From owner-chemistry@ccl.net Sun Sep 13 00:57:01 2015 From: "Susi Lehtola susi.lehtola===alumni.helsinki.fi" To: CCL Subject: CCL: net atomic charges Message-Id: <-51733-150912231045-15925-I0wan5JuQk9EydnR84yNPA##server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Sat, 12 Sep 2015 20:10:32 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola]|[alumni.helsinki.fi] On 09/12/2015 01:23 PM, Thomas Manz thomasamanz#%#gmail.com wrote: > But my overall point is that it is possible to make scientific study > of atomic population analysis methods and the notion that these are > arbitrary is not accurate. Yes, there are different schemes and > methodologies, but these are constructed for defined reasons not > arbitrary ones. Yes, atomic population analyses may be useful. As I was trying to say in my earlier message, there are indeed a number of valid schemes for determining partial charges, each of which are justified in their own domain. But, every scheme gives a different answer, and a big reason to this is that atomic partial charges are not observables. Sure, you can write down a simplified model (like a MM force field) and introduce variables that represent partial charges, but they carry a certain ambiguousness to them. The same can be said about orbital analysis, although we pretty much know that orbitals are not real since they represent a fundamentally one-particle picture, and since the Hamiltonian is a two-electron operator, orbitals cannot represent the whole truth. Also, orbitals are not observables. There is a large amount of ways to achieve localization of orbitals: Edmiston-Ruedenberg, Foster-Boys and its newer variant, the fourth moment localization method, the von Niessen method, as well as Pipek-Mezey and its variants [some of which we recently proposed in JCTC 10, 642 (2014)]. No scheme is a priori better than the other, since none are really physical. > To put this in perspective would most quantum chemists describe > different exchange-correlation functionals as "arbitrary"? Would most > quantum chemists say "constructing exchange-correlation functionals > is an arbitrary process"? There shouldn't be a double standard here. > If we are not going to describe exchange-correlation functionals as > arbitrary we shouldn't use this term for atomic population analysis > methods (except those which truly are arbitrary because they are > malformed such as lacking a basis set limit or having other gross > defects). But here there is a *huge* difference. We *know* that there is *an exact functional*, whereas for atomic partial charges or orbital localization we know the opposite result, that there can't be one because partial charges and orbitals aren't observable. The reason why there is a zoo of functionals is that we simply don't know the form of the exact functionals, but we can derive its behavior in model systems (LDA and the ab initio functionals), or present an educated guess for its form and optimize the model parameters by minimizing deviation from ab initio or experimental data (e.g. the Minnesota zoo, or the B97 style functionals). -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola*_*alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA ----------------------------------------------------------------------- From owner-chemistry@ccl.net Sun Sep 13 03:07:01 2015 From: "Peeter Burk peeter.burk::ut.ee" To: CCL Subject: CCL: atomic population analysis Message-Id: <-51734-150913023541-16163-98BATifLAWO6+3brC2uz7g[]server.ccl.net> X-Original-From: Peeter Burk Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Sun, 13 Sep 2015 09:35:33 +0300 MIME-Version: 1.0 Sent to CCL by: Peeter Burk [peeter.burk_+_ut.ee] Dear Tom, I can understand your passion against atomic charges, and I do believe that your work on them is methodologically as scientific as it can be. But if you compare the atomic charges with airplane, then for tha airplane there is a clear "moment of truth" - will it fly? What is the similar thing for atomic charges? Can you provide experimental charges? How are those MEASURED? To my limited knowledge there are no such experiment, which will measure atomic point charges... If you could convince me that comparison to experiment is possible I would not argue any more, but at the moment the discussion reminds me rather a theology than science as one party does not believe that atomic point charges can be obtained from experiment and other one does... Best regards Peeter On 09/12/2015 04:24 PM, Thomas Manz thomasamanz]-[gmail.com wrote: > Hi Robert, > > The notion of atomic population analysis methods as being arbitrary > reflects the practical state of affairs in decades past. It is certainly > true that the earliest methods such as Mulliken and Lowdin populations > are inherently arbitrary because they lack a basis set limit. But, the > notion of arbitrariness doesn't accurately characterize the most > recently developed methods which not only have a well-defined basis set > limit but also have been developed with extensive and rigorous > comparisons to experimental data. > > At the time the textbooks you mentioned were written, things had only > begun to improve in the area of atomic population analysis. I'm sure the > authors of those textbooks did the best they could with the information > available at that time. Since those textbooks were written, newer > methods have been developed that are at least an order of magnitude more > accurate in comparisons to experiments than the crude, early methods. If > one were going to write a textbook today, it would be appropriate to say > that many of the early atomic population analysis methods were arbitrary > but that some of the most recent ones have been developed through a > legitimate scientific design process. > > This is an area in which I currently do research. In my research group, > atomic population analysis methods are developed using scientific > methods. The procedure we use is not unlike the one used to design > airplanes. Yes, there is some flexibility in the design of an airplane. > One could make it longer or shorter, for example. Yet, it is not quite > accurate to say the design of an airplane is arbitrary. Airplanes, like > my atomic population analysis methods, are designed to meet certain > performance criteria. An airplane should fly, for example. Not only > should it fly, but it should have stable control, take off and land > smoothly, etc. There is some flexibility when choosing the shape of > airplane, but it is not quite accurate to say the shape of an airplane > is arbitrary. Proposed airplane shapes are tested in wind tunnels to see > how they react to air turbulence, how much drag they produce, etc. There > is a real engineering design element involved with scientific process of > engineering and testing prototypes to continuously improve the design. > Saying that airplane designs are arbitrary somehow doesn't do justice to > the enormous amount of design work, prototype building, and scientific > testing that goes into producing an efficient airplane. > > The same principle applies to the development of accurate atomic > population analysis methods in my research group. We use a legitimate > and rigorous process that involves engineering design, prototype > building and scientific testing with comparisons to experimental data. I > realize that many other research groups do not use such a rigorous > process, but if you are going to say that atomic population analysis > methods are arbitrary, please restrict this designation to those that > actually are arbitrary and mention that some of the recent efforts use a > legitimate scientific design process. > > The diborane molecule you mentioned does present an interesting example. > Please find below the net atomic charges and bond orders I computed for > this molecule: > > B atomic charge: -0.0221 > bridging H atomic charge: 0.131 > outer H atomic charge: -0.054 > > B-H(bridging) bond order: 0.423 > B-B bond order: 0.627 > B-H(outer) bond order: 0.940 > > sum of bond orders for B atom: 3.39 > sum of bond orders for bridging H atom: 0.91 > sum of bond orders for outer H atom: 1.01 > > Sincerely, > > Tom > > > On Fri, Sep 11, 2015 at 2:25 PM, Robert Molt > r.molt.chemical.physics%x%gmail.com . ccl.net > wrote: > > There is nothing problematic with saying "there is no such thing as > the quantum mechanical operator for atomic charge." Any atomic > charge model requires an /arbitrary /partitioning of density as > "belonging" to certain atoms. None of the laws of physics are > written in terms of atoms! We don't write the force between atoms, > we write the force between charges. Trivializing the problem of > partitioning is brushing under the rug the inherent problem: we > cannot partition it without arbitrary choices. > > An atomic charge model is especially problematic when the electron > density is delocalized. There is no way to say to "whom" the density > "belongs" in diborane or a metal conducting a current. > > Moreover, this is the accepted view of the community. See Cramer, > chapter 9; see Jensen's book (don't recall the chapter; see Szabo > and Ostlund, chapters 1-3. > From owner-chemistry@ccl.net Sun Sep 13 18:37:01 2015 From: "Jim Kress jimkress35 * gmail.com" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51735-150912202129-23256-Vj2MaYDSxCq7XZsOMHmBxg a server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 12 Sep 2015 20:21:34 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35!A!gmail.com] Bill Goddard and his group at Caltech have a vast body of work that deals with the successful use of Quantum Chemistry in solving real problems. Adri van Duin also is doing the same at Penn State. You should investigate their work. Jim Kress