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Archive 1 |
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)
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.
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.
I don't think Computational chemistry is the branch of theoretical chemistry.
LiDaobing 16:07, 25 Jun 2004 (UTC)
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
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 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)
I think the logical heirarchy of computational chemistry is:
Ed Sanville 15:51, 23 July 2005 (UTC)
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)
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)
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)
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)
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)
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)
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)
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)
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:-
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)
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)
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)
The following suggestions were generated by a semi-automatic javascript program, and might not be applicable for the article in question.
You may wish to browse through User:AndyZ/Suggestions for further ideas.
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)
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)
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)
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)
These two might help to get a little bit more of the computational stonage.-- Stone 15:18, 2 May 2007 (UTC)
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)
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)
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)
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)
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)
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)
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:
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)
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).
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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![]() | This is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page. |
Archive 1 |
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)
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.
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.
I don't think Computational chemistry is the branch of theoretical chemistry.
LiDaobing 16:07, 25 Jun 2004 (UTC)
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
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 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)
I think the logical heirarchy of computational chemistry is:
Ed Sanville 15:51, 23 July 2005 (UTC)
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)
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)
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)
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)
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)
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)
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)
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)
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:-
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)
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)
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)
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)
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)
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)
These two might help to get a little bit more of the computational stonage.-- Stone 15:18, 2 May 2007 (UTC)
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)
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)
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)
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)
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)
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)
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:
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)
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).
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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