Molecular self-assembly is the process by which molecules adopt a defined arrangement without guidance or management from an outside source. There are two types of self-assembly. These are intramolecular self-assembly and intermolecular self-assembly. Commonly, the term molecular self-assembly refers to intermolecular self-assembly, while the intramolecular analog is more commonly called folding.
Molecular self-assembly is a key concept in supramolecular chemistry. This is because assembly of molecules in such systems is directed through noncovalent interactions (e.g., hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, π-π interactions, and/or electrostatic) as well as electromagnetic interactions. Common examples include the formation of micelles, vesicles, liquid crystal phases, and Langmuir monolayers by surfactant molecules. Further examples of supramolecular assemblies demonstrate that a variety of different shapes and sizes can be obtained using molecular self-assembly.
Molecular self-assembly allows the construction of challenging molecular topologies. One example is Borromean rings, interlocking rings wherein removal of one ring unlocks each of the other rings. DNA has been used to prepare a molecular analog of Borromean rings. More recently, a similar structure has been prepared using non-biological building blocks. While a mechanistic understanding of how supramolecular self-assembly occurs remains largely unknown, both experimental and theoretic work has been pursued on this topic.  
Molecular self-assembly underlies the construction of biologic macromolecular assemblies in living organisms, and so is crucial to the function of cells. It is exhibited in the self-assembly of lipids to form the membrane, the formation of double helical DNA through hydrogen bonding of the individual strands, and the assembly of proteins to form quaternary structures. Molecular self-assembly of incorrectly folded proteins into insoluble amyloid fibers is responsible for infectious prion-related neurodegenerative diseases. Molecular self-assembly of nanoscale structures plays a role in the growth of the remarkable β-keratin lamellae/setae/spatulae structures used to give geckos the ability to climb walls and adhere to ceilings and rock overhangs.
Molecular self-assembly is an important aspect of bottom-up approaches to nanotechnology. Using molecular self-assembly the final (desired) structure is programmed in the shape and functional groups of the molecules. Self-assembly is referred to as a 'bottom-up' manufacturing technique in contrast to a 'top-down' technique such as lithography where the desired final structure is carved from a larger block of matter. In the speculative vision of molecular nanotechnology, microchips of the future might be made by molecular self-assembly. An advantage to constructing nanostructure using molecular self-assembly for biological materials is that they will degrade back into individual molecules that can be broken down by the body.
DNA nanotechnology is an area of current research that uses the bottom-up, self-assembly approach for nanotechnological goals. DNA nanotechnology uses the unique molecular recognition properties of DNA and other nucleic acids to create self-assembling branched DNA complexes with useful properties. DNA is thus used as a structural material rather than as a carrier of biological information, to make structures such as two-dimensional periodic lattices (both tile-based as well as using the "DNA origami" method) and three-dimensional structures in the shapes of polyhedra. These DNA structures have also been used as templates in the assembly of other molecules such as gold nanoparticles and streptavidin proteins.
The spontaneous assembly of a single layer of molecules at interfaces is usually referred to as two-dimensional self-assembly. Early direct proofs showing that molecules can assembly into higher-order architectures at solid interfaces came with the development of scanning tunneling microscopy and shortly thereafter. Eventually two strategies became popular for the self-assembly of 2D architectures, namely self-assembly following ultra-high-vacuum deposition and annealing and self-assembly at the solid-liquid interface. The design of molecules and conditions leading to the formation of highly-crystalline architectures is considered today a form of 2D crystal engineering at the nanoscopic scale.
- Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N.R.; Kantorovich, L.; Moriarty, P. (2014). "Mapping the force field of a hydrogen-bonded assembly". Nature Communications. 5. Bibcode:2014NatCo...5E3931S. doi:10.1038/ncomms4931.
- Hapala, Prokop; Kichin, Georgy; Wagner, Christian; Tautz, F. Stefan; Temirov, Ruslan; Jelínek, Pavel (2014-08-19). "Mechanism of high-resolution STM/AFM imaging with functionalized tips". Physical Review B. 90 (8): 085421. doi:10.1103/PhysRevB.90.085421.
- Hämäläinen, Sampsa K.; van der Heijden, Nadine; van der Lit, Joost; den Hartog, Stephan; Liljeroth, Peter; Swart, Ingmar (2014-10-31). "Intermolecular Contrast in Atomic Force Microscopy Images without Intermolecular Bonds". Physical Review Letters. 113 (18): 186102. doi:10.1103/PhysRevLett.113.186102. PMID 25396382.
- Pham, Tuan Anh; Song, Fei; Nguyen, Manh-Thuong; Stöhr, Meike (2014). "Self-assembly of pyrene derivatives on Au(111): Substituent effects on intermolecular interactions". Chem. Commun. 50 (91): 14089–14092. doi:10.1039/C4CC02753A.
- Lehn, J.-M. (1988). "Perspectives in Supramolecular Chemistry-From Molecular Recognition towards Molecular Information Processing and Self-Organization". Angew. Chem. Int. Ed. Engl. 27 (11): 89–121. doi:10.1002/anie.198800891.
- Lehn, J.-M. (1990). "Supramolecular Chemistry-Scope and Perspectives: Molecules, Supermolecules, and Molecular Devices (Nobel Lecture)". Angew. Chem. Int. Ed. Engl. 29 (11): 1304–1319. doi:10.1002/anie.199013041.
- Lehn, J.-M. Supramolecular Chemistry: Concepts and Perspectives. Wiley-VCH. ISBN 978-3-527-29311-7.
- Rosen, Milton J. (2004). Surfactants and interfacial phenomena. Hoboken, NJ: Wiley-Interscience. ISBN 978-0-471-47818-8.
- Ariga, Katsuhiko; Hill, Jonathan P; Lee, Michael V; Vinu, Ajayan; Charvet, Richard; Acharya, Somobrata (2008). "Challenges and breakthroughs in recent research on self-assembly". Science and Technology of Advanced Materials. 9 (1): 014109. Bibcode:2008STAdM...9a4109A. doi:10.1088/1468-6996/9/1/014109. PMC . PMID 27877935.
- Mao, C; Sun, W; Seeman, N. C. (1997). "Assembly of Borromean rings from DNA". Nature. 386 (6621): 137–138. Bibcode:1997Natur.386..137M. doi:10.1038/386137b0. PMID 9062186.
- Chichak, K. S.; Cantrill, S. J.; Pease, A. R.; Chiu, S. H.; Cave, G. W.; Atwood, J. L.; Stoddart, J. F. (2004). "Molecular Borromean Rings". Science. 304 (5675): 1308–1312. Bibcode:2004Sci...304.1308C. doi:10.1126/science.1096914. PMID 15166376.
- Larsen, Randy (2008). "How fast do metal organic polyhedra form in solution? Kinetics of [Cu2(5-OH-bdc)2L2]12 formation in methanol". Journal of the American Chemical Society. 130 (34): 11246–11247. doi:10.1021/ja802605v.
- Alkordi, Mohamed; Belof, Jonathan; Rivera, Edwin; Wojtas, Lukasz; Eddaoudi, Mohamed (2011). "Insight into the construction of metal–organic polyhedra: metal–organic cubes as a case study". Chemical Science. 2 (9): 1695–1705. doi:10.1039/C1SC00269D.
- Min, Younjin; et al. (2008). "The role of interparticle and external forces in nanoparticle assembly". Nature Materials. 7 (7): 527–38. Bibcode:2008NatMa...7..527M. doi:10.1038/nmat2206. PMID 18574482.
- Santos, Daniel; Spenko, Matthew; Parness, Aaron; Kim, Sangbae; Cutkosky, Mark (2007). "Directional adhesion for climbing: theoretical and practical considerations". Journal of Adhesion Science and Technology. 21 (12–13): 1317–1341. doi:10.1163/156856107782328399.
Gecko "feet and toes are a hierarchical system of complex structures consisting of lamellae, setae,and spatulae. The distinguishing characteristics of the gecko adhesion system have been described [as] (1) anisotropic attachment, (2) high pulloff force to preload ratio, (3) low detachment force, (4) material independence, (5) self-cleaning, (6) anti-self sticking and (7) non-sticky default state. ... The gecko’s adhesive structures are made from ß-keratin (modulus of elasticity [approx.] 2 GPa). Such a stiff material is not inherently sticky; however, because of the gecko adhesive’s hierarchical nature and extremely small distal features (spatulae are [approx.] 200 nm in size), the gecko’s foot is able to intimately conform to the surface and generate significant attraction using van der Waals forces.
- Seeman, N. C. (2003). "DNA in a material world". Nature. 421 (6921): 427–431. Bibcode:2003Natur.421..427S. doi:10.1038/nature01406. PMID 12540916.
- Chen, J. & Seeman, N. C. (1991). "Synthesis from DNA of a molecule with the connectivity of a cube". Nature. 350 (6319): 631–633. Bibcode:1991Natur.350..631C. doi:10.1038/350631a0. PMID 2017259.
- Mirkin, C. A.; Letsinger, R. L.; Mucic, R. C.; Storhoff, J. J. (1996). "A DNA-based method for rationally assembling nanoparticles into macroscopic materials". Nature. 382 (6592): 607–609. Bibcode:1996Natur.382..607M. doi:10.1038/382607a0. PMID 8757129.
- Yan, H; Park, S. H.; Finkelstein, G; Reif, J. H.; Labean, T. H. (2003). "DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires". Science. 301 (5641): 1882–1884. Bibcode:2003Sci...301.1882Y. doi:10.1126/science.1089389. PMID 14512621.
- Foster, J. S. & Frommer, J. E. (1988). "Imaging of liquid crystals using a tunnelling microscope". Nature. 333 (6173): 542–545. Bibcode:1988Natur.333..542F. doi:10.1038/333542a0.
- Rabe, J.P. & Buchholz, S. (1991). "Commensurability and Mobility in Two-Dimensional Molecular Patterns on Graphite". Science. 253 (5018): 424–427. Bibcode:1991Sci...253..424R. doi:10.1126/science.253.5018.424. JSTOR 2878886.