemical properties, Chemistry, Dipole, Electric dipole moment, Electromagnetism, energy, Moment, Nature, Physical quantities, Physics, Potential theory
Posted in Interesting chemistry | 11 Comments »
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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.

Tags:bond dissociation energy, City: Aachen, City: Munich, Dieter Cremer, Edward Valeev, energy, Flavour, Jeremy Harvey, Ken Houk, Leo Radom, Peter Scheiner, Physics, Proceedings, Quark matter, Standard Model, Yitzhak Apeloig
Posted in Interesting chemistry, WATOC reports | No Comments »
Friday, June 2nd, 2017
In 2016, the world heard that gravitational waves had been detected and now a third instance is reported.‡ Given that the data associated with these detections are perhaps amongst the most important instances in recent times, I thought I might take a peek at how it was managed.
- The original report in 2016[1] cited (Ref 116) data as DOI: 10.7935/K5MW2F23.
- The second instance[2] also cites (Ref 89) a DOI: 10.7935/K5H41PBP
- Today† a third instance was reported[3] with data cited (Ref 180) as DOI: 10.7935/K53X84K2
- Sixth instance in 2017[4], Data (Ref 80) DOI: 10.7935/K5B8566F.
- A complete list of events is available at losc.ligo.org/events/
Each of these datasets is beautifully presented, with interactive components making the data very accessible and indeed FAIR. Recently, guidelines for how to cite data have emerged and the FORCE11 organisation has interpreted them for authors, publishers and journal editors, and repository administrators and it is good that the data for these detections has adhered to these principles. When implemented, it will identify e.g. Refs 116, 89 or 180 in the above articles with attributes that will trigger something called EventData with the objective that it retrieves and exposes the activity that occurs around research data objects and brings to light links between publications and data, citations, software, reuse, documentation, etc. At the moment I presume that these three data citations do not yet trigger any EventData. However, there are plans to for both CrossRef and DataCite to implement search procedures to find such EventData. When this service goes live, I intend to explore its potential; watch this space.
I did one other check on each of the datasets:
These download the metadata associated with each dataset. Ideally this could contain a host of information about the data and in particular its creators (i.e. the ORCID of each of the many authors describing how the data was acquired and interpreted). I show just the last as an example in full (the others are similar). Its pretty minimal.

Now there is an area that this otherwise magnificent example of open data sharing could improve upon. In a forthcoming post, I will show how rich metadata population of a chemistry dataset can be used to enhance it and also to trigger EventData as noted above.
‡For a famous chemical controversy involving gravitational fields, see here.
References
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Zhang, M. Zhang, T. Zhang, Y. Zhang, C. Zhao, M. Zhou, Z. Zhou, S. Zhu, X. Zhu, A. Zimmerman, M. Zucker, J. Zweizig, and . , "GW170817: Observation of Gravitational Waves from a Binary Neutron Star Inspiral", Physical Review Letters, vol. 119, 2017. https://doi.org/10.1103/physrevlett.119.161101
Tags:Astronomy, Binary stars, Black holes, famous chemical controversy, General relativity, Gravitational wave, Gravity, Physics, search procedures, Technology/Internet, Wave
Posted in Chemical IT | 1 Comment »
Friday, June 2nd, 2017
In 2016, the world heard that gravitational waves had been detected and now a third instance is reported.‡ Given that the data associated with these detections are perhaps amongst the most important instances in recent times, I thought I might take a peek at how it was managed.
- The original report in 2016[1] cited (Ref 116) data as DOI: 10.7935/K5MW2F23.
- The second instance[2] also cites (Ref 89) a DOI: 10.7935/K5H41PBP
- Today a third instance was reported[3] with data cited (Ref 180) as DOI: 10.7935/K53X84K2
Each of these datasets is beautifully presented, with interactive components making the data very accessible and indeed FAIR. Recently, guidelines for how to cite data have emerged and the FORCE11 organisation has interpreted them for authors, publishers and journal editors, and repository administrators and it is good that the data for these detections has adhered to these principles. When implemented, it will identify e.g. Refs 116, 89 or 180 in the above articles with attributes that will trigger something called EventData with the objective that it retrieves and exposes the activity that occurs around research data objects and brings to light links between publications and data, citations, software, reuse, documentation, etc. At the moment I presume that these three data citations do not yet trigger any EventData. However, there are plans to for both CrossRef and DataCite to implement search procedures to find such EventData. When this service goes live, I intend to explore its potential; watch this space.
I did one other check on each of the datasets:
These download the metadata associated with each dataset. Ideally this could contain a host of information about the data and in particular its creators (i.e. the ORCID of each of the many authors describing how the data was acquired and interpreted). I show just the last as an example in full (the others are similar). Its pretty minimal.

Now there is an area that this otherwise magnificent example of open data sharing could improve upon. In a forthcoming post, I will show how rich metadata population of a chemistry dataset can be used to enhance it and also to trigger EventData as noted above.
‡For a famous chemical controversy involving gravitational fields, see here.
References
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- B. Abbott, R. Abbott, T. Abbott, F. Acernese, K. Ackley, C. Adams, T. Adams, P. Addesso, R. Adhikari, V. Adya, C. Affeldt, M. Afrough, B. Agarwal, M. Agathos, K. Agatsuma, N. Aggarwal, O. Aguiar, L. Aiello, A. Ain, P. Ajith, B. Allen, G. Allen, A. Allocca, P. Altin, A. Amato, A. Ananyeva, S. Anderson, W. Anderson, S. Antier, S. Appert, K. Arai, M. Araya, J. Areeda, N. Arnaud, K. Arun, S. Ascenzi, G. Ashton, M. Ast, S. Aston, P. Astone, P. Aufmuth, C. Aulbert, K. AultONeal, A. Avila-Alvarez, S. Babak, P. Bacon, M. Bader, S. Bae, P. Baker, F. Baldaccini, G. Ballardin, S. Ballmer, S. Banagiri, J. Barayoga, S. Barclay, B. Barish, D. Barker, F. Barone, B. Barr, L. Barsotti, M. Barsuglia, D. Barta, J. Bartlett, I. Bartos, R. Bassiri, A. Basti, J. Batch, C. Baune, M. Bawaj, M. Bazzan, B. Bécsy, C. Beer, M. Bejger, I. Belahcene, A. Bell, B. Berger, G. Bergmann, C. Berry, D. Bersanetti, A. Bertolini, J. Betzwieser, S. Bhagwat, R. Bhandare, I. Bilenko, G. Billingsley, C. Billman, J. Birch, I.A. Birney, O. Birnholtz, S. Biscans, A. Bisht, M. Bitossi, C. Biwer, M. Bizouard, J. Blackburn, J. Blackman, C. Blair, D. Blair, R. Blair, S. Bloemen, O. Bock, N. Bode, M. Boer, G. Bogaert, A. Bohe, F. Bondu, R. Bonnand, B. Boom, R. Bork, V. Boschi, S. Bose, Y. Bouffanais, A. Bozzi, C. Bradaschia, P. Brady, V. Braginsky, M. Branchesi, J. Brau, T. Briant, A. Brillet, M. Brinkmann, V. Brisson, P. Brockill, J. Broida, A. Brooks, D. Brown, D. Brown, N. Brown, S. Brunett, C. Buchanan, A. Buikema, T. Bulik, H. Bulten, A. Buonanno, D. Buskulic, C. Buy, R. Byer, M. Cabero, L. Cadonati, G. Cagnoli, C. Cahillane, J. Calderón Bustillo, T. Callister, E. Calloni, J. Camp, M. Canepa, P. Canizares, K. Cannon, H. Cao, J. Cao, C. Capano, E. Capocasa, F. Carbognani, S. Caride, M. Carney, J. Casanueva Diaz, C. Casentini, S. Caudill, M. Cavaglià, F. Cavalier, R. Cavalieri, G. Cella, C. Cepeda, L. Cerboni Baiardi, G. Cerretani, E. Cesarini, S. Chamberlin, M. Chan, S. Chao, P. Charlton, E. 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Hough, E. Houston, E. Howell, Y. Hu, E. Huerta, D. Huet, B. Hughey, S. Husa, S. Huttner, T. Huynh-Dinh, N. Indik, D. Ingram, R. Inta, G. Intini, H. Isa, J. Isac, M. Isi, B. Iyer, K. Izumi, T. Jacqmin, K. Jani, P. Jaranowski, S. Jawahar, F. Jiménez-Forteza, W. Johnson, N. Johnson-McDaniel, D. Jones, R. Jones, R. Jonker, L. Ju, J. Junker, C. Kalaghatgi, V. Kalogera, S. Kandhasamy, G. Kang, J. Kanner, S. Karki, K. Karvinen, M. Kasprzack, M. Katolik, E. Katsavounidis, W. Katzman, S. Kaufer, K. Kawabe, F. Kéfélian, D. Keitel, A. Kemball, R. Kennedy, C. Kent, J. Key, F. Khalili, I. Khan, S. Khan, Z. Khan, E. Khazanov, N. Kijbunchoo, C. Kim, J. Kim, W. Kim, W. Kim, Y. Kim, S. Kimbrell, E. King, P. King, R. Kirchhoff, J. Kissel, L. Kleybolte, S. Klimenko, P. Koch, S. Koehlenbeck, S. Koley, V. Kondrashov, A. Kontos, M. Korobko, W. Korth, I. Kowalska, D. Kozak, C. Krämer, V. Kringel, B. Krishnan, A. Królak, G. Kuehn, P. Kumar, R. Kumar, S. Kumar, L. Kuo, A. Kutynia, S. Kwang, B. Lackey, K. Lai, M. Landry, R. Lang, J. Lange, B. Lantz, R. Lanza, A. Lartaux-Vollard, P. Lasky, M. Laxen, A. Lazzarini, C. Lazzaro, P. Leaci, S. Leavey, C. Lee, H. Lee, H. Lee, H. Lee, K. Lee, J. Lehmann, A. Lenon, M. Leonardi, N. Leroy, N. Letendre, Y. Levin, T. Li, A. Libson, T. Littenberg, J. Liu, R. Lo, N. Lockerbie, L. London, J. Lord, M. Lorenzini, V. Loriette, M. Lormand, G. Losurdo, J. Lough, G. Lovelace, H. Lück, D. Lumaca, A. Lundgren, R. Lynch, Y. Ma, S. Macfoy, B. Machenschalk, M. MacInnis, D. Macleod, I. Magaña Hernandez, F. Magaña-Sandoval, L. Magaña Zertuche, R. Magee, E. Majorana, I. Maksimovic, N. Man, V. Mandic, V. Mangano, G. Mansell, M. Manske, M. Mantovani, F. Marchesoni, F. Marion, S. Márka, Z. Márka, C. Markakis, A. Markosyan, E. Maros, F. Martelli, L. Martellini, I. Martin, D. Martynov, J. Marx, K. Mason, A. Masserot, T. Massinger, M. Masso-Reid, S. Mastrogiovanni, A. Matas, F. Matichard, L. Matone, N. Mavalvala, R. Mayani, N. Mazumder, R. McCarthy, D. McClelland, S. McCormick, L. McCuller, S. McGuire, G. McIntyre, J. McIver, D. McManus, T. McRae, S. McWilliams, D. Meacher, G. Meadors, J. Meidam, E. Mejuto-Villa, A. Melatos, G. Mendell, R. Mercer, E. Merilh, M. Merzougui, S. Meshkov, C. Messenger, C. Messick, R. Metzdorff, P. Meyers, F. Mezzani, H. Miao, C. Michel, H. Middleton, E. Mikhailov, L. Milano, A. Miller, A. Miller, B. Miller, J. Miller, M. Millhouse, O. Minazzoli, Y. Minenkov, J. Ming, C. Mishra, S. Mitra, V. Mitrofanov, G. Mitselmakher, R. Mittleman, A. Moggi, M. Mohan, S. Mohapatra, M. Montani, B. Moore, C. Moore, D. Moraru, G. Moreno, S. Morriss, B. Mours, C. Mow-Lowry, G. Mueller, A. Muir, A. Mukherjee, D. Mukherjee, S. Mukherjee, N. Mukund, A. Mullavey, J. Munch, E. Muniz, P. Murray, K. Napier, I. Nardecchia, L. Naticchioni, R. Nayak, G. Nelemans, T. Nelson, M. Neri, M. Nery, A. Neunzert, J. Newport, G. Newton, K. Ng, T. Nguyen, D. Nichols, A. Nielsen, S. Nissanke, A. Nitz, A. Noack, F. Nocera, D. Nolting, M. Normandin, L. Nuttall, J. Oberling, E. Ochsner, E. Oelker, G. Ogin, J. Oh, S. Oh, F. Ohme, M. Oliver, P. Oppermann, R.J. Oram, B. O’Reilly, R. Ormiston, L. Ortega, R. O’Shaughnessy, D. Ottaway, H. Overmier, B. Owen, A. Pace, J. Page, M. Page, A. Pai, S. Pai, J. Palamos, O. Palashov, C. Palomba, A. Pal-Singh, H. Pan, B. Pang, P. Pang, C. Pankow, F. Pannarale, B. Pant, F. Paoletti, A. Paoli, M. Papa, H. Paris, W. Parker, D. Pascucci, A. Pasqualetti, R. Passaquieti, D. Passuello, B. Patricelli, B. Pearlstone, M. Pedraza, R. Pedurand, L. Pekowsky, A. Pele, S. Penn, C. Perez, A. Perreca, L. Perri, H. Pfeiffer, M. Phelps, O. Piccinni, M. Pichot, F. Piergiovanni, V. Pierro, G. Pillant, L. Pinard, I. Pinto, M. Pitkin, R. Poggiani, P. Popolizio, E. Porter, A. Post, J. Powell, J. Prasad, J. Pratt, V. Predoi, T. Prestegard, M. Prijatelj, M. Principe, S. Privitera, G. Prodi, L. Prokhorov, O. Puncken, M. Punturo, P. Puppo, M. Pürrer, H. Qi, J. Qin, S. Qiu, V. Quetschke, E. Quintero, R. Quitzow-James, F. Raab, D. Rabeling, H. Radkins, P. Raffai, S. Raja, C. Rajan, M. Rakhmanov, K. Ramirez, P. Rapagnani, V. Raymond, M. Razzano, J. Read, T. Regimbau, L. Rei, S. Reid, D. Reitze, H. Rew, S. Reyes, F. Ricci, P. Ricker, S. Rieger, K. Riles, M. Rizzo, N. Robertson, R. Robie, F. Robinet, A. Rocchi, L. Rolland, J. Rollins, V. Roma, J. Romano, R. Romano, C. Romel, J. Romie, D. Rosińska, M. Ross, S. Rowan, A. Rüdiger, P. Ruggi, K. Ryan, M. Rynge, S. Sachdev, T. Sadecki, L. Sadeghian, M. Sakellariadou, L. Salconi, M. Saleem, F. Salemi, A. Samajdar, L. Sammut, L. Sampson, E. Sanchez, V. Sandberg, B. Sandeen, J. Sanders, B. Sassolas, B. Sathyaprakash, P. Saulson, O. Sauter, R. Savage, A. Sawadsky, P. Schale, J. Scheuer, E. Schmidt, J. Schmidt, P. Schmidt, R. Schnabel, R. Schofield, A. Schönbeck, E. Schreiber, D. Schuette, B. Schulte, B. Schutz, S. Schwalbe, J. Scott, S. Scott, E. Seidel, D. Sellers, A. Sengupta, D. Sentenac, V. Sequino, A. Sergeev, D. Shaddock, T. Shaffer, A. Shah, M. Shahriar, L. Shao, B. Shapiro, P. Shawhan, A. Sheperd, D. Shoemaker, D. Shoemaker, K. Siellez, X. Siemens, M. Sieniawska, D. Sigg, A. Silva, A. Singer, L. Singer, A. Singh, R. Singh, A. Singhal, A. Sintes, B. Slagmolen, B. Smith, J. Smith, R. Smith, E. Son, J. Sonnenberg, B. Sorazu, F. Sorrentino, T. Souradeep, A. Spencer, A. Srivastava, A. Staley, M. Steinke, J. Steinlechner, S. Steinlechner, D. Steinmeyer, B. Stephens, S. Stevenson, R. Stone, K. Strain, G. Stratta, S. Strigin, R. Sturani, A. Stuver, T. Summerscales, L. Sun, S. Sunil, P. Sutton, B. Swinkels, M. Szczepańczyk, M. Tacca, D. Talukder, D. Tanner, M. Tápai, A. Taracchini, J. Taylor, R. Taylor, T. Theeg, E. Thomas, M. Thomas, P. Thomas, K. Thorne, K. Thorne, E. Thrane, S. Tiwari, V. Tiwari, K. Tokmakov, K. Toland, M. Tonelli, Z. Tornasi, C. Torrie, D. Töyrä, F. Travasso, G. Traylor, D. Trifirò, J. Trinastic, M. Tringali, L. Trozzo, K. Tsang, M. Tse, R. Tso, D. Tuyenbayev, K. Ueno, D. Ugolini, C. Unnikrishnan, A. Urban, S. Usman, K. Vahi, H. Vahlbruch, G. Vajente, G. Valdes, M. Vallisneri, N. van Bakel, M. van Beuzekom, J. van den Brand, C. Van Den Broeck, D. Vander-Hyde, L. van der Schaaf, J. van Heijningen, A. van Veggel, M. Vardaro, V. Varma, S. Vass, M. Vasúth, A. Vecchio, G. Vedovato, J. Veitch, P. Veitch, K. Venkateswara, G. Venugopalan, D. Verkindt, F. Vetrano, A. Viceré, A. Viets, S. Vinciguerra, D. Vine, J. Vinet, S. Vitale, T. Vo, H. Vocca, C. Vorvick, D. Voss, W. Vousden, S. Vyatchanin, A. Wade, L. Wade, M. Wade, R. Wald, R. Walet, M. Walker, L. Wallace, S. Walsh, G. Wang, H. Wang, J. Wang, M. Wang, Y. Wang, Y. Wang, R. Ward, J. Warner, M. Was, J. Watchi, B. Weaver, L. Wei, M. Weinert, A. Weinstein, R. Weiss, L. Wen, E. Wessel, P. Weßels, T. Westphal, K. Wette, J. Whelan, B. Whiting, C. Whittle, D. Williams, R. Williams, A. Williamson, J. Willis, B. Willke, M. Wimmer, W. Winkler, C. Wipf, H. Wittel, G. Woan, J. Woehler, J. Wofford, K. Wong, J. Worden, J. Wright, D. Wu, G. Wu, W. Yam, H. Yamamoto, C. Yancey, M. Yap, H. Yu, H. Yu, M. Yvert, A. Zadrożny, M. Zanolin, T. Zelenova, J. Zendri, M. Zevin, L. Zhang, M. Zhang, T. Zhang, Y. Zhang, C. Zhao, M. Zhou, Z. Zhou, X. Zhu, A. Zimmerman, M. Zucker, J. Zweizig, and . , "GW170104: Observation of a 50-Solar-Mass Binary Black Hole Coalescence at Redshift 0.2", Physical Review Letters, vol. 118, 2017. https://doi.org/10.1103/physrevlett.118.221101
Tags:Astronomy, Binary stars, Black holes, famous chemical controversy, General relativity, Gravitational wave, Gravity, Physics, search procedures, Technology/Internet, Wave
Posted in Chemical IT | 1 Comment »
Sunday, March 5th, 2017
Cyclobutadiene is one of those small iconic molecules, the transience and instability of which was explained theoretically long before it was actually detected in 1965.[1] Given that instability, I was intrigued as to how many crystal structures might have been reported for this ring system, along with the rather more stable congener cyclo-octatetraene. Here is what I found.
The Conquest search query shown (with no disorder, no errors and R < 0.1 also specified). 
There are 23 instances (February 2017 database; see DOI: 10.14469/hpc/2231 for search query) of the supposedly unstable cyclobutadiene motif!

The three clusters deserve explanations. The orange cluster reveals a long C-C bond (rather longer than normal C-C bonds), accompanied by short C=C bonds, as indicated by the valence bond form shown below. Take particular note that the arrow connecting the two forms is NOT a resonance arrow but an equilibrium arrow. The “bond shifting” is not fast but slow, allowing long and short bonds to be measured in a crystal structure.

The rather larger blue cluster exhibits much more equal bonds. These arise from the presence of “push-pull” substituents on the ring which serve to delocalise the unfavourable cyclobutadiene ring and hence decrease the unfavourable anti-aromaticity. A typical example is shown below (EACBUT):

The small red cluster shows a long C=C bond and a short C-C bond! I have commented previously on apparently abnormally long C=C bonds, which in fact all turned out to be errors, and I suspect the same is true here. The bond orders in the indexing in the CSD data base have probably been mis-assigned, as per below for GANBII;

The Conquest search query is shown (with no disorder, no errors and R < 0.1 specified) for the 8-ring, which further specifies a torsion angle about a C-C bond to determine how planar the ring might be.

The “normal” cluster in the top left exhibits long C-C bonds and short C=C bonds. The colour code indicates how planar the ring is (red-blue spectrum = twisted ⇒ planar). The majority of examples are twisted about the C-C bond(s), but there are a few interesting examples that are not, as shown by the blue dots. There are only a few “bond-equalised” examples in the centre; perhaps “push-pull” induced equalisation is more difficult or perhaps few examples have been made?

The members of the red cluster in the bottom right all reveal short “C-C” bonds and long “C=C” bonds. Intriguingly they all also have low values of the torsion about one C-C bond (although not always about all four C-C bonds). A typical example (BAQVUK, DOI: 10.5517/CC4GWWB ) is shown below. These all need careful inspection and possibly reversal of the C-C and C=C indexing.

It was interesting to discover how many crystalline examples of this archetypal “unstable” cyclobutadiene motif have been made, and the means by which some of them at least have been stabilized. In the more abundant cyclo-octatetraene system, I learnt that one has to be cautious about blindly accepting the bond order designations in the database. Perhaps we might learn here that some of these have indeed been re-assigned in the next release of the database.
References
- L. Watts, J.D. Fitzpatrick, and R. Pettit, "Cyclobutadiene", Journal of the American Chemical Society, vol. 87, pp. 3253-3254, 1965. https://doi.org/10.1021/ja01092a049
Tags:antiaromaticity, Chemistry, cyclobutadiene, Instability, Nature, Physical organic chemistry, Physics, search query
Posted in crystal_structure_mining | 4 Comments »
Sunday, March 5th, 2017
Cyclobutadiene is one of those small iconic molecules, the transience and instability of which was explained theoretically long before it was actually detected in 1965.[1] Given that instability, I was intrigued as to how many crystal structures might have been reported for this ring system, along with the rather more stable congener cyclo-octatetraene. Here is what I found.
The Conquest search query shown (with no disorder, no errors and R < 0.1 also specified). 
There are 23 instances (February 2017 database; see DOI: 10.14469/hpc/2231 for search query) of the supposedly unstable cyclobutadiene motif!

The three clusters deserve explanations. The orange cluster reveals a long C-C bond (rather longer than normal C-C bonds), accompanied by short C=C bonds, as indicated by the valence bond form shown below. Take particular note that the arrow connecting the two forms is NOT a resonance arrow but an equilibrium arrow. The “bond shifting” is not fast but slow, allowing long and short bonds to be measured in a crystal structure.

The rather larger blue cluster exhibits much more equal bonds. These arise from the presence of “push-pull” substituents on the ring which serve to delocalise the unfavourable cyclobutadiene ring and hence decrease the unfavourable anti-aromaticity. A typical example is shown below (EACBUT):

The small red cluster shows a long C=C bond and a short C-C bond! I have commented previously on apparently abnormally long C=C bonds, which in fact all turned out to be errors, and I suspect the same is true here. The bond orders in the indexing in the CSD data base have probably been mis-assigned, as per below for GANBII;

The Conquest search query is shown (with no disorder, no errors and R < 0.1 specified) for the 8-ring, which further specifies a torsion angle about a C-C bond to determine how planar the ring might be.

The “normal” cluster in the top left exhibits long C-C bonds and short C=C bonds. The colour code indicates how planar the ring is (red-blue spectrum = twisted ⇒ planar). The majority of examples are twisted about the C-C bond(s), but there are a few interesting examples that are not, as shown by the blue dots. There are only a few “bond-equalised” examples in the centre; perhaps “push-pull” induced equalisation is more difficult or perhaps few examples have been made?

The members of the red cluster in the bottom right all reveal short “C-C” bonds and long “C=C” bonds. Intriguingly they all also have low values of the torsion about one C-C bond (although not always about all four C-C bonds). A typical example (BAQVUK, DOI: 10.5517/CC4GWWB ) is shown below. These all need careful inspection and possibly reversal of the C-C and C=C indexing.

It was interesting to discover how many crystalline examples of this archetypal “unstable” cyclobutadiene motif have been made, and the means by which some of them at least have been stabilized. In the more abundant cyclo-octatetraene system, I learnt that one has to be cautious about blindly accepting the bond order designations in the database. Perhaps we might learn here that some of these have indeed been re-assigned in the next release of the database.
References
- L. Watts, J.D. Fitzpatrick, and R. Pettit, "Cyclobutadiene", Journal of the American Chemical Society, vol. 87, pp. 3253-3254, 1965. https://doi.org/10.1021/ja01092a049
Tags:antiaromaticity, Chemistry, cyclobutadiene, Instability, Nature, Physical organic chemistry, Physics, search query
Posted in crystal_structure_mining | 4 Comments »
Wednesday, February 15th, 2017
This post arose from a comment attached to the post on Na2He and relating to peculiar and rare topological features of the electron density in molecules called non-nuclear attractors. This set me thinking about other molecules that might exhibit this and one of these is shown below.
The topology of the electron density is described by just four basic types, designed formally by the notation [3,-3], [3,-1], [3,1] and [3,3] and more colloquially by the terms nuclear attractor (NNA), line (or bond) critical point, a ring critical point and a cage critical point respectively. Mostly, the nuclear critical points coincide exactly with the actual nuclear positions, but more rarely these points are not found centered at a nucleus. It was such an NNA that was suggested as a comment on the post on Na2He. There I replied that another example of an NNA is to be found in H3+ and so its a short step to take a look at H42+ in a tetrahedral arrangement (DOI: 10.14469/hpc/2165). Since only two electrons are available for bonding, it is tempting to represent it as below, with dashed partial bonds connnecting the six edges of the tetrahedron and is associated with real normal vibrational modes; ν 416, 1490 and 1861 cm-1. A brief search on Scifinder, which appears to reference this species as hydrogen, ion (H42+), does not identify any publications associated with it (there are studies on H41+ however); if any reader here knows of any discussion please alert us!

Analysing the density however gives a different result. A NNA is located at the centre of the tetrahedron and a line (bond) critical point connects this to each of the four hydrogen nuclei. This result is similar to the obtained for H3+. It is rather odd that these non-nuclear attractors have not entered into the vocabulary used to describe the bonding in simple molecules, but this picture is certainly different from the more empirical dashed lines between the four nuclei that one is instinctively drawn to use (above).

The ELF analysis (performed using multiWFN) is more interesting. The nuclear basins associated with the hydrogens reveal each has 0.425e, but the central one (green below) has its own basin with 0.301e.

The NICS value associated with the non-nuclear attractor is -27 ppm, which is indicative of strong spherical aromaticity.
All of which goes to show that even the simplest of molecular species may still have properties that are unexpected or certainly not well-known!
Tags:Attractor, brief search, Chemistry, Electron, Electron density, Hydrogen, Molecule, Nature, Physics, Quantum chemistry
Posted in Interesting chemistry | 11 Comments »
Saturday, February 11th, 2017
On February 6th I was alerted to this intriguing article[1] by a phone call, made 55 minutes before the article embargo was due to be released. Gizmodo wanted to know if I could provide an (almost)† instant‡ quote. After a few days, this report of a stable compound of helium and sodium still seems impressive to me and I now impart a few more thoughts here.
The discovery originates from 17 authors based in 17 different institutions, an impressive illustration of global science and cooperation. I illustrate with this diagram, to be found not in the main article body but in its supporting information and for which the caption reads:

Computed charge density (eÅ-3) of Na2He at 300 GPa, plotted in the [110] plane of the conventional cell. The color bar gives the scale.
The nuclei carry of course the greatest charge density, but the density labelled “2e” is not nuclear-centered. This is typical of species known as electrides, where positive cations are associated with just electrons acting as the counter-anion and about which there was an extensive debate earlier on this blog. There is much discussion in the article[1] about the essential role of the He atoms in bringing about the formation of such an electride, an effect that is summarised in a second diagram also found in the supporting information:

I found myself thinking that it would be great to have the first diagram represented as a movie, evolving as the pressure is increased from say ambient to 300 GPa, and presumably showing the “2e” feature (which means diamagnetic electrons) forming as the pressure increases. Would their evolution be abrupt (a step change) or gradual as the pressure increases and the interatomic distances all decrease? As I understand it, this chemical phenomenon is due not so much to the usual coulombic attraction between positive nuclei and negative charge density from the electronic wavefunction leading to e.g. covalent bonds, but to electron repulsions induced by decreasing nuclear separations resulting in electride-like ionisation and hence electron localisation into the “interstitial cavities” of the lattice. Without pressure, you would just have sodium and helium atoms!
The urge to obtain this intriguing electronic wavefunction for myself now appeared (wavefunctions are rarely if ever included in supporting information). To do this you must have atom coordinates available, But such data was not to be found in the supporting information. It was eventually tracked down (by a crystallographer; thanks Andrew!) to the caption in Figure 2.

However, you probably do need to be a crystallographer to convert this data into a set of coordinates. This was done and is here deposited as a CIF file for you to play with if you wish (DOI:10.14469/hpc/2154)[2]. I have reduced the packing of the unit cell obtained from this CIF file (198 atoms) to just 60 and you can enjoy them by clicking on the diagram below. I should point out that if one uses a program that can recognise the periodic lattice such as Crystal (used in the article discussed here), there is no need to make such reductions, but in this instance I wanted to use a program such as Gaussian in discrete (non-periodic) mode, for which the calculation (B3LYP/Def2-SVPD) has DOI: 10.14469/hpc/2156[3] and where you can also find a wavefunction file to play with if you wish.

Click for 3D model
An ELF analysis for this non-periodic wavefunction looks as below. The ELF basins labelled “2e” located in the centre of the cube show an integrated electron population of ~1.9e and correspond to the localised electron pairs noted in the article above.

Click for 3D
The basins on the boundaries of this non-periodic unit show reduced integrations (red arrows below, 0.08 – 1.7e) and are artefacts of the non-periodic approximation introduced.

The ionization into an electride is brought about by the close proximity of the atoms as induced by high pressure. Releasing the pressure would allow the ionized electrons to re-attach themselves to the valence shell of the sodium atoms, thus destroying the unique properties of the system. It is certainly true that this system challenges our normal concepts of what a molecule is. The presence of He is essential and yet its electrons are hardly involved in the re-organised wavefunction. I cannot wait for more examples to be discovered!
†To meet the 55 minute deadline, I was given about 15 minutes thinking time!
‡Instant responses on social media now seem a sine qua non of the political world, so why not the scientific one?!
References
- X. Dong, A.R. Oganov, A.F. Goncharov, E. Stavrou, S. Lobanov, G. Saleh, G. Qian, Q. Zhu, C. Gatti, V.L. Deringer, R. Dronskowski, X. Zhou, V.B. Prakapenka, Z. Konôpková, I.A. Popov, A.I. Boldyrev, and H. Wang, "A stable compound of helium and sodium at high pressure", Nature Chemistry, vol. 9, pp. 440-445, 2017. https://doi.org/10.1038/nchem.2716
- H. Rzepa, "Na2He: a stable compound of helium and sodium at high pressure.", 2017. https://doi.org/10.14469/hpc/2154
- H. Rzepa, "He20Na40", 2017. https://doi.org/10.14469/hpc/2156
Tags:10.1038, Atom, Chemical elements, chemical phenomenon, Chemistry, Company: P. Acucar-CBD, Electride, Electron, Food Retail & Distribution - NEC, helium, Hydrogen, Matter, Oxygen, Physics, social media
Posted in Bond slam, crystal_structure_mining, Interesting chemistry | 11 Comments »
Saturday, December 24th, 2016
The previous posts produced discussion about the dipole moments of highly polar molecules. Here to produce some reference points for further discussion I look at the dipole moment of glycine, the classic zwitterion (an internal ion-pair).
Dielectric relaxation studies of glycine–water mixtures yield values that range from 15.7D[1] to 11.9D[2] although these have to be derived using various approximations and assumptions for up to 4 independent Debye processes. Before proceeding to calculations, I looked at the properties of ionized amino acids in the solid state, using the following search query for the Cambridge structure database (CSD).

The distance measures hydrogen bonds to the carboxylate oxygens and the torsion their orientation. The O…H hydrogen bond distances vary between 1.7-1.85Å, which are short. The orientation of the hydrogen bond can be to the in-plane oxygen “σ-lone pair” (torsion 0 or 180°) and also an out-of-plane ~π form (torsion ~60-90°).

In aqueous solution, it is normally assumed that glycine sustains five such strong H-bonds (three to the H3N+ group and two[3] to the carboxylate anion), forming a polarised “salt bridge” across the ion-pair. Two model types were subjected to calculation using ωB97XD/Def2-TZVPP/SCRF=water. Aqueous glycine without any added explicit water molecules yields a dipole moment of 12.9D (DOI: 10.14469/hpc/2000), which is within the range noted above.‡

The solvated form is shown below, in one specific conformation of the three studied (ωB97XD/Def2-TZVPP/SCRF=water). The calculated O…H hydrogen bond lengths fall into the range revealed from crystal structures. The calculated dipole moments range from 12.6 (DOI: 10.14469/hpc/2007), 15.3 (DOI: 10.14469/hpc/2006) and 14.9D (DOI: 10.14469/hpc/2005), which is a modest increase over the model with no explicit water molecules. The actual dipole is of course a Boltzmann average over these and other as yet unexplored conformations, as well as other values for the number of water molecules.

Given the difficulties in interpreting the dipole moment of a complex Debye system such as hydrated glycine, the agreement between the limited range of solvated models and the measured values seems reasonable, and provides at least some measure of “calibration” for the polar molecules commented on previously.
‡Optimized with the solvent field on. If a vacuum model is used, the proton transfers from the N to the O.
References
- M.W. Aaron, and E.H. Grant, "Dielectric relaxation of glycine in water", Transactions of the Faraday Society, vol. 59, pp. 85, 1963. https://doi.org/10.1039/tf9635900085
- T. Sato, R. Buchner, . Fernandez, A. Chiba, and W. Kunz, "Dielectric relaxation spectroscopy of aqueous amino acid solutions: dynamics and interactions in aqueous glycine", Journal of Molecular Liquids, vol. 117, pp. 93-98, 2005. https://doi.org/10.1016/j.molliq.2004.08.001
- T. Shikata, "Dielectric Relaxation Behavior of Glycine Betaine in Aqueous Solution", The Journal of Physical Chemistry A, vol. 106, pp. 7664-7670, 2002. https://doi.org/10.1021/jp020957j
Tags:aqueous solution, Chemical polarity, Chemistry, dielectric, Dipole, Electric dipole moment, Electromagnetism, Magnetism, Moment, Nature, Physical quantities, Physics, Potential theory, zwitterion
Posted in crystal_structure_mining, Interesting chemistry | 1 Comment »
Thursday, September 1st, 2016
Bromoallene is a pretty simple molecule, with two non-equivalent double bonds. How might it react with an electrophile, say dimethyldioxirane (DMDO) to form an epoxide?[1] Here I explore the difference between two different and very simple approaches to predicting its reactivity. 
Both approaches rely on the properties of the reactant and use two types of molecule orbitals derived from its electronic wavefunction. The first of these is very well-known as the molecular orbital (MO), which has the property that it tends to delocalise over all the contributing atoms (the “molecule”). MOs are often used in this context; the highest energy occupied MO is thought of as being associated with the most nucleophilic (electron donating) regions of the molecule and so such a HOMO would be expected to predict the region of nucleophilic attack. The second is known as the natural bond orbital (NBO), which is evaluated in a manner that tends to localise it on bonds (the functional groups or reaction centres) and atom centres. What do these respective orbitals reveal for bromoallene?
| The MOs |
| HOMO, -0.3380 |
HOMO-1, -0.3692 au |
 Click for 3D |
 Click for 3D |
| The NBOs |
| HONBO, -0.3769 |
HONBO-2, -0.3898 |
 Click for 3D |
 Click for 3D |
The table above shows the energies (in Hartrees) of the four relevant orbitals. The less negative (less stable) the orbital, the more nucleophilic it is. The (heavily) delocalized HOMO is located on the C=C bond bond carrying the C-Br bond, Δ1,2 alkene, but it also has a large component on the Br. The more stable HOMO-1 is located on the C=C bond located away from the Br, the Δ2,3 alkene and also with a (different type of) component on the Br.
In contrast, the HONBO is located on the Δ2,3 alkene and it is the HONBO-2 that is on the Δ1,2 alkene. Both these orbitals have very little “leakage” onto other atoms, they are almost completely localised.
Well, now we have a problem since these two analyses lead to diametrically opposing predictions! So what does experiment say? A recent article[1] addresses this issue by isolating the initially formed epoxide from reaction with DMDO and characterising it using crystallography. But here comes the catch; such isolation only proved possible if the allene was also substituted with large sterically bulky groups such as t-butyl or adamantyl. And the isolated product was the Δ1,2 epoxide. So does that mean that the MO method was correct and the NBO method wrong? Well, not necessarily. Those large groups play an additional role via steric effects. To factor in such effects one has to look at the transition state model for the reaction rather than depending purely on the reactant properties. And the steric effects in this case appear to win out over the electronic ones.[1]
The Klopman[2]-Salem[3] equation (shown in very simplified, and original, form below for just the covalent term) casts some light on what is going on. This term is a double summation over occupied/unoccupied (donor-acceptor) orbital interactions, involving the coefficients of the orbitals (the overlap integrals in effect) in the numerator and the energy difference between the occupied/unoccupied orbital pair as denominator.

Performing such a double summation is rarely attempted; instead the equation is reduced to just one single term involving the donor of highest energy and the acceptor of lowest energy, ensuring the energy difference is a minimum and hence the term itself is (potentially) the largest in the summation. There is still the issue of the orbital coefficients, and here we get to the crux of the difference between the use of MOs and NBOs. You can see by inspection that the two π-MOs for bromoallene have different coefficients on the two atoms of interest, the two carbons of the double bond. One really has to evaluate the size of this term in the summation by using quantitative values for the respective coefficients and to very probably include the further terms in the summation for any other orbitals which also have significantly non-zero coefficients on these two atoms. But with the NBOs, the localisation procedure used to derive them has reduced the coefficients to just the carbon atoms and effectively no other atoms; all the other terms in the double summation in effect do drop out entirely. So with NBOs, the only number that matters is the energy difference between the occupied/empty orbitals (the denominator). But since the acceptor (the electrophile, DMDO in this case) is the same for both regiochemistries, things reduce even further to just comparing the donor energies for the two alternatives (Table above). The higher/less stable of these will have the greater contribution in the Klopman-Salem equation.
This little molecule teaches the important lesson that electronic and steric effects both play a role in directing reactions, and in this system they may well oppose each other. Simple interpretations based on reactant orbitals may give only a partial and even potentially misleading answer.
References
- D. Christopher Braddock, A. Mahtey, H.S. Rzepa, and A.J.P. White, "Stable bromoallene oxides", Chemical Communications, vol. 52, pp. 11219-11222, 2016. https://doi.org/10.1039/c6cc06395k
- G. Klopman, "Chemical reactivity and the concept of charge- and frontier-controlled reactions", Journal of the American Chemical Society, vol. 90, pp. 223-234, 1968. https://doi.org/10.1021/ja01004a002
- L. Salem, "Intermolecular orbital theory of the interaction between conjugated systems. I. General theory", Journal of the American Chemical Society, vol. 90, pp. 543-552, 1968. https://doi.org/10.1021/ja01005a001
Tags:chemical bonding, chemical reaction, Chemistry, Delocalized electron, double bond, energy, energy difference, HOMO/LUMO, lowest energy, Molecular orbital, Natural bond orbital, Nature, Physics, Quantum chemistry, stable HOMO-1
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