What is Molecular Engineering?

Molecular engineering is simply the design and synthesis of molecules with specific properties and functions in mind. Certain chemical groups and atoms incorporated into molecules results in them having certain characteristics. When these molecules are used within a larger system their properties impact the overall function of the system. Atomic-scale changes to a molecule can result in huge changes in the properties of a complex system such as an electronic device or diagnostic test.

Molecular engineering is often described as “bottom-up” engineering as it involves using molecules and atoms as building blocks to build functional materials and devices. It is a rapidly growing field which is relevant to researchers from science, engineering and medical backgrounds.

Engineering Molecules

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Molecular Design

In molecular engineering, a molecule is designed based on its desired application or function. For example, it may be a drug for treating a specific disease or a catalyst for a specific chemical reaction. Once the purpose of the molecule is defined then it’s components can be selected.

An existing molecule may be modified with new chemical groups. By introducing specific functional groups, a molecules hydrophobicity and electronic environment can be altered. This is tuned so that the molecule is compatible with its target application.

Inspired by nature

One of the key figures in nanotechnology, K. Drexler, described biochemical systems as "microtechnology". He drew comparisons between classic engineering technology and molecular components. By using natures molecular machines which can carry out similar functions we can create devices with precise atomic specifications.

Engineering Technology	Function	Natures Molecular Example
Struts, beans, casings	Transmit force, hold positions	Microtubules, cellulose, mineral structures
Fasteners, glue	Connects parts	Intermolecular forces
Pumps	Move fluids	Flagella, membrane proteins
Tools	Modify workpieces	Metallic complexes, functional groups
Programmable Control System	Store and read programs	Genetic system

Dexeler stated: "Development of the ability to design protein molecules will, by analogy between features of natural macromolecules and components of existing machines, make possible the construction of molecular machines. These machines can build second-generation machines able to perform extremely general synthesis of three-dimensional molecular structures, thus permitting construction of devices and materials to complex atomic specifications."

Essentially he said by using what we know about natural biomolecules and their functions we can use them as "molecular machines" to create molecules. Because the molecular machines operate on a molecular scale, we can control the properties of the synthesized molecules at an atomic level.

De Novo Design

De novo design is to create a molecule from scratch, not using a previous molecule as a template. Designing a brand-new chemical structure that meets the requirements of the desired function. This is done using knowledge of the target application. This is common in protein design and engineering.

Computational Modelling

Computational molecular modelling is also used in molecular engineering for visualizing molecular structures, predicting properties, and understanding interactions. It uses mathematical models and algorithms to make the predictions. This process often involves machine learning. As a result, it has accelerated drug discovery by predicting ligand-target interactions, aided in designing advanced materials like polymers and nanomaterials, and optimized chemical reactions and catalysts.

Molecular Synthesis

Molecular synthesis is vital to molecular engineering. As well as selecting the components of a molecule, the way they are bonded together is important. Getting the key functional groups in the correct arrangement is crucial. Selecting the most suitable synthetic method will allow control over stereochemistry and molecular weight which is essential for ensuring the engineered molecules have the desired properties and function.

Some common synthesis techniques include:

• Solution-phase synthesis
• Solid-phase synthesis
• Click Chemistry
• Flow Chemistry
• Photo/electrochemistry
• Metal-Catalyzed coupling reactions
• Biocatalysis
• Total Synthesis

Characterization of Molecules

Another crucial aspect of molecular engineering is the characterization of molecules. Without complete understanding of the properties of the molecules that are designed and synthesized, molecular engineering is useless. Characterization also means that we can take inspiration from molecules that already exist in nature. Understanding how they already exist and perform amazing functions helps us learn how to artificially engineer useful molecules for a huge variety of applications.

Characterization methods include:

Spectroscopic Techniques	Microscopy Techniques	Crystallography	Thermal Analysis	Chromatographic Techniques	Electrophoretic Techniques	Other Analytical Techniques
NMR Spectroscopy Mass Spectroscopy IR Spectroscopy Raman Spectroscopy UV Spectroscopy Fluorescence Spectroscopy X-ray Spectroscopy Circular Dichroism Spectroscopy	Electron Microscopy: TEM, SEM,Cryo-EM Scanning prove Microscopy: AFM, STM Optical Microscopy: confocal, fluorescence, STORM, PALM	X-ray Crystallography Neutron Diffraction Electron Diffraction	Differential Scanning Calorimetry (DSC) Thermogravimetric Analysis (TGA) Differential Thermal Analysis (DTA) Thermomechanical Analysis (TMA)	Gas Chromatography (GC) Liquid Chromatography (LC) High-Performance Liquid Chromatography (HPLC) Ultra-Performance Liquid Chromatography (UPLC) Size Exclusion Chromatography (SEC) Thin Layer Chromatography (TLC)	Gel Electrophoresis Polyacrylamide Gel Electrophoresis (PAGE) Agarose Gel Electrophoresis Capillary Electrophoresis (CE)	Elemental Analysis: Combustion Analysis (CHN Analysis) Isothermal Titration Calorimetry (ITC) Dynamic Light Scattering (DLS) Zeta Potential Analysis Surface Plasmon Resonance (SPR) Quartz Crystal Microbalance (QCM)	Circular Dichroism (CD) Atomic Absorption Spectroscopy (AAS) Inductively Coupled Plasma (ICP) Spectroscopy ICP Optical Emission Spectroscopy (ICP-OES) ICP Mass Spectrometry (ICP-MS)

Applications of Molecular Engineering

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Electronics

The progress of electronic device development has seen some of the greatest benefit as a result of molecular engineering techniques. Miniaturization of electronic devices for more efficient and portable electronics required working on the molecular scale. In fact, this area of research is so big it has its own term - molecular electronics.

Molecular engineering can be used to modify components of electronic devices including:

• Conductive Polymers
• Optoelectronic Materials
• Semiconducting Molecules
• Quantum Dots
• Graphene materials and Carbon Nanotubes
• Fullerenes and Non-Fullerene Acceptors
• Molecular Dyes
• Conductive Inks
• Interface Materials
• Perovskite Materials
• Self-Assembled Monolayers

Medicine and Healthcare

Molecular engineering is being used to make progress in disease diagnostics, prognosis and treatment. There are a huge variety of medical applications that have been improved by molecular engineering including:

Medical Application	Description
Drug discovery	Creating molecules with therapeutic effects to treat diseases
Drug delivery	Using specially designed nanomaterials to deliver drugs to target sites
In vivo imaging	Imaging inside the body to monitor illness using molecular components that target specific sites
Cancer therapy	Molecules that target cancerous cells and are toxic to them
Neuroengineering	Building, repairing or improving neurological pathways
Antibacterial/microbial agents	Molecules designed to kill specific bacteria and microbes
Diagnostic assays	Microarrays and microfluidics using engineered molecules to detect diseases

Biotechnology

Biotechnological developments have been at the heart of molecular engineering since its inception. Drexler compared classic engineering components to biological components in his seminal work on nanotechnology. With the discovery of recombinant DNA which allowed the manipulation of genetic material there has been a boom in biotechnology.

Genetic engineering has seen the development of:

• More resilient crops and animals
• Potential cures for genetic disorders
• Recombinant proteins and hormones such as insulin and growth factors
• Industrial enzymes such as subtilisin, a protease used extensively in laundry detergents and other cleaning products
• Antibodies used in diagnostics and therapies

Nanomaterial research

Molecular engineering has been used in to inform the discovery and development of nanoparticles and nanostructures, including some of the most famous examples:

• Fullerenes
• Carbon Nanotubes
• Graphene

Whilst all these examples are only made of carbon, they have brilliant electronic properties that has seen their use in a huge range of applications, driving the cutting edge of research in electronics. Other popular nanomaterials that have come about as a result of molecular engineering include:

• Quantum Dots
• Silver Nanoparticles
• Metal-organic frameworks

Smart Materials

Smart materials are a category of advanced materials known for their ability to adapt to their environment. Molecular engineering has been used to design molecules that can respond to specific stimuli as the building blocks for such materials.

Smart materials are classified based on their responses to various stimuli, which can be physical (such as pressure, temperature, humidity, light, electric fields, and magnetic fields), chemical (such as pH and CO2 levels), or biological. For example pH responsive materials can change color as a response to a specific pH. This is useful in bandages that can help medicine to indicate any change of burned patient for example.

Environmental science

Many aspects of environmental science have been developed using molecular engineering. This field has seen a significant amount of molecular biological research such as using microorganisms to monitor environmental changes and develop biofuels. Here is a brief summary of how molecular engineering has been use in the environmental sciences:

Application	Description
Biofuels	Engineering microorganisms and enzymes to convert biomass into biofuels
Pollution Control	Designing molecules that can break down pollutants and toxins in the environment
Sustainable Chemistry	Creating green chemical processes that reduce waste and environmental impact
Pesticides and Herbicides	Developing more effective and environmentally friendly agrochemicals
Genetic Modification	:Engineering plants with desirable traits, such as pest resistance, improved yield, and enhanced nutritional content

History of Molecular Engineering

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• 1959: Nobel Laureate Richard Feynman - "There's Plenty of Room at the Bottom " Lecture – “arrange the atoms the way we want”
• 1972: Paul Berg first produced recombinant DNA which allowed the manipulation of genetic material
• 1985: Harold Kroto, Robert Curl, and Richard Smalley discover fullerenes, a new form of carbon with unique properties and applications in nanotechnology.
• 1986: K. Eric Drexler published the first book on nanotechnology: “Engines of Creation: The Coming Era of Nanotechnology.”
• 1991: Sumio Iijima discovers carbon nanotubes, which exhibit extraordinary mechanical and electrical properties, sparking extensive research in nanomaterials.
• 2000: Alan Heeger, Alan MacDiarmid, and Hideki Shirakawa are awarded the Nobel Prize in Chemistry for the discovery and development of conductive polymers.
• 2004: Andre Geim and Konstantin Novoselov isolate graphene, a single layer of carbon atoms with remarkable properties, leading to a surge in research and potential applications.
• 2012: Jennifer Doudna and Emmanuelle Charpentier develop CRISPR-Cas9, a revolutionary gene-editing technology that allows precise modification of DNA sequences.
• 2016: Jean-Pierre Sauvage, Sir J. Fraser Stoddart and Bernard L. Feringa win Nobel Prize in Chemistry for their development of molecular machines.
• 2018: Frances H. Arnold, George P. Smith, and Sir Gregory P. Winter receive the Nobel Prize in Chemistry for directed evolution of enzymes and phage display of peptides and antibodies, respectively, advancing protein engineering.

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