Structural chemistry

Short description: Branch of chemistry which studies 3D structure of molecules

Structural chemistry is a part of chemistry and deals with spatial structures of molecules (in the gaseous, liquid or solid state) and solids (with extended structures that cannot be subdivided into molecules). For structure elucidation[1] a range of different methods is used. One has to distinguish between methods that elucidate solely the connectivity between atoms (constitution) and such that provide precise three dimensional information such as atom coordinates, bond lengths and angles and torsional angles.

## Contents

* 1 Determination methods
* 2 Gaseous state
* 2.1 Electron diffraction
* 2.2 Microwave spectroscopy
* 3 Liquid state
* 3.1 NMR spectroscopy
* 4 Solid state
* 4.1 X-ray diffraction
* 4.2 Electron diffraction
* 4.3 Neutron diffraction
* 5 Importance and contributions
* 5.1 Contributions
* 5.1.1 Drug discovery and design
* 5.1.2 Materials science
* 5.1.3 Catalysis
* 5.1.4 Biological research
* 5.1.5 Environmental science
* 6 Challenges
* 6.1 Complexity of systems
* 6.2 Technological limitations
* 6.3 Data analysis
* 7 Future directions
* 8 See also
* 9 References

## Determination methods

The determination of chemical structure include (mainly):

* for the gaseous state: gas electron diffraction[2] and microwave spectroscopy[3]
* for the liquid state: NMR spectroscopy[4] (note, obtaining precise structural information from liquids and solutions is still rather difficult compared to gases and crystalline solids)
* for the solid state: X-ray,[5] electron diffraction[6] and neutron diffraction[7]

To identify connectivity and the presence of functional groups a variety of methods of molecular spectroscopy and solid state spectroscopy can be used.

## Gaseous state

### Electron diffraction

Main article: Physics:Gas electron diffraction

Gas electron diffraction focuses on determining the geometrical arrangement of atoms in a gaseous molecule. It does this by interpreting the electron diffraction patterns that result when a molecule is intersected by a beam of electrons. Studies have used gas electron diffraction to obtain equilibrium and vibrationally averaged structures of gases.[8] Gas electron diffraction is also crucial for acquiring data on both stable and unstable free molecules, radicals, and ions, providing essential structural information.[9] For instance, the structure of gaseous fluorofullerene C60F36 was determined using electron diffraction supplemented with quantum chemical calculations.[10]

### Microwave spectroscopy

Microwave rotational spectroscopy measures the energies of rotational transitions through microwave radiation for a gaseous molecule. The electric dipole moment of the molecules interacts with the electromagnetic field of the exciting microwave photon, which facilitates the measurement of these transitions.[11] It employs chirped-pulse Fourier transform microwave (FTMW) spectroscopy to determine the rotational constants of compounds.[3] This method has long been regarded as robust for the precise determination of structures, with the ability to discern different conformational states of molecules.[12] Its accuracy is highlighted by its application in providing molecular structure in the gas phase, with rotational transitions being particularly informative when ΔJ = ±1.[13]

## Liquid state

### NMR spectroscopy

Liquid-state NMR spectroscopy has become a principal method for molecular structure elucidation in liquids.[4] It is a flexible method that accommodates a wide array of applications, including structure determination, in situ monitoring, and analysis of mixtures.[14] Techniques like SHARPER (Sensitive, Homogeneous And Resolved PEaks in Real time) have further enhanced the sensitivity of NMR, particularly in reaction monitoring by removing J splittings, which creates very narrow signals that are crucial for accurate analysis.[4] NMR spectroscopy also enables the determination of 3D structures of molecules in the liquid state by measuring interproton distances through Nuclear Overhauser Effect (NOE) experiments.[15]

## Solid state

### X-ray diffraction

Main articles: Physics:X-ray diffraction and X-ray crystallography

X-ray diffraction is a powerful technique for determining the atomic and molecular structure of crystalline solids.[5] It relies on the interaction of X-rays with the electron density of the crystal lattice, producing diffraction patterns that can be used to deduce the arrangement of atoms.[5] This method has been instrumental in elucidating the structures of a wide range of materials, including organic compounds, inorganic compounds, and proteins.

Using X-ray diffraction to determine the structure of membrane protein

### Electron diffraction

Main article: Physics:Electron diffraction

Electron diffraction involves firing a beam of electrons at a crystalline sample.[6] Similar to X-ray diffraction, it produces diffraction patterns that can be used to determine the structure of the sample.[6] Electron diffraction is particularly useful for the study of small organic molecules and complex organic compounds.

### Neutron diffraction

Main article: Physics:Neutron diffraction

Neutron diffraction is a technique that employs a beam of neutrons instead of X-rays or electrons.[7] Neutrons interact with atomic nuclei and are sensitive to the positions of light atoms, such as hydrogen.[7] This method is vital for understanding the structure of materials where hydrogen plays a significant role, such as in hydrogen-bonded systems.

## Importance and contributions

Structural chemistry is pivotal in understanding the fundamental nature of matter and the properties of materials. Structural chemists play a crucial role in various scientific and industrial fields.[16] The prospective of structural chemistry lies in its ability to address real-world challenges, fuel scientific innovation, and contribute to advancements in various fields. Collaboration, technological advancements, and a multidisciplinary approach will continue to shape the future of structural chemistry, paving the way for groundbreaking discoveries and applications.

### Contributions

#### Drug discovery and design

Structural chemists contribute significantly to drug discovery by elucidating the three-dimensional structures of biological molecules, enabling the design of targeted drugs with higher efficacy and fewer side effects.[17]

#### Materials science

Understanding the atomic and molecular arrangements in materials helps in developing new materials with specific properties, leading to innovations in electronics, energy storage, and nanotechnology.[18]

#### Catalysis

Structural chemistry provides insights into the active sites of catalysts, enabling the design of efficient catalysts for chemical reactions, including those used in sustainable energy technologies.[19]

#### Biological research

Structural biologists use techniques like X-ray crystallography and NMR spectroscopy to determine the structures of biomolecules, contributing to our understanding of biological processes and diseases.[20]

#### Environmental science

Structural chemistry aids in analyzing pollutants, understanding their behavior, and developing methods to mitigate environmental impact.[21]

## Challenges

### Complexity of systems

As researchers delve into more complex materials and biological systems, determining their structures accurately becomes challenging due to the intricate interactions and large molecular sizes involved. Recent study has found unprecedented applications in the biological context and for the first time enables scientists to address complex questions in biology on the level of molecules, cells, tissues and entire organs, as well as to begin to address important challenges imposed by cardiovascular diseases, cancer, and in digestive and reproductive biology.[22]

### Technological limitations

The development of advanced experimental techniques and computational methods is essential. High-resolution techniques like cryo-electron microscopy and advancements in computational simulations are addressing some challenges.[23]

### Data analysis

Handling vast amounts of structural data requires sophisticated algorithms and data analysis techniques to extract meaningful information, posing challenges in data interpretation and storage.[24] However, with the advent of deep learning, a branch of machine learning and artificial intelligence, and it has become possible to analyze large datasets with greater accuracy and efficiency.[24] However, method also has its own limitations, such as the lack of training data, imbalanced data, and overfitting.[24]

## Future directions

Combining various experimental and computational techniques can provide comprehensive insights into complex structures. Integrating data from X-ray crystallography, NMR spectroscopy, and computational modeling enhances accuracy and reliability. Continued progress in computational simulations, including quantum chemistry and molecular dynamics, will allow researchers to study larger and more complex systems, aiding in predicting and understanding novel structures.[18][17] Open-access databases and collaborative efforts enable researchers worldwide to share structural data, accelerating scientific progress and fostering innovation.[24]

Structural chemistry can contribute to the design of eco-friendly materials and catalysts, promoting sustainable practices in the chemical industry. Structural chemistry can contribute to the design of eco-friendly materials and catalysts, promoting sustainable practices in the chemical industry. Recent development of metal-free nanostructured catalysts is one of the advancements in the field of structural chemistry that has the potential to drive organic transformations in a sustainable manner.[25]

## See also

* Chemical structure

## References

1. ↑ David W. H. Rankin, Norbert W. Mitzel, Carole A. Morrison (2013). Structural Methods in Molecular Inorganic Chemistry. Chichester: John Wiley & Sons. ISBN 978-0-470-97278-6.
2. ↑ "The use of neutrons for materials characterization". Analysis of Residual Stress by Diffraction using Neutron and Synchrotron Radiation. CRC Press. 2003. pp. 15–39. doi:10.1201/9780203608999-6. ISBN 978-0-429-21190-4.
3. ↑ 3.0 3.1 Martin-Drumel, Marie-Aline; McCarthy, Michael C.; Patterson, David; McGuire, Brett A.; Crabtree, Kyle N. (2016-03-24). "Automated microwave double resonance spectroscopy: A tool to identify and characterize chemical compounds". The Journal of Chemical Physics 144 (12). doi:10.1063/1.4944089. ISSN 0021-9606. PMID 27036441. Bibcode: 2016JChPh.144l4202M.
4. ↑ 4.0 4.1 4.2 Peat, George; Boaler, Patrick J.; Dickson, Claire L.; Lloyd-Jones, Guy C.; Uhrín, Dušan (2023-07-21). "SHARPER-DOSY: Sensitivity enhanced diffusion-ordered NMR spectroscopy" (in en). Nature Communications 14 (1): 4410. doi:10.1038/s41467-023-40130-2. ISSN 2041-1723. PMID 37479704. Bibcode: 2023NatCo..14.4410P.
5. ↑ 5.0 5.1 5.2 "X-ray diffraction | Definition, Diagram, Equation, & Facts | Britannica" (in en). https://www.britannica.com/science/X-ray-diffraction.
6. ↑ 6.0 6.1 6.2 Asadabad, Mohsen Asadi; Eskandari, Mohammad Jafari (2016). "Electron Diffraction". in Janecek, Milos; Kral, Robert (in en). Modern Electron Microscopy in Physical and Life Sciences. InTech. doi:10.5772/61781. ISBN 978-953-51-2252-4. http://www.intechopen.com/books/modern-electron-microscopy-in-physical-and-life-sciences/electron-diffraction. Retrieved 2023-11-07.
7. ↑ 7.0 7.1 7.2 "7.5: Neutron Diffraction" (in en). 2016-07-14. https://chem.libretexts.org/Bookshelves/Analytical_Chemistry/Physical_Methods_in_Chemistry_and_Nano_Science_(Barron)/07:_Molecular_and_Solid_State_Structure/7.05:_Neutron_Diffraction.
8. ↑ Vishnevskiy, Yury V.; Blomeyer, Sebastian; Reuter, Christian G. (2020-04-01). "Gas standards in gas electron diffraction: accurate molecular structures of CO2 and CCl4" (in en). Structural Chemistry 31 (2): 667–677. doi:10.1007/s11224-019-01443-5. ISSN 1572-9001.
9. ↑ Demaison, Jean; Vogt, Natalja (2020), "Molecular Structures from Gas-Phase Electron Diffraction" (in en), Accurate Structure Determination of Free Molecules, Lecture Notes in Chemistry (Cham: Springer International Publishing) 105: pp. 167–204, doi:10.1007/978-3-030-60492-9_7, ISBN 978-3-030-60492-9
10. ↑ Belyakov, Alexander V.; Kulishenko, Roman Yu.; Johnson, Robert D.; Shishkov, Igor F.; Rykov, Anatolii N.; Markov, Vitaliy Yu.; Khinevich, Viktor E.; Goryunkov, Alexey A. (2020-12-10). "Structure of C 60 F 36: A Gas-Phase Electron Diffraction and Quantum Chemical Computational Study of a Remarkably Distorted Fluorofullerene" (in en). The Journal of Physical Chemistry A 124 (49): 10216–10224. doi:10.1021/acs.jpca.0c05714. ISSN 1089-5639. PMID 33200926. Bibcode: 2020JPCA..12410216B. https://pubs.acs.org/doi/10.1021/acs.jpca.0c05714.
11. ↑ "1.10: Microwave Spectroscopy" (in en). 2023-01-10. https://chem.libretexts.org/Courses/Grinnell_College/CHM_363:_Physical_Chemistry_1_(Grinnell_College)/01:_Energy_Levels_and_Spectroscopy/1.10:_Microwave_Spectroscopy.
12. ↑ Bernstein, Elliot R. (2020) (in en). Intra- and Intermolecular Interactions Between Non-covalently Bonded Species. Elsevier. pp. 97–98. ISBN 978-0-12-817586-6.
13. ↑ 1\. Purusottam 2. A. Welford, 1.Jena 2. Castleman (2010) (in en). Science and Technology of Atomic, Molecular, Condensed Matter & Biological Systems. Elsevier. pp. 173–175. ISBN 978-0-444-53440-8.
14. ↑ Aggarwal, Priyanka; Kumari, Pooja; Bhavesh, Neel Sarovar (2022-01-01), Tripathi, Timir; Dubey, Vikash Kumar, eds., "Chapter 16 - Advances in liquid-state NMR spectroscopy to study the structure, function, and dynamics of biomacromolecules", Advances in Protein Molecular and Structural Biology Methods (Academic Press): pp. 237–266, doi:10.1016/b978-0-323-90264-9.00016-7, ISBN 978-0-323-90264-9, https://www.sciencedirect.com/science/article/pii/B9780323902649000167, retrieved 2023-12-08
15. ↑ Purslow, Jeffrey A.; Khatiwada, Balabhadra; Bayro, Marvin J.; Venditti, Vincenzo (2020-01-28). "NMR Methods for Structural Characterization of Protein-Protein Complexes". Frontiers in Molecular Biosciences 7: 9. doi:10.3389/fmolb.2020.00009. ISSN 2296-889X. PMID 32047754.
16. ↑ Maier, Joachim (2004-04-02). Physical Chemistry of Ionic Materials. Wiley. doi:10.1002/0470020229. ISBN 978-0-471-99991-1.
17. ↑ 17.0 17.1 Provasi, Davide; Filizola, Marta (2023-08-07). "Enhancing Opioid Bioactivity Predictions through Integration of Ligand-Based and Structure-Based Drug Discovery Strategies with Transfer and Deep Learning Techniques". BioRxiv: The Preprint Server for Biology. doi:10.1101/2023.08.04.552065. PMID 37609329.
18. ↑ 18.0 18.1 Eguchi, Miharu; Han, Minsu; Asakura, Yusuke; Hill, Jonathan P.; Henzie, Joel; Ariga, Katsuhiko; Rowan, Alan E.; Chaikittisilp, Watcharop et al. (2023-11-13). "Materials Space-Tectonics: Atomic-level Compositional and Spatial Control Methodologies for Synthesis of Future Materials" (in en). Angewandte Chemie International Edition 62 (46). doi:10.1002/anie.202307615. ISSN 1433-7851. PMID 37485623.
19. ↑ Liu, Lichen; Corma, Avelino (April 2021). "Structural transformations of solid electrocatalysts and photocatalysts" (in en). Nature Reviews Chemistry 5 (4): 256–276. doi:10.1038/s41570-021-00255-8. ISSN 2397-3358. PMID 37117283. https://www.nature.com/articles/s41570-021-00255-8.
20. ↑ Brito, José A.; Archer, Margarida (2020-01-01), Crichton, Robert R.; Louro, Ricardo O., eds., "Chapter 10 - Structural biology techniques: X-ray crystallography, cryo-electron microscopy, and small-angle X-ray scattering", Practical Approaches to Biological Inorganic Chemistry (Second Edition) (Elsevier): pp. 375–416, doi:10.1016/b978-0-444-64225-7.00010-9, ISBN 978-0-444-64225-7, https://www.sciencedirect.com/science/article/pii/B9780444642257000109, retrieved 2023-12-08
21. ↑ "How chemistry is helping to improve the environment around us" (in en-GB). https://www.rsc.org/policy-evidence-campaigns/environmental-sustainability/global-challenges/environment/.
22. ↑ "Complex rheology in biological systems | Royal Society". 6 August 2017. https://royalsociety.org/blog/2022/10/complex-rheology-in-biological-systems/.
23. ↑ "Cryo-Electron Microscopy - What it is, How it Works and Pros and Cons". https://www.microscopemaster.com/cryo-electron-microscopy.html.
24. ↑ 24.0 24.1 24.2 24.3 Sarker, Iqbal H. (2021-08-18). "Deep Learning: A Comprehensive Overview on Techniques, Taxonomy, Applications and Research Directions" (in en). SN Computer Science 2 (6): 420. doi:10.1007/s42979-021-00815-1. ISSN 2661-8907. PMID 34426802.
25. ↑ Gholipour, Behnam; Shojaei, Salman; Rostamnia, Sadegh; Naimi-Jamal, Mohammad Reza; Kim, Dokyoon; Kavetskyy, Taras; Nouruzi, Nasrin; Jang, Ho Won et al. (2021-08-31). "Metal-free nanostructured catalysts: sustainable driving forces for organic transformations" (in en). Green Chemistry 23 (17): 6223–6272. doi:10.1039/D1GC01366A. ISSN 1463-9270. https://pubs.rsc.org/en/content/articlelanding/2021/gc/d1gc01366a.

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