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Molecular engineering is any means of manufacturing molecules or creating new manufacturing materials using them. It may be used to create, on an extremely small scale, most typically one at a time, new molecules which may not exist in nature, or be stable beyond a very narrow range of conditions.
Today this is an extremely difficult process, requiring manual manipulation of molecules using such devices as a scanning tunneling microscope. Eventually it is expected to exploit lifelike self-replicating 'helper molecules' that are themselves engineered. Thus the field can be seen as a precision form of chemical engineering that includes protein engineering, the creation of protein molecules, a process that occurs naturally in biochemistry, e.g., prion reproduction. However, it provides far more control than genetic modification of an existing genome, which must rely strictly on existing biochemistry to express genes as proteins, and has little power to produce any non-proteins.
Emergence of scanning tunneling microscopes and picosecond-burst lasers in the 1990s, plus discovery of new carbon nanotube applications to motivate mass production of these custom molecules, drove the field forward to commercial reality in the 2000s.
As it matures, it is seeming to converge with mechanical engineering, since the molecules being designed often resemble small machines. A general theory of molecular mechanosynthesis to parallel that of photosynthesis and chemosynthesis (both used by living things) is the ultimate goal of the field. This may lead to a molecular assembler, according to some, such as K. Eric Drexler, Ralph Merkle, and Robert Freitas, and of the potential for integrating vast numbers of assemblers into a kg-scale nanofactory.
Molecular engineering is sometimes called generically "nanotechnology", in reference to the nanometre scale at which its basic processes must operate. That term is considered to be vague, however, due to misappropriation of the word in association with other techniques, such as X-ray lithography, that are not used to create new free-floating ions or molecules.
Future developments in molecular engineering hold out the promise of great benefits, as well as great risks. See the nanotechnology article for an extensive discussion of the more speculative aspects of the technology. Of these, the one that sparks the most controversy is that of the molecular assembler.
A 2013 paper published in the journal Science details a new method of synthesizing a peptide in a sequence-specific manner by using an artificial molecular machine that is guided by a molecular strand. This functions in the same way as a ribosome building proteins by assembling amino acids according to a messenger RNA blueprint. The structure of the machine is based on a rotaxane, which is a molecular ring sliding along a molecular axle. The ring carries a thiolate group which removes amino acids in sequence from the axle, transferring them to a peptide assembly site. 
In two dimensions
The study and fabrication of molecular-precise architectures confined at interfaces (i.e., molecular thick architectures) has rapidly emerged as a scientific approach towards supramolecular and molecular engineering. The fabrication step of such architectures (often referred as molecular self-assembly depending on the deposition process and interactions involved) relies in the use of solid interfaces to create adsorbed monolayers. Just recently, have such two-dimensional (or "on-surface") chemistry and physics yielded large-scale molecular-precise structures of technological relevance. Albeit spatial control and working devices remain to be evidenced in the field, predictive (computational) models as well as advances in the thermo- and photo- chemical physics of monolayers are expected to bring the field to technology within the next 10 years.
It is worth noting that the ansatz of a molecular assembler or STM manipulation experiments aim at achieving atom-by-atom fabrication, i.e. fabrication with resolutions of ca. 3Åx3Åx3Å. On the other hand (2D) on-surface molecular engineering will be intrinsically limited to the size of the molecules which are capable of encoding complex physico-chemical information. This might be considered a technique having a maximum resolution of ca. 20Åx20Åx3Å. In contrast, state-of-the art lithography methods, a form of less-precise molecular engineering, is expected to achieve a resolution of 50Åx50Åx50Å by 2016.
- Chemical Engineering
- Biomolecular engineering
- Weapons of mass destruction
- Technological singularity
- Molecular modelling
- Molecular design software
Corporations specializing in molecular engineering
- Sequence-Specific Peptide Synthesis by an Artificial Small-Molecule Machine
- J.V. Barth, G. Constantini, K. Kern (2005). "Engineering atomic and molecular nanostructures at surfaces". Nature 437: 671–679. doi:10.1038/nature04166.
- A. Ciesielski, C.-A. Palma, M. Bonini, P. Samori (2010). "Towards Supramolecular Engineering of Functional Nanomaterials: Pre-Programming Multi-Component 2D Self-Assembly at Solid-Liquid Interfaces". Advanced Materials 22: 3506–3520. doi:10.1002/adma.201001582.
- Jinming Cai, Pascal Ruffieux, Rached Jaafar, Marco Bieri, Thomas Braun, Stephan Blankenburg, Matthias Muoth, Ari P. Seitsonen, Moussa Saleh, Xinliang Feng, Klaus Müllen & Roman Fasel (2010). "Atomically precise bottom-up fabrication of graphene nanoribbons". Nature 466: 470. doi:10.1038/nature09211.
- C.-A. Palma, P. Samori (2011). "Blueprinting macromolecular electronics". Nature Chemistry 3: 431–436. doi:10.1038/nchem.1043.