Editing Computational chemistry (section)

== Applications ==

There are several fields within computational chemistry.
* The prediction of the molecular structure of molecules by the use of the simulation of forces, or more accurate quantum chemical methods, to find stationary points on the energy surface as the position of the nuclei is varied.<ref>{{Cite journal |last1=Musil |first1=Felix |last2=Grisafi |first2=Andrea |last3=Bartók |first3=Albert P. |last4=Ortner |first4=Christoph |last5=Csányi |first5=Gábor |last6=Ceriotti |first6=Michele |date=2021-08-25 |title=Physics-Inspired Structural Representations for Molecules and Materials |journal=Chemical Reviews |language=en |volume=121 |issue=16 |pages=9759–9815 |doi=10.1021/acs.chemrev.1c00021 |pmid=34310133 |issn=0009-2665|doi-access=free |arxiv=2101.04673 }}</ref>
* Storing and searching for data on chemical entities (see [[chemical database]]s).<ref>{{Citation |last1=Muresan |first1=Sorel |title=Mapping Between Databases of Compounds and Protein Targets |date=2012 |url=https://doi.org/10.1007/978-1-61779-965-5_8 |work=Bioinformatics and Drug Discovery |pages=145–164 |editor-last=Larson |editor-first=Richard S. |access-date=2023-12-03 |series=Methods in Molecular Biology |place=Totowa, NJ |publisher=Humana Press |language=en |doi=10.1007/978-1-61779-965-5_8 |isbn=978-1-61779-965-5 |pmc=7449375 |pmid=22821596 |last2=Sitzmann |first2=Markus |last3=Southan |first3=Christopher|volume=910 }}</ref>
* Identifying [[correlation]]s between [[chemical structure]]s and properties (see ''quantitative structure–property relationship'' (QSPR) and ''[[quantitative structure–activity relationship]]'' (QSAR)).<ref>{{Cite book |last1=Roy |first1=Kunal |title=Understanding the basics of QSAR for applications in pharmaceutical sciences and risk assessment |last2=Kar |first2=Supratik |last3=Das |first3=Rudra Narayan |date=2015 |publisher=Elsevier/Academic Press |isbn=978-0-12-801505-6 |location=Amsterdam Boston}}</ref>
* Computational approaches to help in the efficient synthesis of compounds.<ref>{{Cite journal |last1=Feng |first1=Fan |last2=Lai |first2=Luhua |last3=Pei |first3=Jianfeng |date=2018 |title=Computational Chemical Synthesis Analysis and Pathway Design |journal=Frontiers in Chemistry |volume=6 |page=199 |doi=10.3389/fchem.2018.00199 |issn=2296-2646 |pmc=5994992 |pmid=29915783 |doi-access=free |bibcode=2018FrCh....6..199F }}</ref>
* Computational approaches to design molecules that interact in specific ways with other molecules (e.g. [[drug design]] and [[catalysis]]).<ref name="doi.org">{{Cite journal |last1=Tsui |first1=Vickie |last2=Ortwine |first2=Daniel F. |last3=Blaney |first3=Jeffrey M. |date=2017-03-01 |title=Enabling drug discovery project decisions with integrated computational chemistry and informatics |url=https://doi.org/10.1007/s10822-016-9988-y |journal=Journal of Computer-Aided Molecular Design |language=en |volume=31 |issue=3 |pages=287–291 |doi=10.1007/s10822-016-9988-y |pmid=27796615 |bibcode=2017JCAMD..31..287T |s2cid=23373414 |issn=1573-4951|url-access=subscription }}</ref>
These fields can give rise to several applications as shown below.

=== Catalysis ===
[[File:CatalysisScheme.png|thumb|Computational chemistry can help predict values like activation energy from catalysis. The presence of the catalyst opens a different reaction pathway (shown in red) with lower activation energy. The final result and the overall thermodynamics are the same.]]
Computational chemistry is a tool for analyzing catalytic systems without doing experiments. Modern [[Electronic structure|electronic structure theory]] and [[density functional theory]] has allowed researchers to discover and understand [[Catalysis|catalysts]].<ref>{{Cite journal |last1=Elnabawy |first1=Ahmed O. |last2=Rangarajan |first2=Srinivas |last3=Mavrikakis |first3=Manos |date=2015-08-01 |title=Computational chemistry for NH3 synthesis, hydrotreating, and NOx reduction: Three topics of special interest to Haldor Topsøe |url=https://www.sciencedirect.com/science/article/pii/S0021951714003534 |journal=Journal of Catalysis |series=Special Issue: The Impact of Haldor Topsøe on Catalysis |volume=328 |pages=26–35 |doi=10.1016/j.jcat.2014.12.018 |issn=0021-9517}}</ref> Computational studies apply theoretical chemistry to catalysis research. Density functional theory methods calculate the energies and orbitals of molecules to give models of those structures.<ref name="Patel-2020">{{Cite journal |last1=Patel |first1=Prajay |last2=Wilson |first2=Angela K. |date=2020-12-01 |title=Computational chemistry considerations in catalysis: Regioselectivity and metal-ligand dissociation |journal=Catalysis Today |series=Proceedings of 3rd International Conference on Catalysis and Chemical Engineering |volume=358 |pages=422–429 |doi=10.1016/j.cattod.2020.07.057 |s2cid=225472601 |issn=0920-5861|doi-access=free }}</ref> Using these methods, researchers can predict values like [[activation energy]], [[Active site|site reactivity]]<ref name="van Santen-1996">{{Cite journal |last=van Santen |first=R. A. |date=1996-05-06 |title=Computational-chemical advances in heterogeneous catalysis |url=https://dx.doi.org/10.1016/1381-1169%2895%2900161-1 |journal=Journal of Molecular Catalysis A: Chemical |series=Proceedings of the 8th International Symposium on the Relations between Homogeneous and Heterogeneous Catalysis |volume=107 |issue=1 |pages=5–12 |doi=10.1016/1381-1169(95)00161-1 |s2cid=59580128 |issn=1381-1169}}</ref> and other thermodynamic properties.<ref name="Patel-2020" />

Data that is difficult to obtain experimentally can be found using computational methods to model the mechanisms of catalytic cycles.<ref name="van Santen-1996" /> Skilled computational chemists provide predictions that are close to experimental data with proper considerations of methods and basis sets. With good computational data, researchers can predict how catalysts can be improved to lower the cost and increase the efficiency of these reactions.<ref name="Patel-2020" />

=== Drug development ===
Computational chemistry is used in [[drug development]] to model potentially useful drug molecules and help companies save time and cost in drug development. The drug discovery process involves analyzing data, finding ways to improve current molecules, finding synthetic routes, and testing those molecules.<ref name="doi.org"/> Computational chemistry helps with this process by giving predictions of which experiments would be best to do without conducting other experiments. Computational methods can also find values that are difficult to find experimentally like [[Acid dissociation constant|pKa]]'s of compounds.<ref>{{Cite journal |last1=van Vlijmen |first1=Herman |last2=Desjarlais |first2=Renee L. |last3=Mirzadegan |first3=Tara |date=March 2017 |title=Computational chemistry at Janssen |url=https://pubmed.ncbi.nlm.nih.gov/27995515/ |journal=Journal of Computer-Aided Molecular Design |volume=31 |issue=3 |pages=267–273 |doi=10.1007/s10822-016-9998-9 |issn=1573-4951 |pmid=27995515|bibcode=2017JCAMD..31..267V |s2cid=207166545 }}</ref> Methods like density functional theory can be used to model drug molecules and find their properties, like their [[HOMO and LUMO|HOMO and LUMO energies]] and molecular orbitals.  Computational chemists also help companies with developing informatics, infrastructure and designs of drugs.<ref>{{Cite journal |last1=Ahmad |first1=Imad |last2=Kuznetsov |first2=Aleksey E. |last3=Pirzada |first3=Abdul Saboor |last4=Alsharif |first4=Khalaf F. |last5=Daglia |first5=Maria |last6=Khan |first6=Haroon |date=2023 |title=Computational pharmacology and computational chemistry of 4-hydroxyisoleucine: Physicochemical, pharmacokinetic, and DFT-based approaches |journal=Frontiers in Chemistry |volume=11 |bibcode=2023FrCh...1145974A |doi=10.3389/fchem.2023.1145974 |issn=2296-2646 |pmc=10133580 |pmid=37123881 |doi-access=free}}</ref>

Aside from drug synthesis, [[drug carrier]]s are also researched by computational chemists for [[nanomaterials]]. It allows researchers to simulate environments to test the effectiveness and stability of drug carriers. Understanding how water interacts with these nanomaterials ensures stability of the material in human bodies. These computational simulations help researchers optimize the material find the best way to structure these nanomaterials before making them.<ref>{{Cite journal |last1=El-Mageed |first1=H. R. Abd |last2=Mustafa |first2=F. M. |last3=Abdel-Latif |first3=Mahmoud K. |date=2022-01-02 |title=Boron nitride nanoclusters, nanoparticles and nanotubes as a drug carrier for isoniazid anti-tuberculosis drug, computational chemistry approaches |url=https://www.tandfonline.com/doi/full/10.1080/07391102.2020.1814871 |journal=Journal of Biomolecular Structure and Dynamics |language=en |volume=40 |issue=1 |pages=226–235 |doi=10.1080/07391102.2020.1814871 |issn=0739-1102 |pmid=32870128 |s2cid=221403943|url-access=subscription }}</ref>

=== Computational chemistry databases ===
[[Database]]s are useful for both computational and non computational chemists in research and verifying the validity of computational methods. Empirical data is used to analyze the error of computational methods against experimental data. Empirical data helps researchers with their methods and basis sets to have greater confidence in the researchers results. Computational chemistry databases are also used in testing software or hardware for computational chemistry.<ref name="Muresan-2012">{{Citation |last1=Muresan |first1=Sorel |title=Mapping Between Databases of Compounds and Protein Targets |date=2012 |work=Bioinformatics and Drug Discovery |volume=910 |pages=145–164 |editor-last=Larson |editor-first=Richard S. |series=Methods in Molecular Biology |place=Totowa, NJ |publisher=Humana Press |language=en |doi=10.1007/978-1-61779-965-5_8 |isbn=978-1-61779-964-8 |pmc=7449375 |pmid=22821596 |last2=Sitzmann |first2=Markus |last3=Southan |first3=Christopher}}</ref>

Databases can also use purely calculated data. Purely calculated data uses calculated values over experimental values for databases. Purely calculated data avoids dealing with these adjusting for different experimental conditions like zero-point energy. These calculations can also avoid experimental errors for difficult to test molecules. Though purely calculated data is often not perfect, identifying issues is often easier for calculated data than experimental.<ref name="Muresan-2012" />

Databases also give public access to information for researchers to use. They contain data that other researchers have found and uploaded to these databases so that anyone can search for them. Researchers use these databases to find information on molecules of interest and learn what can be done with those molecules. Some publicly available chemistry databases include the following.<ref name="Muresan-2012" />

* [[BindingDB]]: Contains experimental information about protein-small molecule interactions.<ref>{{Cite journal |last1=Gilson |first1=Michael K. |last2=Liu |first2=Tiqing |last3=Baitaluk |first3=Michael |last4=Nicola |first4=George |last5=Hwang |first5=Linda |last6=Chong |first6=Jenny |date=2016-01-04 |title=BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology |journal=Nucleic Acids Research |volume=44 |issue=D1 |pages=D1045–1053 |doi=10.1093/nar/gkv1072 |issn=1362-4962 |pmc=4702793 |pmid=26481362}}</ref>
* [[Protein Data Bank|RCSB]]: Stores publicly available 3D models of macromolecules (proteins, nucleic acids) and small molecules (drugs, inhibitors)<ref>{{Cite journal |last1=Zardecki |first1=Christine |last2=Dutta |first2=Shuchismita |last3=Goodsell |first3=David S. |last4=Voigt |first4=Maria |last5=Burley |first5=Stephen K. |date=2016-03-08 |title=RCSB Protein Data Bank: A Resource for Chemical, Biochemical, and Structural Explorations of Large and Small Biomolecules |journal=Journal of Chemical Education |language=en |volume=93 |issue=3 |pages=569–575 |doi=10.1021/acs.jchemed.5b00404 |bibcode=2016JChEd..93..569Z |issn=0021-9584|doi-access=free }}</ref>
* [[ChEMBL]]: Contains data from research on drug development such as assay results.<ref name="Muresan-2012" />
* [[DrugBank]]: Data about mechanisms of drugs can be found here.<ref name="Muresan-2012" />