Talk:Computational chemistry

Wiki Education assignment: CHEM 300
— 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:

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.

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.

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)