Talk:Computational chemistry

Wiki Education assignment: CHEM 300

This article was the subject of a Wiki Education Foundation-supported course assignment, between 6 September 2023 and 7 December 2023. Further details are available on the course page. Student editor(s): Erdabravest2001, Bird flock (article contribs). Peer reviewers: User19228, Dev1 0302, LegoMagneto, GurkiratSinghNijjar.

— 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)

Wiki Education assignment: CHEM 300 II

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:

References

Wiki Education assignment: CHEM 300 III

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)~

Update the Chemistry Computational Chemistry Page

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.

GA Review

This review is transcluded from Talk:Computational chemistry/GA1. The edit link for this section can be used to add comments to the review.

Reviewer: Esculenta (talk · contribs) 00:06, 5 December 2023 (UTC)

I'm quickfailing this article because it is a far ways from meeting Good Article criteria 2b and 2c. Essentially, every statement needs a source so that it can be verified. Looking at the article, there are dozens of sentences ending paragraphs without citations, and there also many paragraphs that are completely uncited. It would take longer than the week or so timeframe of a GA to find sources for all of these statements. Esculenta (talk) 00:06, 5 December 2023 (UTC)

Hi there,

We are currently in the process of editing our page. Please be patient as we add more citations sources (which will be done by this coming Wednesday) — Preceding unsigned comment added by Erdabravest2001 (talk • contribs) 01:37, 5 December 2023 (UTC)

Hi there ,

I hope this message finds you well. 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 yourself. Please continue to review the computational chemistry page. Erdabravest2001 (talk) 02:58, 5 December 2023 (UTC)

Lol! I think you and your team are going have a rough time on Wikipedia if you continue to use ChatGPT to interface with other humans. This review has been already been closed, and despite your admirably quick efforts to tack on citations to the unsourced bits (there's still more left uncited BTW), the article is still far from meeting the GA standards, and will take lots of line-by-line editing work, evaluation, and comparison to the original sources for text-source verification. If you're serious about this, read Wikipedia:Make technical articles understandable and apply liberally throughout the article. Esculenta (talk) 03:16, 5 December 2023 (UTC)

Hi there,

Fortunately, I do not use ChatGPT when writing my emails, as it frustrates me. Could you please specify the sections with unsourced citations that were mentioned earlier? This info would be greatly helpful for ensuring accuracy and completeness in our work. Erdabravest2001 (talk) 03:30, 5 December 2023 (UTC)

Start of section "Applications", and section "Methods#Chemical dynamics". Esculenta (talk) 03:37, 5 December 2023 (UTC)

Hi there,

Understood. My team and I will endeavor to incorporate additional citations. Also could you clarify where we could simplify or try to better explain the technical language/jargon? This would also help us as well. Erdabravest2001 (talk) 03:42, 5 December 2023 (UTC)

Try reading the entire article, from top to bottom, as if you had the background knowledge of a bright high school student. Read the paragraph that starts with this sentence: "The simplest type of ab initio electronic structure calculation is the Hartree–Fock method (HF), an extension of molecular orbital theory, in which the correlated electron-electron repulsion is not specifically taken into account; only its average effect is included in the calculation." Then follows more bleeding-edge quantum mechanical theory. Why do I say that? The publication it's cited to is dated 2024 (isn't it still 2023?), and as I struggle to understand the abstract for this publication (I'm not a complete idiot, I've taken advanced uni chem. courses and intro comp. sci.), I'm wondering why it's even being used as a source for a Wikipedia article, which is supposed to be a layman-friendly introduction to the field, understandable by the hypothetical bright high school student. The entire article's not quite as bad as that specific example I pointed out, but it really needs a top-to-bottom check in this manner. Is there not a recently published, general purpose textbook on computational chemistry that could be used as a main reference? Esculenta (talk) 03:58, 5 December 2023 (UTC)

Hi,

I agree that our content should be easily understood by an informed high school student. Currently, I am fine-tuning my approach to balance detailed coverage with succinctness. I'm committed to identifying the appropriate level of detail for different situations. While my background in writing for a newspaper has equipped me with skills in clear communication, I am continually developing my ability to maintain neutrality and prevent any perceived bias.

I would also like to offer my apologies regarding the source in question. It appears legitimate, but there is a chance it might be a pre-print, necessitating further verification.

Another comment that I want to address:

"The simplest type of ab initio electronic structure calculation is the Hartree–Fock method (HF), an extension of molecular orbital theory, in which the correlated electron-electron repulsion is not specifically taken into account; only its average effect is included in the calculation." Then follows more bleeding-edge quantum mechanical theory.

Although my team and I were not directly responsible for writing this specific section of the methods, we acknowledge the need for revision. We plan to revise this paragraph soon and will work on simplifying the language in the coming days.

Additionally, I'd like to inquire about the adherence to Wikipedia's guidelines concerning source diversity, particularly regarding the predominant use of a single textbook. Is this practice in line with Wikipedia's standards? Erdabravest2001 (talk) 04:24, 5 December 2023 (UTC)

Check out WP:PST to see what Wikipedia's standards are for sourcing. Ok, I've had enough of talking to GPT, good luck with your assignment. Esculenta (talk) 04:29, 5 December 2023 (UTC)

Hi there,

Thank you for your help and support. Have a good evening. Erdabravest2001 (talk) 04:54, 5 December 2023 (UTC)

Just In case we need this

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.

GA Review

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

---

This review is transcluded from Talk:Computational chemistry/GA2. The edit link for this section can be used to add comments to the review.

Reviewer: Ldm1954 (talk · contribs) 03:09, 8 December 2023 (UTC)

I will be making some more detailed review comments in the next week. At the moment two things stand out:

• Resubmitting for a GA after less than 1 day is extraordinary.
• The article rambles on and on. Parts are OK, but then there is the sudden appearance of a massive section Computational chemistry#Quantum computational chemistry which contains many specialized sections, many of which are speculations that do not belong. They are not core to computational chemistry. Ldm1954 (talk) 03:09, 8 December 2023 (UTC)

I personally have expressed my concerns that the Quantum Computational Chemistry should be it's own wikipedia page. Erdabravest2001 (talk) 19:59, 9 December 2023 (UTC)

Then I suggest that you move it. If you do not have the rights, then perhaps post to WT:Chemistry and/or WT:Physics. I am not going to do this while reviewing.

The current draft rambles, with the Quantum computational chemistry stuck in there. This needs to be removed and the methods and complexity sections consolidated as they are redundant.

If I do not see any indications of action in a week or so I will do a quick fail. Ldm1954 (talk) 09:28, 10 December 2023 (UTC)

Hi there,

Understood. I will consolidate within the next 2 weeks. Please give me some time as I am undergraduate with final exams.

Regards Erdabravest2001 (talk) 23:13, 10 December 2023 (UTC)

Ok. I will check back after Xmas. Ldm1954 (talk) 01:56, 11 December 2023 (UTC)

Hi there,

I removed the computational Chemistry page using my non-school wikipedia account:

It's still in Draft mode:

https://en.wikipedia.org/wiki/User:Erdabravest/Quantum_Computational_Chemistry

I am currently in the process of adding a brief subsection about Quantum Computational Chemistry within the Methods Section. Erdabravest (talk) 10:25, 19 December 2023 (UTC)

Ok. I will wait until you have edited the page. Ldm1954 (talk) 11:47, 19 December 2023 (UTC)

Hi @Ldm1954,

You say the following:

The article rambles on and on. Parts are OK.

Other than quantum computational chemistry which I am working on, can you provide some more details on where in the methods and computational complexity they could improve? This feedback could help me edit this page as well.

What I want to do is ensure that the reader gets a thorough understanding of computational chemistry and how chemists think about which algorithm/computational method to use. In my experience of learning computational chemistry, I learned how to use algorithms not by learning about computational methods but by learning the computational complexity of the problems required to solve them. Hence, this is why I wrote the computational complexity section.

Maybe I could combine the Methods/ Computational Complexity into a new section. I could describe the methods used here and a computational complexity subsection.

For example:

Ab Initio

Computational Complexity:

  - Discusses the rationale for selecting these algorithms, emphasizing their computational efficiency and complexity.

Algorithms:

  - This section delves into the specifics of the algorithms.

The Applications section should be dedicated to exploring the use of these methods in chemistry, highlighting practical examples. It should clearly demonstrate the relevance and significance of these algorithms in daily chemical applications, providing insights that prompt the reader to recognize their importance.

Let me know what your thought are on this! :)

Erdabravest (talk) 21:40, 21 December 2023 (UTC)

Removing the material was good. I have an international flight in 30 mins, so it will be a bit before I can give you a good answer. Ldm1954 (talk) 22:29, 21 December 2023 (UTC)

@Ldm1954 I have finished the subsection titled Quantum computational chemistry. I am still waiting for approval.

Regards Erdabravest (talk) 21:08, 23 December 2023 (UTC)

I have moved the article back to Draft:Quantum computational chemistry -- it should keep this name until it is reviewed. It looks roughly OK, although it should have Quantum computational chemistry in the first line. I won't be able to review the original article until after Christmas. Ldm1954 (talk) 09:15, 24 December 2023 (UTC)

Happy 2024! I have properly linked the Quantum Computational Chemistry Page to the methods sections and am now awaiting further instructions. Regards Erdabravest (talk) 01:28, 3 January 2024 (UTC)

That looks appropriate. I will try and look over more closely the main page this week. One thing, I suggest moving the whole "Computational costs" section to before (or after) the "Accuracy" section. It makes sense to describe the methods before describing their computational cost. Ldm1954 (talk) 20:38, 7 January 2024 (UTC)

I am finished moving all of the Computational Cost section. Erdabravest (talk) 10:19, 8 January 2024 (UTC)

Now starting the real review. Overall it is good. There are some places where I might say things differently, but I am not going to edit it to my style. Some initial important things:

History

• First paragraph: please add a reference to VBT Y
• Second paragraph, please ensure that everything has a reference, for instance the LCAO paper by Roothaan needs oneY
• Third paragraph. You need an overview review or specific sources, it is not appropriate to just have the Allinger paper.Y

Applications

• Looks fine. Others may add to it -- let them

Methods

• All three paragraphs are misplaced, these are for optimizing positions, and specifics of ab-initio methods. They should be deletedY
• The 'Methods for solids section is not appropriate, as DFT is also often for solids. I suggest deleting. (Move the Main to see also)Y
• In Chemical Dynamics need to mention that this is for ab-initio calculationsY
• Split operator technique should be a subheading of Chemical DynamicY

Accuracy

• I noticed that the first sentence uses "our" and "us". Remember that we cannot use words like this in Wikipedia.

Ldm1954 (talk) 16:56, 15 January 2024 (UTC)Y

Hi @Ldm1954,

I've contributed to the History section of the computational chemistry segment by incorporating the original papers referenced there.

I haven't made any changes to the Applications section, anticipating that others might wish to contribute to it, so I've left it open for edits.

Regarding the Methods section, the current three paragraphs are not appropriately placed. They pertain to optimizing positions and details of ab initio methods and therefore should be removed.

On another note, I'm considering whether an Applications subsection for Ab Initio methods is necessary. Since it's already mentioned elsewhere, would adding this subsection be redundant? I'm inclined to delete it unless it's deemed essential. What I will do is I will delete it and put it on the talk page of the article for now and if we would like to keep some things please let me know.

Regarding the Accuracy section, it's been corrected. Sorry.

Regards Erdabravest (talk) 02:39, 16 January 2024 (UTC)

HI @Ldm1954,

I removed the section. I have decided to leave it to the Ab initio folks.

Other than that it seems good. Erdabravest (talk) 04:31, 18 January 2024 (UTC)

Good revisions, a few more needed:

• In Ab initio, 4-6 paragraphs all cite [48]. That paper is only on one specific approach, it is not general. Please revise the references.
• The heading Applications of ab-initio algorithms is not needed, what you have below are a list of them. Please remove it.

Ldm1954 (talk) 17:50, 18 January 2024 (UTC)

Just a brief ping to @Erdabravest about the additional requested changes. Ldm1954 (talk) 22:46, 18 January 2024 (UTC)

Hi @Ldm1954,

Will implement these additional requested changes tonight at 7 PM PST.

Regards Erdabravest (talk) 22:53, 18 January 2024 (UTC)

Hi @Ldm1954,

I was injured so I had to delay my additions. Please find them added just now.

Regards Erdabravest (talk) 06:39, 21 January 2024 (UTC)

As a GA reviewer I am not supposed to edit the article. Therefore I will ask you to revert the recent edits by @Dcdiehardfan. While those were well meaning edits, unfortunately they are inaccurate and your prior version was (much) more accurate. Ldm1954 (talk) 15:56, 22 January 2024 (UTC)

Also, @Erdabravest the Figures are a bit misplaced -- many are in the are in the section on Computational costs, whereas they should be in the prior section on methods. Please also look in some other Wikipedia pages. For instance, in Catalysis there is a nice potential energy diagram that you could use. There may be others you can find on Wikimedia. Reordering the images, plus a few more will be helpful. Ldm1954 (talk) 16:20, 22 January 2024 (UTC)

Hi @Ldm1954,

For the figures will edit them and place them properly.

As for @Dcdiehardfan, it seems that they were intending to correct the History section. Erdabravest (talk) 19:00, 22 January 2024 (UTC)

They made changes which alter the sense, and make the sentences incorrect. I suggest you replace them by what you had. Ldm1954 (talk) 19:05, 22 January 2024 (UTC)

Hi @Ldm1954,

I undid the changes.

Will attempt to edit the figures now. Erdabravest (talk) 19:16, 22 January 2024 (UTC)

Hi @Ldm1954,

I added more figures to the computational chemistry page and have reordered the images. Let me know what you think. Erdabravest (talk) 20:21, 22 January 2024 (UTC)

GA review (see here for what the criteria are, and here for what they are not)

1. It is reasonably well written.

   a (prose, spelling, and grammar): Y b (MoS for lead, layout, word choice, fiction, and lists): Y

2. It is factually accurate and verifiable.

   a (reference section): Y b (inline citations to reliable sources): Y c (OR): Y d (copyvio and plagiarism):

3. It is broad in its coverage.

   a (major aspects): Y b (focused): Y

4. It follows the neutral point of view policy.

   Fair representation without bias: Y

5. It is stable.

   No edit wars, etc.: Y

6. It is illustrated by images and other media, where possible and appropriate.

   a (images are tagged and non-free content have non-free use rationales): Y b (appropriate use with suitable captions): Y

7. Overall:

   Pass/Fail: ✓ Pass

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Methods for Solids

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)