Talk:Computational chemistry/Archive 1

Archive 1

Semiempirical methods

As it stands, the article implies that classical force-field MM is considered a semiempirical method. I've never heard these methods described as semi-empirical, that term usually being reserved for parameterized quantum mechanical models like PM3, AM1, MNDO, etc. I think we need a separate section for the classical methods, since they are in practice a whole different animal from quantum calculations. Ed Sanville 03:33, 7 December 2005 (UTC)

I've moved the molecular mechanics section out of the semiempirical method section. They are classified as distinct topics in every book and article I've seen. Itub 00:44, 4 January 2006 (UTC)

The statement: "The opinion that computational chemistry would be ultimately able to predict mechanisms of such complex processes as biochemical reactions is now looked upon as unjustifiably optimistic."

Is not NPOV.. There are a number of highly regarded researchers in the field who do study biochemical reactions with quantum-chemical methods.

This is not entirely without controversy (no field of research really is), but the previous remark is not-neutral on the issue, rather it takes a rather damning view which is not representative of the general opinion within the field either.

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Apart from the intro, this articles concentrates on QM methods to the exclusion of all others. It would be nice to have more balance and in particular some sort of list of all methods (force field, statistical mechanics, QM/DFT etc.) at the beginning in order of complexity/computational cost.

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I don't think Computational chemistry is the branch of theoretical chemistry.

LiDaobing 16:07, 25 Jun 2004 (UTC)

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As there is already a page for quantum chemistry, I think this page needs some revision. I'd agree that comp. chem. is a branch of theoretical chemistry -- but comp. chem. can also focus on the properties of molecular clusters, molecular dynamics, etc. -- not just "molecular properties."

I think some of the discussion of quantum-chemical methods belongs under quantum chemistry.

While I just created some stubs for the programs mentioned, I think it might be better to link to community pages like CCL.net and other directories of comp. chem. resources and databases than particular products. There are hundreds of programs and including some but not others might be construed as bias or advertising for particular packages.

Ghutchis 28 Jul 2004

Merge

I personnaly believe theoretical, quantum and computational chemistry should all be merged under the title theoretical chemistry. Vb 08:05, 19 July 2005 (UTC)

I think this would be a far too wide generalization. Karol 08:54, July 19, 2005 (UTC)

I agree with Karol. While there is significant overlap between theoretical, quantum and computational chemistry, they are definitely separate fields of endeavour. Theoretical chemistry does need expanding though, maybe with a brief summary of comp. chem., qm, stat. mech., chemical information, etc. I don't necessarily agree with what the current article states. I guess that's something else for my to-do list... Stewart Adcock 10:08, 19 July 2005 (UTC)

OK. I understand those three articles have distinct topics but I think they have such overlaps that a common article (with, of course, subsections and preliminary remarks, like the ones which are already in computational chemistry) could be less confusing for newcomers. For example it is sometimes difficult to decide whether a topic like Carr-Parrinello or molecular mechanics is something which belongs to theoretical, quantum or computational chemistry. But well, if you have ideas how to improve the theoretical and quantum chemistry articles so that they show clearly how they are separated from computational chemistry, I am of course a keen supporter Vb 14:26, 19 July 2005 (UTC)

If I can lend my own viewpoint, I would say that there is a clear methodological difference. Computational chemistry and quantum chemistry are narrow branches of theoretical chemistry, which is no dsicovery, I think. Therefore, theoretical chemistry encompasses alot more than these two fields put together - reaction kinetic theory, statistical mechanics used for chemical applications, mathematical chemistry, and even chemical database theory, to name a few. Whereas quantum chemistry uses quantum mechanics to solve question that are chemical in nature and thus restricts itself to providing reliable formulas based on decent approximations, computational chemistry aims to implement these formulas in actual computer code and thus is seen by some to be more in the computer science domain than a chemical science. Obviously, quantum and computational chemistry are very intimate with each other, but still are very distinct, just as theory and experiment are in physics. Hope this is all clear enough, and that it is in line with other quantum/computational chemists ideas of the trade. Karol 15:51, July 19, 2005 (UTC)

Now I understand a bit better. I don't know enough of theoretical chemical methods which are not within quantum or computational chemistry. So I think the conclusion is that the Wikipedia does not show up the full extend of theoretical chemistry and require strong expansion. But on the other hand, relative to the topic merging quantum/computational chemistry, the difference with experimental and theoretical physics is that both quantum and computational chemistry are usually performed by the same persons and are therefore sometimes very difficult to distinguish from each other. Of course there are people doing computational chemistry without knowing anything of quantum chemistry but is that really a reason to separate so clearly the two articles? 10:01, 20 July 2005 (UTC)

Re your last question: yes and no :) But still, computational chemistry (and even more computational biochemistry/biology) uses tools that aren't ab initio (read quantum chemistry). These are molecular mechanics, molecular dynamics, monte carlo and so forth. In any case, there are alot of computational techniques used to solve chemical problems that are empirical or semiempirical, so saying that computational chem. = quantum chem. is also probably not too good an idea. You're right that the information on Wikipedia is neither clear nor concise on this topic, but that is not a reason to merge ar delete articles - it is a reason for adding stub tags, however... Karol 11:20, July 20, 2005 (UTC)

OK. I agree.

Ab initio

I really like the multitude of edits people have made recently - the articles on computational/quantum chemistry are growing! I am wondering, however, if we should perhaps place Molecular Dynamics in this article beyond the scope of the Ab Initio section? I mean, it's just a question of terminology, as you can have Ab initio MD (AIMD), but maybe MD generally is not considered ab initio. What do other editors think? Karol 07:24, July 23, 2005 (UTC)

Nowadays, many article are published with names like "Ab initio study of...". They often present both the computation of the potential energy surface and the wave packet dynamics on it. Ab initio means solving the Schroedinger equation with the total molecular Hamiltonian without experimental parameters. The title they use is therefore fully legitimate. --131.220.68.177 10:28, 25 July 2005 (UTC)

I think the logical heirarchy of computational chemistry is:

• Quantum
  • ab initio
  • semiempirical
  • DFT
  • MD (which can be any of the above)
• Classical
  • MM
  • MD

Ed Sanville 15:51, 23 July 2005 (UTC)

From my point of view, this discussion must be done within an entire concept with the article quantum chemistry and theoretical chemistry. Please have a look to the discussion on the quantum chemistry article. As said there : there are NO classical treatment possible of the molecular electronic structure! I insist. :-) --131.220.68.177 10:00, 25 July 2005 (UTC)

I don't agree with Ed Sanville. I suggest this structure :

• electronic structure
  • ab initio
  • DFT (whether DFT is ab initio or not is controversial)
  • semiempirical
    • semiempirical approximation to Hamiltonian matrix
    • molecular mechanics (MM)
• chemical dynamics
  • Quantum
  • Semi-classical
  • Classical (MD)

See discussion on quantum chemistry to see my argumentation. --131.220.68.177 10:14, 25 July 2005 (UTC)

But, in that scheme, where would quantum MD methods come into play? And why is MM under semiempirical electronic structure, when MM typically means classical Newtonian physics with no reference whatever to the electronic structure of the system? Ed Sanville 06:05, 4 January 2006 (UTC)

Mills' Spreadsheet

I understand that the math and theory behind RL Mills' Hydrino theory is highly suspect. However, he has published a spreadsheet that purports to exactly solve the first twenty ionization levels of the first twenty elements, using only physical constants and basic algebra (i.e. non-iterative, closed-form solutions). Unless this spreadsheet derivation can be impeached in some way (and I haven't been able to yet), it would seem like a fairly significant event in the field of computational chemistry. Even assuming that Mills' is indeed 100% wrong, the mere existence of a closed-form model that derives even approximately close results would appear to be a useful tool. Can someone with more subject matter expertise please comment. Ronnotel 19:44, 25 November 2005 (UTC)

I don't think it's worthwhile to mention. Even if it has susbtance, it's not a core part of computational chemistry. Karol 20:00, 29 November 2005 (UTC)

I entirely agree with Karol. This should have no place here, at least at this stage. I looked through some of his stuff. He seems, for example, to have no idea that the many-body problem is the issue and thinks the failure to handle molecules in a closed form is a feature of quantum theory.Bduke 20:33, 29 November 2005 (UTC)

OK - you guys seem to know more about this than I do. Although I must wonder at what stage would it be relevant? Is it not the case that a closed-form solution to this problem, if it really worked, would be a pretty powerful tool? Working out protein folding in Excel would be kinda cool. Just sayin' Ronnotel 02:34, 30 November 2005 (UTC)

Current science would say that a closed form solution to this problem, which is a many-body problem, is not possible. It is not a matter of quantum theory. A closed-form equation for the motion of the moon is not possible because of the many gravitational forces on the moon (from sun, earth, other planets, etc.). Also, to put it bluntly, the time to add this to wikipedia is when it becomes widely accepted normal science and it is very far from that at present. We should not present new wild and unconventional ideas in wikiperia.Bduke 07:39, 30 November 2005 (UTC)

One more note. That something works doesn't make it all that hot of a science, only engineering, and that maybe for a year or two until something better comes around. Good scientific ideas must allow us to make predictions, beyond the subject we originally formulated them for. What we see here is a tool, which doesn't give us any information outside of what it is designed for. Karol 08:22, 30 November 2005 (UTC)

After looking at the spreadsheet for a little bit, it makes me very curious as to what's going on here. His calculated values for ionizations of multi-electron atoms are consistently within 1% of the experimental values. It would take a post-Hartree-Fock method with a large basis set to obtain such accurate values. This guy HAS to be doing some fudging of his data or something. I would say that if this model does what it claims to do, (i.e. calculate an analytical solution for the ionization energies of multi-electron systems), then it would be very, very, very interesting indeed. Of course, everything I know and learned says that's impossible, which makes it that much more interesting, (if it works). What is claimed here is far more than simply a tool, and it kind of freaks me out. Could somebody smarter than me figure out what this guy has done wrong, so I can sleep at night? Ed Sanville 02:24, 4 January 2006 (UTC)

Mills has expanded on his work and built out solutions to 19 different molecules. If I were about to spend >$100M on a protein-folding super-computer architecture, I'd be more than a little interested in what he's got. Unless his new work can be impeached, this article should be amended to reference him. 19 molecular solutions Ronnotel 15:35, 14 January 2006 (UTC)

I see that the core of his work is the assertion that the hydrogen atom can be shrunk to smaller than the known ground state. He calls it a 'hydrino' and claims that it will give unlimited cheap energy. He has raised 25 million dollors to set up Blacklight Power in New Jersey. He promised cheap power by 2000, but as far as I can see he still has not delivered. Nothing he has done has been subjected to peer review. There is some criticism of Mills' hydrino theory here, although some of the links from that page do not work. The later stuff on atoms and molecules flows from hydrino theory. If he is wrong at the beginning, everything is wrong. If he wants his work to be accepted, he should write up the molecular stuff for the Journal of Chemical Physics and then it will get proper peer review. I certainly do not have time to go through everything in detail. I do not think this has a place on the computational chemistry page unless other scientists can support it. However I think that the story of Randell Mills, Blacklight Power and his various theories does deserve a page on Wikipedia and it has already been done - see Hydrino theory and Randell Mills. The former page is in Category:Pseudophysics. Finally, I would hope that in the computational chemistry pages we could avoid topics that are controversial and may be pseudoscience, as this will lead to real arguments, delete/revert wars, etc. Bduke 20:48, 14 January 2006 (UTC)

I believe a number of his papers have been peer-reviewed in quality journals.Ronnotel 20:04, 17 January 2006 (UTC)

I think that is correct, but that they are not on the topic we are discussing. They are experimental papers on hydrides. If you know of a peer review paper on this material, please let me know and I'll check it out. I am following this up. I have asked about him on the Computational Chemistry e-mail list and so far nobody has given information of either a peer review of this work or an analysis that proves it is wrong. There is an analysis or perhaps attack on him in a book. The bookshop is holding it for me and I'll collect it today. More below. Bduke 22:06, 17 January 2006 (UTC)

I don't think it should be mentioned here until it is published in a stricter journal, cited by someone other by himself, confirmed by someone else, and/or shown to be useful. Itub 16:10, 16 January 2006 (UTC)

Galileo offered his inquisitor an opportunity to peer through a telescope and observe for himself the Jovian moons that, according Church-approved Ptolemaic celestial mechanics, could not exist. He was refused. Look at the spreadsheets. They're quite simple and they do what is claimed. Ronnotel 19:15, 17 January 2006 (UTC)

I have to still agree with Itub. The spreadsheets may be simple, but the derivation of the equations is very unclear. The online book is verbose yet fails to mention things that should be mentioned. I could perhaps accept that a classical approach could replace a quantum approach but I fail to see how he can get round the three body problem. An analytical solution for a problem with two or more electrons is not solvable analytically either in classical mechanics or quantum mechanics. In calculating the motion of satallites, moons etc., a serious numerical iteration process is needed. The situation in atoms and molecules is worse as none of the pair repulsion or attraction forces is small. The forces between the particles (electrons and nuclei) are all of comparable magnitude. Let us wait until his new work on molecules has been addressed by people other than himself. The atom calculations would not be relevant to this page anyway - more one on atomic physics. Bduke 22:06, 17 January 2006 (UTC)

I believe Mills' approach avoids the three-body problem because he does not assume that the electron is a point-charge, but a dirac-like 'shell' of rotating charge. The resulting 'force-balance' equation is a much simpler and more tractable approach. Regardless of whether the fundamental physics is correct or not, I believe directly observered results from the spreadsheets clearly meet the threshold of what would be of use to the reader, and therefore should be addressed in some way, as a highly-qualified link or whatever. Ronnotel 00:41, 18 January 2006 (UTC)

That makes no sense to me, but that is not the point. Let's just wait until someone other than Mills publishes something about it. This would make any WP comment more balanced. He only wrote the chapters of his on-line book in the last few weeks. Bduke 01:40, 18 January 2006 (UTC)

Semiempirical methods

This section is very thin and largely deals with pi electron models. I am thinking about having a go at a complete rewrite. I would first mention empirical methods - Huckel theory and extended Huckel theory as precursors of semi-empirical pi electron and all-valence electron methods. This would be a new page. I would then move the PPP stuff to a new pi electron semi-empirical page and add a link to a new page on valence electron semi-empirical methods. The later page would have links to Dewar (MOPAC) methods, ZINDO, SINDO etc. In turn these would link to existing links for AM1, PM3, etc which currently are only linked to in the program section, particularly the MOPAC link. What do people think? Add ideas here or on my talk page.

I would add that there has been some discussion on the computational chemistry list recently about there being no recent comprehensive review of all semi-empirical methods rather than a review on just MOPAC methods or just ZINDO or whatever. This is a big job, but maybe it could develop here on wikipedia.Bduke 06:13, 6 December 2005 (UTC)

I have largely done what I suggested above. I would welcome comments and criticism.Bduke 05:31, 21 December 2005 (UTC)

Famous Computational Chemists

I think on wikipedea we should honour those computational chemists who have made significant contributions. The link to the International Academy of Quantum Molecular Science gives a list of members, both still living and dead. This is a good place to start. Only a small proportion of members have a page. Most do not. I have added a few. Can others add some? I have also in many other places changed the link to people so that it is identical to the link on the list of Academy members. For example, the link to Rod Bartlett on the ACES program page, is now the same as on the Academy page. Perhaps others could check names in this way also. In this way, any new bio should work from other links.Bduke 05:31, 21 December 2005 (UTC)

I've just added Clemens Roothaan, George Hall and Frank Boys. Please add to them. Also, which others do you think are higher priority than other famous computation/theoretical/quantum chemists? --Bduke 05:37, 26 January 2006 (UTC)

I have added Isaiah Shavitt. I have a gap in his bio after his Ph D with Boys in 1957 to starting at the Technion in 1962. Can anyone fill that gap? --Bduke 02:21, 27 January 2006 (UTC)

Columbus Program

To the unregistered editor (67.169.1.106) who added COLUMBUS. Please register and then we can discuss your edits more directly. There are real advantages in registering. This is program that is worthy of being described in Wikipedia, but just a mention in this table is not enough. Are you going to write the page for it? I have recently added pages for JAGUAR, PQS and some others, but I do not know much about COLUMBUS and what I do will be confused by the fact that I have used some of the old COLUMBUS code from Pitzer's group. but not the current release or anything like it. Bduke 23:00, 13 January 2006 (UTC)

Good to see that User:Karol Langner has done the page. Thanks. Bduke 23:18, 15 January 2006 (UTC)

as SPR comment

Wikipedia is not only for experts on the field!

The intro is short but OK. But from than on nobody searching for a a good explenation for computational chemistry only gets the methodes which can also go into a small list at the end of the article.

Examples what computational chemistry is doing, are missing. There are a few words with no explenation in the intro giving no clue how and why you get IR-spectra or something else from a computer. For every major use there should be one section or a exapmle.

TS and IM for reactions or searching for the most stable conformer are exaples which can be shown in a small picture and everybody will get a picture what this stuff is about.

Then ther should be a description of why you do it at all. Most of the data you get from CC you can get by measurments. What are the benefits and the problems with CC. And beeing onest with problems is OK.

But for SPR this article is far more easy to comment than the aricle about science.

--Stone 07:57, 3 April 2006 (UTC)

Review

I have created the review page linked from Wikipedia:Scientific peer review and have taken the liberty of copying into the page the above review by Stone which I found a helpfull contribution. I have added a first draft of my review. Having done that, I must get back to other tasks, but when I have time, I will add this article to the normal WP:PR process and see whether anything comes of that and will edit Wikipedia:Scientific peer review to reflect the current situation. --Bduke 03:08, 7 April 2006 (UTC)

Recent edits

Karol Langner started to edit the software table by removing the pure DFT entries. I have completed this by writing Semi-empirical quantum chemistry methods (Pi electron semiempirical methods and Valence electron semiempirical methods are now included in there and are made redirects as is Semiempirical method which was a copy of part of the main article made by Itub some time ago but went nowhere) and Computational chemical methods in solid state physics. The software table now has no column for periodic systems and the codes that do this are listed in Computational chemical methods in solid state physics. The purely semi-empirical codes are deleted from the table and all are listed in Semi-empirical quantum chemistry methods. This leaves the article a bit of mess, but it will be OK when I do a similar article for ab initio methods, reorganise material and clean-up. I will get to it ASAP. --Bduke 08:05, 9 April 2006 (UTC)

This is a good movement, but aren't those names a bit long? Karol 09:03, 9 April 2006 (UTC)

Maybe. I wanted to be clear and with solid state I wanted to not overlap with any of the solid state physics articles which are nowhere near close to what we want to add the software list to. --Bduke 12:03, 9 April 2006 (UTC)

I have done more extensive work on the article and it as all roughly in the order I want. I have written Ab initio quantum chemistry methods. In the main article, in the section now headed "Interpreting molecular wave functions", I propose another sub-article. This would include not just the Bader stuff, but localised orbitals, NBO, Mulliken charges and several other similar things. I want to add several examples including the one I had in my review. The last four of this list from early in the article:-

• The prediction of the molecular structure of molecules by the use of the simulation of forces to find stationary points on the energy hypersurface as the position of the nuclei is varied.
• Storing and searching for data on chemical entities (see chemical databases).
• Identifying correlations between chemical structures and properties (see QSPR and QSAR).
• Computational approaches to help in the efficient synthesis of compounds.
• Computational approaches to design molecules that interact in specific ways with other molecules (e.g. drug design).

all need brief sections. The section on "Chemical dynamics" needs work. The whole needs checking, sourcing and tidying, but it is getting there. --Bduke 12:03, 9 April 2006 (UTC)

Also the para near your (Karol's) image needs rewriting to explain the image. The image perhaps should also go on the ab initio article. --Bduke 12:25, 9 April 2006 (UTC)

Encyclopedia of Computational Chemistry

The "Encyclopedia of Computational Chemistry", 5 Volume Set (Hardcover), Ed. by Paul von Ragué Schleyer, is available from Amazon at US$5,375.00. It has been said that WP is not just trying to outdo Brittanica but all specialist encyclopedias. So this article is the potential portal to pages that would fill 5 volumes. Is that where we are going? The book is of course massively expensive, in part I guess because more free copies were sent to people who were asked to contribute articles than was actually sold. I have only ever seen it on shelves of people who contributed. Sadly, I'm not one of them. It would be a good place to look for ideas for articles. --Bduke 06:48, 10 April 2006 (UTC)

This is kind of off-topic, but I've seen on on the shelf of a person who bought it :) Karol 07:39, 10 April 2006 (UTC)

Still off-topic. Are you sure he did not contribute a small article. There were lots of authors and they all got a free copy. --Bduke 07:54, 10 April 2006 (UTC)

Educational Approach

In the wikipedia article named "Chemistry", the definition of Computational Chemistry is formulated by using the following statements: [..."Since the end of the Second World War, the development of computers has allowed a systematic development of computational chemistry, which is the art of developing and applying computer programs for solving chemical problems."...]- Going to the wikipedia page on Computational Physics, a similar idea can be read: [..."Computational Physics also englobes the tuning of the software/hardware structure to solve the problems (as the problems usually can be very large, in processing power need or in memory requests)."]- Now, then again, if we search the wikipedia article on Scientific Computation, we may find a statement related to those on that Chemistry and Computational Physics article of wikipedia. This statement goes as follows: [..."The term computational scientist is used to describe someone skilled in scientific computing. This person is usually a scientist, an engineer or an applied mathematician who applies high-performance computers in different ways to advance the state-of-the-art in their respective applied disciplines in physics, chemistry or engineering. Scientific computing has increasingly also impacted on other areas including economics, biology and medicine."...];- That same article (Scientific Computing) continues with:[..."Programming languages commonly used for the more mathematical aspects of scientific computing applications include Fortran, MATLAB, GNU Octave, Num-Python, Sci-Python and PDL. The more computationally-intensive aspects of scientific computing will often utilize some variation of C or Fortran."...] -and with : [..."Scientists and engineers develop computer programs, application software, that model systems being studied and run these programs with various sets of input parameters. Typically, these models require massive amounts of calculations (usually floating-point) and are often executed on supercomputers or distributed computing platforms."...]- On that same article (Scientific Computing) there's a part that give us info on the education that can be achieve to obtain a degree on Scientific Computing, and it tell us that:[..."There are also programs in areas such as computational physics, computational chemistry, etc."]- With all the information above in this page the message of an expert in Chemistry programs and this capacity to develop those computer programs may arise, and that is the point. I don't mean to define what is it that a Computational Chemist do,exactly, but the question remains: Do a Compuational Chemist develop a computational program for Chemistry (at least in theory, at least as capacity gained, no matter how untraditional these days that might be)?. It may sound like a stupid question, but by reading this article on Computational Chemistry I was left with the impresion that a Computational Chemist is nothing more than a chemist playing nintendo with a molecules-related videogame, without the capacity to really implement or develop a computer program or a computational knowledge high enough to make the neccesary changes if they are needed. I was planing a M.S. degree in this area of both Chemistry and Computational Sciences, but I need to know if by definition a Computational Chemist have at least some level of knowledge on computer programming and/or computer science; I know the mathematical aspect of theoretical chemistry must be regular enough before it can be implemented,and that maybe not the computational chemist job, really, but, if the mathematical approach is ready to be implement on a computer software, do the computational chemist have the knowledge or skills to do that software, or at least do some "computational chemist specific computer programming job" ? Do it depends on something? On what?. Forgive my weird questions, but I didn't know who could I ask Thank you —The preceding unsigned comment was added by 206.248.83.151 (talk) 09:50, 17 December 2006 (UTC).

This raises some interesting questions. It is rather late at night here in Australia, so I will be brief for now. I think there are two sorts of computational chemists, but with a lot of overlap. There are those who use the codes with a lot of chemical intuition to get chemical answers, and there are those who write codes. There are however many people like me who do both, but I use codes I probably could not write, and I write code that I do not sufficiently employ to get chemical answers. If you want to get into computational chemistry, then the ability to write the codes is an advantage, but you still need the ability to use them to tackle chemical problems. I hope this helps. --Bduke 11:50, 17 December 2006 (UTC)

Thank you Mr.Bduke; Please allow me to ask just a simple questions ( and this is rather a clarification, hoping you have the patience on these kind of questions- Here it is: When you wrote -[..."There are those who use the codes with a lot of chemical intuition to get chemical answers, and there are those who write codes. There are however many people like me who do both,"...]- Is the distinction beetween these two sorts of computational chemistry a clear , formal one or is it just a matter of different kinds of jobs for the same title of computational chemist?. I'm a chemistry major interested in computers and Chemistry, but with no prior computer degree, hope that explain a lot; I'm looking for an advance level of chemical knowledge, not necesarily the most advanced of them all but more than a undergraduate degree. I only want to know the neccesary about computer programming and hardware so that I use it for chemical information systems . Pratically I want to be a computational chemist, but I'm not sure what kind of preparation that would give me. I feel a personal need to cover these two areas (computer science with -at least- basic level, and, of course, Chemistry -advanced level-.Maybe you could help me. The article on computational chemistry should adress the issue of educational pathways toward Computational Chemistry degree or preparation, as well as the advantage and limitations of the discipline. It should clarify what task do computational chemist could be doing, and not just what the majority of them prefer to do or traditionaly do (it should focus on potential applications as well as common trends on the field); Thank you again. (The above was by User:206.248.83.151

Please sign you posts on talk pages with ~~~~. Sometimes those who write the codes, and of course develop the methods that the code embodies, describe themselves as theoretical chemists or quantum chemists depending on what the method is. However the term computational chemist is becoming more widespread and dominant. I get the impression that people who have entered the field in the last decade or two are generally people with a chemistry degree and a strong interest in computers. They have often learn to program on their own to write a game or similar. It helps to have a minor in mathematics and some physics too. Maybe other people would care to come in here and say what the best preparation for P/G wotk in comp chem is. I first learnt to program 46 years ago and I have not been on a programming course since, but I have learnt several other languages and have not programmed in my first language for 42 years. My degree was in chemistry with no minor. I did do a degree in maths for fun but that was well after my D Phil. --Bduke 20:57, 17 December 2006 (UTC)

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I carried out this automatic review to give me some ideas to improve the article. Maybe you have some ideas too. Thanks, Bduke 07:41, 11 March 2007 (UTC)

Discussions (moved here from: User talk:Bduke)

Computational chemistry (History?)

There is no history section for this article, could you write a short one or simply tell me what the start date is for this branch of chemistry? Thanks: --Sadi Carnot 02:23, 25 April 2007 (UTC)

Hi Sadi, I will have a go, but it will have to wait for about 12 days or so. I'm really busy in real life and that will force me to take a wikibreak next week. The question is a complex one. The term is later than the practice. When I started doing calculations in quantum chemistry, I thought of myself as a theoretical chemist or a quantum chemist. The term "computational chemistry" is much later, but it brought into the fold people who called themselves other things such as molecular modellers and so on. It needs to be handled carefully. --Bduke 06:30, 25 April 2007 (UTC)

Yes, thanks. Based on the history section of the computer article, I'm guessing that computational chemistry started developing in the 1970s (slowly) and then gained momentum in the 1980s? I plan to buy a basic computational chemistry textbook soon; maybe then I'll be able to contribute to the history section a bit. Later: --Sadi Carnot 14:40, 25 April 2007 (UTC)

As you know theoretical calculations in Chemistry go back to Heitler and London in 1927. The first calculations carried out on digital computers was much earlier than you think. It was in the early 1950s, when what we now call semiempirical calculations were carried out. The first ab initio calculations on diatomic molecules were in 1956 at MIT. The first polyatomic calculation using Gaussian orbitals was in the late 1950s at Cambridge. Huckel calculations, generated by computer in Berkeley and Oxford were published in 1964. The first version of GAUSSIAN (Pople's program) was 1970, but other codes - ATMOL, POLYAYTOM, IBMOL, and others - all predate GAUSSIAN. The first bibliography (200+ pages) on ab initio molecular calculations was published in 1971. The 1960s were extremely active. I myself first used a computer in 1961. Molecular mechanics started in the 60s or at least the 70s. However, none of this was called computational chemistry. That term was I think first used in the late 1980s. The series "Reviews in Computational Chemistry" going back to around 1990 have had a number of articles outlining the history of computational chemistry in different countries - USA, UK, France, Canada and Germany at least. They contain stuff about hardware and the organisation of computer centres to facilitate large numerical calculations that could well be used in some of the history of computer articles that are linked from the place you mention. Those articles are pretty poor. Geeks have no sense of history. --Bduke 21:49, 25 April 2007 (UTC)

Very nice information. It would be interesting to find out who first coined or used the term "computational chemistry" in its current sense? We'll have to keep our eyes open. Let me know when you start putting some of the above information into the article. Also, yes I agree writing computer code and writing articles are two different things. Talk soon: --Sadi Carnot 23:39, 25 April 2007 (UTC)

Hi guys. I just want to add that the Journal of Computational Chemistry was first published in 1980, so the term goes at least as early as that. I would guess that it came into use in the mid to late 1970s (but I'm too young to remember ;-). Another milestone worth mentioning is the paper of Metropolis et al in 1953 which introduced the Metropolis Monte Carlo method also widely used in computational chemistry for fluid simulations among other things. Of course, they didn't call it computational chemistry at the time. --Itub 06:14, 26 April 2007 (UTC)

Itub, good data facts. We'll have to add some of this to the history section whenever it gets started. Thanks for the input. --Sadi Carnot 07:18, 26 April 2007 (UTC)

New history stubby

I'm going to use some of the above information to start a history stubby for this article. Please feel free to clean and join in. --Sadi Carnot 07:35, 26 April 2007 (UTC)

Good start. I'll add references over the weekend. --Bduke 08:38, 26 April 2007 (UTC)

Good. I just looked in google books, and the earliest one I could find that uses the term computational chemistry is from 1970: Computers and Their Role in the Physical Sciences By Sidney Fernbach, Abraham Haskell Taub. Unfortunately google only shows tiny snippets for this book, but in one of the search results it used the term in quotation marks: 'It seems, therefore, that "computational chemistry" can finally be more and more of a reality'. [1] This suggests that the term must have been pretty new at the time. --Itub 07:57, 26 April 2007 (UTC)

I’m watching. Ema--or (talk) 21:36, 7 August 2023 (UTC) I meant I will be watching. To think this was already such a long time ago.

I would want to have a good look at that book. I do not recall it and I am sure it had little influence on the field. One place to start is the preface of the first volume of "Reviews in Computational Chemistry", VCH, around 1990. Editors are Kenny Lipkowitz and Donald Boyd. It is not labelled as volume 1, but it started a series and the next was labelled volume 2. That preface discusses a definition of "computational chemistry" certainly and it may discuss the history of the term. I forget and do not have a copy. --Bduke 08:33, 26 April 2007 (UTC)

Yes, I agree it doesn't seem to be influential. Probably many people used the words "computational chemistry" in various random occasions but it didn't catch on. Reviews in Computational Chemistry is now available online, and I think the front matter of each volume is available for free. Check out http://www3.interscience.wiley.com/cgi-bin/bookhome/114034476 . They say that "it began emerging as a distinct discipline about 10 years ago" (this was written in 1989). --Itub 09:05, 26 April 2007 (UTC)

Good data, I’ll add this to the article. If someone finds older or better references please feel free to change them. I will also reason that Pauling and Wilson’s 1935 Introduction to Quantum Mechanics – with Applications to Chemistry and Heitler’s 1945 Elementary Wave Mechanics – with Applications to Quantum Chemistry were influential to the early development of computational chemistry? If I am wrong please feel free to change my edits. Talk later: --Sadi Carnot 17:31, 26 April 2007 (UTC)

• G. G. Hall (1973). "The growth of computational quantum chemistry from 1950 to 1971". Chemical Society Reviews. 2 (1): 21–28. doi:10.1039/CS9730200021.
• Arthur L. Robinson (1976). "Computational Chemistry: Getting More from a Minicomputer". Science. 193 (4252): 470–472.

These two might help to get a little bit more of the computational stonage.--Stone 15:18, 2 May 2007 (UTC)

"Computational quantum chemistry" is not the same as "Computational chemistry" and may well predate the latter use for the wider field. I do not think that the Robinson book used the term with its modern meaning. I've been away. I will try to look at this over the weekend. --Bduke 09:20, 4 May 2007 (UTC)

I agree. It is hard for us to really decide when computational chemistry began by looking at the original literature, because it might border on original research. What we can say is what other people say about when it began (as in the intro of vol. 1 of Reviews in Computational Chemistry), or plain facts such as the publication dates of journals. However, the articles provided by Stone are certainly interesting and provide insight into the "stone age" or pre-history of computational chemistry. Given what we have, I believe that the best date is somewhere in the late 1970s. --Itub 09:33, 4 May 2007 (UTC)

Marking all of these for a future historical or timeline article. Ema--or (talk) 21:42, 7 August 2023 (UTC)

Huckel calculations

The article says "In 1964, Hückel method calculations, which are a simple LCAO method for the determination of electron energies of molecular orbitals of π electrons in conjugated hydrocarbon systems, such as ethene, benzene and butadiene, were generated on computers at Berkeley and Oxford". I don't have access to the reference provided. Although I remember seeing one of those old books that consisted solely of Huckel calculation results (basically computer printouts), I don't think that ethene, benzene, and butadiene are good examples when talking about calculations done in the sixties. Those molecules can be solved with paper and pencil on the back of an envelope, so I imagine that they were done around 1930! For larger molecules the computer becomes more important. :-) --Itub 08:03, 5 May 2007 (UTC)

Yes, you are right. The references list a very large number of molecules. I have added what I think is the largest, ovalene. I have added some more references. However, this section on history is too narrow. It only deals with computational quantum chemistry. It needs more, such a mention of molecular mechanics and Allinger. --Bduke 09:13, 5 May 2007 (UTC)

Another interesting reference

There's a book called Theory and Applications of Computational Chemistry: The First Forty Years (ISBN 0444517197). I don't have it and it's insanely expensive, but you can read most of the first chapter on Amazon for free. They obviously consider a much earlier date for "computational chemistry" than Reviews in Computational Chemistry (ca 1965 vs ca 1979). But that's almost always the case with new fields: by the time the name becomes popular and journals appear, people have usually been working "in the field" for decades without noticing. ;-) --Itub 15:41, 22 May 2007 (UTC)

Interesting and as you say insanely expensive. I found I could read the first 3 pages of each chapter. Those from chapter 1 are full of errors. They talk about the first ab initio calculations in the mid 1960s. No, they were in the 1950s. They say that 40 years ago, the only high level language was FORTRAN IV. No, the early Boys work was not coded in FORTRAN. I used Mercury autocode, Elliott autocode and Algol 60 from 1960 onwards and did not learn Fortran until about 1966. It points to 1962 and the start of QCPE as the start of computational chemistry, but says nothing about whether the term was used then. I do not recall it being used by QCPE, which is after all, the Quantum Chemistry Program Exchange. Quantum Chemistry was the term used then. Then Molecular Mechanics was introduced and that term used. The collective term for both and other methods, Computational Chemistry, was much later. They are really just talking about when calculations that we now call computational chemistry were were carried out and are saying nothing about the use of the term. The first 3 pages of chapter 6 by Clementi are better history, but he does not use the term computational chemistry once (at a quick read). Looks like a useful book though. On a different matter, I have "Quantum Chemistry: the development of ab initio methods in molecular electronic structure theory" by Henry F, Schaefer III, published in 1984. It gives a brief summary of many key papers in the field. He now widely uses the term computational chemistry, but he does not use the term in that book. I think the term computational chemistry was not used, at least widely, until after that date, although the term computational quantum chemistry was used. --Bduke 00:49, 23 May 2007 (UTC)

I have just realized that I have on my shelves a book entitled "Computational Chemistry" by A. C. Norris published in 1981 by John Wiley. The interesting thing is that none of the book is about what we now call computational chemistry. The sub-title is "An introduction to numerical methods". The blurb on the back starts "This book provides a practical introduction to numerical methods at a level suitable for undergraduate chemists". This, I think, supports the view that the modern usage of the term was not in use prior to 1980, when the author signed off on the preface. --Bduke 00:47, 24 May 2007 (UTC)

That is pretty good evidence. I think we could also add some of the history of textbooks in computational chemistry in the modern sense. I'm not sure which one was first, but it was possibly published after 1990. The real boom came after 2000. Two of the earlier books that I remember are Leach's Molecular Modelling (1996) and Jensen's Introduction to Computational Chemistry (1999). Leach doesn't use "computational chemistry" in the title, but the scope is basically the same as other computational chemistry books. But maybe I'm too young and don't know of much earlier books. ;-) --Itub 05:34, 24 May 2007 (UTC)

accuracy

This is merely a qualitative discipline which can guess orders of magnitude at best. Errors of 1% are the most accurate they can go, and 40%-50% errors would not be considered bad.—Preceding unsigned comment added by 137.205.132.170 (talk • contribs)

Your statement is so vague as to be completely meaningless. Percent of what? Calculating what? For molecular energies, errors much smaller than 1% are the rule. For heats of formation, errors of about 1 kcal/mol are common for small molecules, but for this type of measure it makes no sense to talk about percentages. For equilibrium constants, errors are much larger than 1%, and are often better measured in terms of orders of magnitude. For yet other observables the errors will be different. It makes absolutely no sense to talk about percent errors without reference to the observable and system size in question. --Itub 13:14, 6 June 2007 (UTC)

A real revert war while I slept! I entirely agree with Itub. Coulson once said that we are trying to calculate the mass of the captain of the Queen Mary by measuring the displacement of the liner with the captain on the bridge and then with him on the dock. We can get 1% in the total, but it is'nt good enough. As chemists we need energy differences. I would also point out that 1% in a bond length is 1 - 2 pm. We can do that fairly easily for small molecules. The current wording is fine. --Bduke 01:05, 7 June 2007 (UTC)

its a school example of weasel words. i had in mind energies, and looking just what has been acomplished for a simplest helium 2-electron system (see computational chemistry wiki) where errors are atrocious 1-4%, I would say that its rather a qualitative science. If you have another data, please put links. "very high accuracy" is weasel word and is a misleading lie, as errors of 1-10% are far from high accuracy. The percentage error needs to be quoted to quantify the statement. For energy levels of simple molecules, for chemical potentials etc - quote of percetntages in necessary. And of course, saying that for heats of formation talk of percentages is impossible is nonsense, as there are absolute values to compared with, as with any measurable quantity. Experimental results always come with relative errors, and it is a first and foremost question how does theory compare - and in this case, theory is next to useless.

I think you need to look at sources other than the computational chemistry wiki. First, all energies of helium have been calculated to within experimental error and indeed are most certainly known to far more decimal digits (probably 10 or more digits) from theory than from experiment. Indeed those calculations go back to the 1930s. Secondly, various good methods based on high order coupled cluster methods can give energies of formation to within experimental error. Such methods are the W2 and W3 methods and those using CCSDTQ with accurate relativistic corrections. Indeed, I have heard it argued that as the number of experimentalists who measure thermodynamic properties is decreasing (the field seems to now longer attract people) we are going to have to rely on theoretical calculations for such data. The person who made that remark is one of the people who is meeting that demand for high accurate calculations. Thirdly for small molecules, there are now several examples where theoretical predictions of bond lengths and bond angles forced the experimentalists to look again at their data. The earliest case is perhaps methylene, but there have been many larger examples more recently than that work. The scope of accurate calculations is rapidly moving to larger systems. --Bduke 03:10, 7 June 2007 (UTC)

I like Bduke's recent edit, and I'm all for adding more details for the article about the accuracy for predicting specific properties, as some are harder than others. To clarify my statement about heats of formation, it's really not useful to give the error in percentage for two reasons: 1) a heat of formation is a difference, which can be zero. If you calculate that the heat of formation of H2 is 0.0000001 kcal/mol, instead of the correct 0 kcal/mol, what is the percent error? Infinite? 2) What matters for heats of formation is having the absolute error within "chemical accuracy"; that is, within what has a noticeable effect on experimentally observable properties. In many cases an error of about 1 kcal/mol is as good or better than experiment, and is good enough for predicting other properties. --Itub 06:17, 7 June 2007 (UTC)

On another accuracy related matter: just a little query about the mention of accuracy in the introduction. It says that ab initio calculations are the most accurate. I was under the impression that semi-empirical calculations could be as good as ab initio for molecules similiar to the basis set, and that the advantage of ab initio came with its ability to deal with 'exotic' molecules. i'm not an expert, but is the intro a bit misleading?Brokencalculator 10:29, 15 November 2007 (UTC)

That is a good point. The question is that semi-empirical can give accurate results but you can not rely on them doing so. With ab initio you have a better view of whether it is going to be accurate. --Bduke 10:52, 15 November 2007 (UTC)

GA Re-review

As part of classifying GAs in WP:UCGA, I noticed that how this article came to get a GA tag is a bit weird (it was done by anon IP directly involved with editing of the article over a year ago, it seems). I know you've got a scientific review so the information seems ok, but the style and writing in the article may need to be fixed up some for purposes of a GA re-review. --Masem 04:11, 30 July 2007 (UTC)

I think it became classified as a good article before I started edited WP at the end of October, 2005. I certainly did not think it was that good at that time, but thanks to several people it has become a lot better. I have been intending to put it forward for a GA re-view, but have not got around to it. Could you, or User:Giggy who added cleanup tags to the article, give us any suggestions about what does need to be fixed up? Thanks. --Bduke 07:32, 30 July 2007 (UTC)

This comment from Masem and the cleanup tag on the article has prompted me to do some more work on the article. Could others join me and let us see whether we can can get it really to GA status? In particular we need more examples, I think, and the sections on "Interpreting molecular wave functions" and "Chemical dynamics" in particular appear to need a lot of attention. Other things that have come to my mind are a brief mention of QSPR, QSAR and chemical databases in the lead and more detail further down. The list in the introduction of five major areas is not reflected in the content either below or above in the lead. Please either be bold and just edit or make suggestions here. --Bduke 09:21, 30 July 2007 (UTC)

After all these years on Wikipedia, I still have no idea what a "good article" is, because the criteria seem to be shifting, subjective, and arbitrary. So I don't really care about "good articles". I care more about featured articles because the criteria and process seems more transparent to me. In order to become featured, an article has to be comprehensive and balanced, which is not the case with here. It is too focused on quantum mechanics, with barely a mention of the classical methods. Besides the sections and topics you mention, here are other important omissions:

• Monte Carlo is just a "see also" link.
• The section on software is only about QM software
• No mention of QM/MM or free energy calculations
• Very little on classical MD; no mention of protein simulations, solvation, solvent models
• No link to the molecular orbital article!
• Not much mention of conformational analysis or reaction coordinate calculations
• No mention of computational thermochemistry

These are many topics, to be sure. To be balanced and of reasonable length, the article whould all have to be written in "summary style", which might require making some sections shorter and moving the acetylene example to a more specific article. I'm also tempted to remove the table with software packages. --Itub 10:01, 30 July 2007 (UTC)

Lots of good points there. I suspect that this article is always going to be too technical to get to FA but we could try. Just a few minor quibbles about your 7 dot points, I hope to help us all to learn how to address them.

• Point 2 - the table is supposed to be about codes that match 2 criteria. None have only HF and post HF, and it includes MM, so the 2 has to at least include one of MM, semi-empirical or DFT. I agree we should move it to a separate article like the other software lists. What about Quantum chemistry computer programs for a title?
• Point 3. The table of software has but it is not obvious - Tinker with Gamess(US) and ONIOM in Gaussian, It needs something in the text.
• Point 5. The MO article is terrible. I prefer the links to be articles one or two down the tree such as Hartree-Fock, but they are largely missing too. I'll look at that.
• Point 7. I wrote an article on the composite methods the other day. It needs expanding. It is linked from Post-HF but it could also be a link from a section here.

Most of your points are areas I do not know too much about. Can you help out on them? --Bduke 10:38, 30 July 2007 (UTC)

I have copied this from the talk page of User:Masem, where he responded to my plea for help in much the same words as my reply to him above:

"For some, take a look at what some of the other editors have said over at Good Article Review. You do need a lot more in-line references (doesn't have to be new references if the existing ones adequately state the necessary details, use the (ref name="") tags to repeat them, but you do need more); make sure to properly format references using the correct WP:CITET; the article structure is a bit in question - I think you can move History to be the first section, and then have "Concept" (your current "Introduction"), "Methods" (which covers most of the rest of the article) and "Computer software". I'd also look at other articles in the Physics and Astronomy section of WP:GA to compare against. You also could probably do easily with one or two more pictures to help enhance the understanding of the article - make sure that that tone is written for general understanding (which mostly seems to be there) which pictures can be used to help significantly. --Masem 13:23, 30 July 2007 (UTC)"

I think we can do much of what he suggests but I can not think of a single photpgraph that would help. Any thoughts? --Bduke 22:29, 30 July 2007 (UTC)

Perhaps not photographs, but figures (the only photographs I can think of are of people or computers for the history section). For example, a figure showing the ball-and-spring concept of MM; a figure showing a PES; a figure showing molecular orbitals or electron density distribution; a figure (maybe even an animation) showing the idea of MD; a figure showing the LCAO concept (or an MO energy diagram); a figure depicting the docking or ligand binding concept; a figure of the quantum chemical topology concept. I'll try to help at some point but I need time to really sit down and work on it. On a separate note, I personally hate using citation templates but I don't mind if others use them. But the guidelines clearly say that they are optional, so that's not a valid reason for questioning the "goodness" of an article. --Itub 08:28, 31 July 2007 (UTC)

By unanimous consensus, the article has been delisted. The archived discussion can be seen here. Once the article is brought up to standards, it may be renominated at WP:GAC. Regards, Lara♥Love 21:45, 2 August 2007 (UTC)

Well, none of us knew this was going on and I have told them so. They need to communicate better. It is however no problem, as it never was really a good article. We can nominate it when we are ready. --Bduke 22:23, 2 August 2007 (UTC)

missing balance concerning references on software suites

Gaussian is mentioned, Gamess is not. Orca is not present in the Wikipedia at all. The article should give an overview of available software instead of promoting software that has been a commercial project for about 20 years, this is advertisement, not information. JPBoyd (talk) —Preceding undated comment added 22:18, 12 August 2011 (UTC).

Both GAMESS(US) (and GAMESS(UK)) and Orca are mentioned at List of quantum chemistry and solid state physics software, as are many more. That is where individual programs are mentioned. Programs can have their own articles if they meet wikipedia notability guidelines. Gaussian is only mentioned in a historical context and I think that is appropriate. --Bduke (Discussion) 15:24, 14 August 2011 (UTC)

First paragraph to be introductory. Yes?

Does this sentence, if it means anything at all, really belong in the first paragraph? "Its necessity arises from the well-known fact that apart from relatively recent results concerning the hydrogen molecular ion (see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form." - Rhodesh (talk) 05:09, 10 October 2013 (UTC)

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