:Talk:Computational chemistry

{{dashboard.wikiedu.org assignment | course = Wikipedia:Wiki_Ed/The_University_of_British_Columbia/CHEM_300_(Fall_2023) | assignments = Erdabravest2001, Bird flock | reviewers = User19228, Dev1 0302, LegoMagneto, GurkiratSinghNijjar | start_date = 2023-09-06 | end_date = 2023-12-07 }}

— Assignment last updated by CHEM 300 UBC CJA (talk) 18:02, 8 November 2023 (UTC)

:Added a small citation at the introductory paragraph. It's meant to show that computational chemistry aids drug development Bird flock (talk) 03:05, 8 October 2023 (UTC)

Added a small citation at the first bullet point in "Several major areas may be distinguished within computational chemistry" It's meant to show that computational chemistry involves using simulations of forces or advanced quantum chemical methods to find stable points on the energy surface as the positions of the nuclei change. Erdabravest2001 (talk) 07:06, 10 October 2023 (UTC)

Want to add:

https://journals.aps.org/rmp/abstract/10.1103/RevModPhys.92.015003

{{talkref}}

Erdabravest2001 (talk) 06:00, 23 October 2023 (UTC)

I am starting to add quantum computational chemistry as part of this page. As I have worked on this type of stuff before I am going to add the Variation Quantum Algorithm here and others as well as a more mathematical formulation for specific parts of computational chemistry. I will try finishing by 2023-11-1st.06:00, 23 October 2023 (UTC)~

We were wondering if we could have someone look over our page before we publish them on wikipedia. They are here: https://en.wikipedia.org/wiki/User:Bird_flock/Computational_chemistry

Please update your thoughts using a peer review.

{{Talk:Computational chemistry/GA1}}

Examples of such properties are structure (i.e., the expected positions of the constituent atoms), absolute and relative (interaction) energies, electronic charge density distributions, dipoles and higher multipole moments, vibrational frequencies, reactivity, or other spectroscopic quantities, and cross sections for collision with other particles.

The methods used cover both static and dynamic situations. In all cases, the computer time and other resources (such as memory and disk space) increase quickly with the size of the system being studied. That system can be a molecule, a group of molecules, or a solid. Computational chemistry methods range from very approximate to highly accurate; the latter is usually feasible for small systems only. Ab initio methods are based entirely on quantum mechanics and basic physical constants. Other methods are called empirical or semi-empirical because they use additional empirical parameters.

Both ab initio and semi-empirical approaches involve approximations. These range from simplified forms of the first-principles equations that are easier or faster to solve, to approximations limiting the size of the system (for example, periodic boundary conditions), to fundamental approximations to the underlying equations that are required to achieve any solution to them at all. For example, most ab initio calculations make the Born–Oppenheimer approximation, which greatly simplifies the underlying Schrödinger equation by assuming that the nuclei remain in place during the calculation. In principle, ab initio methods eventually converge to the exact solution of the underlying equations as the number of approximations is reduced. In practice, however, it is impossible to eliminate all approximations, and residual error inevitably remains. The goal of computational chemistry is to minimize this residual error while keeping the calculations tractable.

In some cases, the details of electronic structure are less important than the long-time phase space behavior of molecules. This is the case in conformational studies of proteins and protein-ligand binding thermodynamics. Classical approximations to the potential energy surface are used, typically with molecular mechanics force fields, as they are computationally less intensive than electronic calculations, to enable longer simulations of molecular dynamics. Furthermore, cheminformatics uses even more empirical (and computationally cheaper) methods like machine learning based on physicochemical properties. One typical problem in cheminformatics is to predict the binding affinity of drug molecules to a given target. Other problems include predicting binding specificity, off-target effects, toxicity, and pharmacokinetic properties. Erdabravest2001 (talk) 01:16, 5 December 2023 (UTC)

:Materialscientist Please do not edit this. My partner, @Bird flock is adding citations as we speak. Erdabravest2001 (talk) 01:45, 5 December 2023 (UTC)

I hope this message finds you well. My partner (@Bird_flock) and I would like to share some updates regarding our recent editorial revisions, guided by the valuable insights from Ian, our Senior Educational Expert.

Upon review, Ian advised that references should be positioned at the end of a paragraph when multiple sentences draw from the same citation. We realized that our previous format, which placed the citation after the first relevant sentence, was not optimal. This oversight led to instances where only a single sentence in a paragraph was cited, which was not our intention.

To enhance the readability and professional appearance of the document, we have now adjusted the citations to follow punctuation marks, ensuring a more streamlined and coherent format. Additionally, we have updated the section headers to adopt sentence case, moving away from the previous numbered format. This change aligns with standard editorial practices and improves the overall structure of the document.

Furthermore, we have addressed the specific issue with the section titled "Algorithm: Investigate the…" by removing the colon from the heading. This alteration brings the section titles in line with our revised formatting standards.

These revisions have been an enlightening process for our team, significantly enhancing our understanding of effective and professional document formatting. We are committed to continuous improvement and appreciate the guidance provided by Ian and the feedback from our readers.

{{Talk:Computational chemistry/GA2}}

I deleted this due to the GA Review.

Computational chemical methods can be applied to solid-state physics problems. The electronic structure of a crystal is in general described by a band structure, which defines the energies of electron orbitals for each point in the Brillouin zone. Ab initio and semi-empirical calculations yield orbital energies; therefore, they can be applied to band structure calculations. Since it is time-consuming to calculate the energy for a molecule, it is even more time-consuming to calculate them for the entire list of points in the Brillouin zone.

The determination of molecular structure by geometry optimization became routine only after efficient methods for calculating the first derivatives of the energy with respect to all atomic coordinates became available. Evaluation of the related second derivatives allows the prediction of vibrational frequencies if harmonic motion is estimated. More importantly, it allows for the characterization of stationary points. The frequencies are related to the eigenvalues of the Hessian matrix, which contains second derivatives. If the eigenvalues are all positive, then the frequencies are all real and the stationary point is a local minimum. If one eigenvalue is negative (i.e., an imaginary frequency), then the stationary point is a transition structure. If more than one eigenvalue is negative, then the stationary point is a more complex one and is usually of little interest. When one of these is found, it is necessary to move the search away from it if the experimenter is looking solely for local minima and transition structures.

The total energy is determined by approximate solutions of the time-dependent Schrödinger equation, usually with no relativistic terms included, and by making use of the Born–Oppenheimer approximation, which allows for the separation of electronic and nuclear motions, thereby simplifying the Schrödinger equation. This leads to the evaluation of the total energy as a sum of the electronic energy at fixed nuclei positions and the repulsion energy of the nuclei. A notable exception is certain approaches called direct quantum chemistry, which treat electrons and nuclei on a common footing. Density functional methods and semi-empirical methods are variants of the major theme. For very large systems, the relative total energies can be compared using molecular mechanics. Erdabravest (talk) 20:35, 22 January 2024 (UTC)

None of these links are within the guidelines of WP:EL, that's why I removed it Dajasj (talk) 15:07, 20 November 2024 (UTC)

:How do they violate any of the guidelines? They follow WP:ELYES #1, WP:ELMAYBE #3. They do not match any of the criteria in WP:ELNO. They are all very much encyclopedic content that is appropriate. If they were not then this would have been an issue as part of the original GAN, it was not. Ldm1954 (talk) 15:17, 20 November 2024 (UTC)

::Also match WP:ELYES #2 Ldm1954 (talk) 15:19, 20 November 2024 (UTC)

:::No, because it says "An article about a book, a musical score, or some other media should link to a site hosting a legally distributed copy of the work". This is not an article about the journal (or WebMO). Dajasj (talk) 15:25, 20 November 2024 (UTC)

::They do not match WP:ELYES: this is not the Wikipedia page for WebMO and it is also not the Wikipedia page for these journals. If they had a separate page, they could be linked there. Also note that the external links should be in section External links (see WP:NOELBODY). WP:ELMAYBE #3 could apply, although it these links are not directories of websites or organisations. In any case, WP:ELMAYBE #3 also says: "Long lists of links in articles are not acceptable.", which applies here. Dajasj (talk) 15:24, 20 November 2024 (UTC)

:::#They are pages that connect directly to those journals which provide papers on the topic of the article. Therefore they are directly relevant, albeit their relevance does require some knowledge of the field. That they do not have WP pages does not mean anything, as I said before they are RS.

:::#That is definitely not a long list.

:::If you want to pursue this then I suggest an RfC which should be posted at WT:Chemistry. Currently I do not agree with you, so the default is to not make the change. Ldm1954 (talk) 15:29, 20 November 2024 (UTC)

::::Both WP:ELYES #1 and #2 specifically say the article should be about the topic. This is simply not about the journals. They do not mention directly related. And external links should not be in the body of the article, which is also made explicit in WP:ELLIST (which is basically the same scenario).

::::Anyway, can we at least agree that the WebMO link can be removed? Dajasj (talk) 15:34, 20 November 2024 (UTC)

:::::Given your request for a RfC, I have posted on Wikipedia:External links/Noticeboard, which I think is the most suitable place for such a request. Dajasj (talk) 15:42, 20 November 2024 (UTC)

::::::I will post to WT:Chemistry and WT:Physics, since it really matters that people who know the subject make comments. If you do not know the relevance of those journals to the content of the article then they will appear to be inappropriate. Ldm1954 (talk) 15:46, 20 November 2024 (UTC)

:::Also note that WP:ELNO #19 applies here (because the journals should not be linked in the list of journals). Perhaps also #14. Dajasj (talk) 15:30, 20 November 2024 (UTC)

::::If there is no current WP page I see no reason not to link, and in fact WP:ELNO#19 supports including them: "they qualify as something that should be linked or considered". Also #14 does not apply to scientific literature.

::::The journals are specialized ones which are on the topic of the page. While I see your point about them as a type of "external link", to me they are more a type of "see also". There are times where rules are made to be broken, at the moment I don't have a solution that preserves the information and is different.

::::For WebMO, in fact that one definitely should not be removed, 100%. The editor who wrote the article is giving proper credit to the source where it came from. Not to do that would violate academic standards. Ldm1954 (talk) 15:45, 20 November 2024 (UTC)

:I would like to know which "these links" you folks are talking about. Johnjbarton (talk) 16:11, 20 November 2024 (UTC)

::The links in the section "specialized journals" and the link to WebMo at the top. I am unable to link it now, but you can see the most recent edit by me in the article history. Dajasj (talk) 16:13, 20 November 2024 (UTC)

:::Thanks! My opinion:

:::The WebMo link in the figure should be converted to

:::* Modelled using the freemium WebMO Basic system.{{Cite web |title=WebMO |url=https://www.webmo.net/ |access-date=2023-12-05 |website=www.webmo.net}}

:::That is, the external link should not be in the caption, but in the ref list.

:::As for the "Specialized journals on computational chemistry", I don't think the links are an issue, but the list is. This is a mix of notable journals (evidenced by their wikipages) and non-notable ones. Why this list? Is there any source that guides editors in creating this content or is it just opinion? If I deleted one, how would discussions about that delete be resolved? "I read it"? I don't think the list is knowledge.

::: Johnjbarton (talk) 16:42, 20 November 2024 (UTC)

::::The change to the caption is OK with me. I disagree about "non-notable" ones, for instance Journal of Computer-aided Molecular Design does not currently exist, but it is a Springer Nature journal while Computational and Theoretical Polymer Science is Elsevier. (I just replaced one which has now got a WP page.) Ldm1954 (talk) 17:06, 20 November 2024 (UTC)

:::::See we already disagree. Is this list really worth arguing over? Johnjbarton (talk) 17:30, 20 November 2024 (UTC)

:::::: Just belonging to a publishing company that is well-established is not a criterion for evaluating either the notability not the credibility of a journal, as far as I can tell. If a journal really is notable and relevant but has no page, just redlink it rather than providing an external link. Perhaps {{u|XOR'easter}} would be able to give a more informed opinion on this.

:::::: As far as I'm concerned, crediting the producer of the software that was used to produce a graphic is inappropriate – it smacks of promotion and does not give the reader useful information about the topic of the article. I would at least add a key and remove the "Modelled using WebMO" entirely. The diagram is not great anyway: it is uninterpretable, and even if what it represents was made clear, it gives little information about what it claims: the electrostatic field. —Quondum 18:41, 20 November 2024 (UTC)

:::::::I agree that {{tq|crediting the producer of the software that was used to produce a graphic is inappropriate}}. How often do you see, e.g., "created by Matplotlib" in a figure caption, either on Wikipedia or in a textbook, journal article, etc.? It might be appropriate sometimes, but by default, it's not a datum we include. Save that for the metadata on the image page itself. I also agree that the specific diagram in question here is not very clear or informative. It's supposed to be {{tq|A dichromium metal complex with electrostatic field surrounding it}}, but the electric field is a vector field, while the picture seems to be using a color map to represent a scalar field on a surface. What do the colors mean? For that matter, what is the surface supposed to be? There's a Tinkertoy rod connecting the two atom balls; what is that supposed to indicate? The picture is just decoration, really. {{pb}} Regarding the list of journals, I don't have strong feelings and can't think of a relevant wiki-precedent with strong consensus, but if there isn't enough to say about a journal that it merits its own article, including external links to it starts to seem link-spammy. XOR'easter (talk) 22:31, 22 November 2024 (UTC)

{{reflisttalk}}