As educational program I cite the material of N.V. Rebrov, a student of the national Donetsk Technical University, who, by the way, is currently being shot by the "National Guard" of Ukraine from heavy guns at the direction of Jewish Kyiv:
SELF-ASSEMBLY IN NANOTECHNOLOGIES
Among the various promising approaches to the formation of nanostructures, nanotechnologies that use self-organization are becoming increasingly important. It is assumed that self-organization will make it possible to create nanostructures from individual atoms as a “bottom-up” technology. Molecular self-assembly, in contrast to the "top-down" approach of nanotechnology, such as lithography, where the desired nanostructure emerges from a larger preform, is an important component of the "bottom-up" approach, where the desired nanostructure is the result of a peculiar programming of the shape and functional groups of molecules.
What nanostructures can be built using these technologies? We are talking about different materials, since these technologies allow you to create devices, forming them from atoms and molecules, using self-organization processes in the way that nature uses them. In nature, such systems really exist and similar processes are carried out. The most striking example is the assembly of the most complex biological objects based on the information recorded in DNA (see Fig. 1).
Figure 1 - An example of self-assembly of a biological structure
As it was before? We took, say, a piece of iron and made a hammer out of it, simply removing everything superfluous (top-down technology). Nanotechnology, in the near future, will make it possible to make products from materials from scratch, and it will not always be necessary to add atom to atom "manually", we will be able to use the phenomenon of self-organization, self-assembly of nanostructures and nanodevices. At the same time, it is rather difficult to expect that at the nanolevel it is possible to artificially manipulate individual nanoobjects in order to "manually" assemble the material. This is not yet practical (slow and requires a lot of work). Therefore, a natural way to obtain nanomaterials can be self-organization.
self-assembly(English self-assembly) is a term for describing the processes as a result of which unorganized systems, due to the specific, local interaction of system components, come to an ordered state.
Self-assembly can be both static and dynamic. In the case of static self-assembly, the organizing system approaches the state of equilibrium, reducing its free energy. In the case of dynamic self-assembly, it is more correct to use the term self-organization.
Self-organization in classical terms can be described as the spontaneous and reversible organization of molecular units into an ordered structure through non-covalent interactions. Spontaneity means that the interactions responsible for the formation of a self-assembled system manifest themselves on a local scale, in other words, the nanostructure builds itself.
Under certain conditions, micro- or nano-objects themselves begin to line up in the form of ordered structures. There is no contradiction with the fundamental laws of nature here - the system in this case is not isolated, and some external influence is exerted on nano-objects. However, this action is directed not to a specific particle, as happens in the “top-down” assembly, but to everything at once. You do not need to build the required structure manually by placing nano-objects at the required points in space one by one - the conditions created are such that nano-objects do it themselves and at the same time. Processes that use the creation of such special conditions are called self-assembly processes, and even now they play a crucial role in many fields of science and technology.
For self-assembling components, all that is required of a person is to place enough of them in a test tube and allow them to automatically assemble into the desired configurations according to their natural properties.
To date, two-dimensional and three-dimensional organized arrays of Pt, Pd, Ag, Au, Fe, Co nanocrystals, Fe-Pt, Au-Ag alloys, CdS/CdSe, CdSe/CdTe, Pt/Fe, Pd/Ni nanostructures, etc. have been synthesized. d. In addition, for anisotropic nanoparticles, it was possible to achieve the formation of orientationally ordered arrays. Nanoparticles of uniform size can be "assembled" into spatially ordered structures, which are one-dimensional "threads", two-dimensional densely packed layers, three-dimensional arrays, or "small" clusters. The type of organization of nanoparticles and the structure of the resulting array depend on the synthesis conditions, particle diameter, and the nature of the external action on the structure.
Today, various self-assembly methods are known that make it possible to obtain useful ordered structures from microparticles. To create special conditions under which self-assembly occurs in a particular system, gravitational, electric or magnetic fields, capillary forces, playing on the wettability-nonwetting of system components, and other techniques can be used. Currently, self-assembly processes are beginning to be actively used in production.
The essence of the phenomenon of self-assembly
In modern science there is a huge factual material of experimental observations of the phenomenon of self-assembly. Particularly impressive are observations of the self-assembly of biological objects, in particular Klug's work on the assembly of plant viruses, awarded the Nobel Prize in 1982. Experimental studies of self-assembly are predominantly ascertaining in nature and provide extensive knowledge about how this happens. The question of why this happens in this way and not otherwise is a challenge to modern natural science.
Let us consider the well-studied T4 bacteriophage virus assembly scenario, which is described in all textbooks and is a classic object of self-assembly study. A simplified version of the scenario is shown in Fig. 2. The assembly involves 54 types of proteins, which are aggregated strictly in a certain sequence into subaggregates of various levels, and then the subaggregates are assembled into a complete viral particle, which includes more than a thousand protein molecules. It makes no sense to model this finely coordinated, branched hierarchical process by means of stochastic representations of randomly colliding molecules.
Figure 2 - Scenario for assembly of bacteriophage T4
Undoubtedly, the virus assembly process is deterministic and controllable, and in order to fully understand this process, it is necessary to determine the means of determination and control mechanisms. Scientific thinking in the second half of the 20th century was fascinated by the creation of a computer and the discovery of a protein synthesis control system. Both systems are ideologically identical and embody the principle of concentrated control. The carrier of concentrated control is a sign system - a linear imperative control language. It is quite natural that the first attempts at mathematical modeling of the processes of self-assembly and self-reproduction were made within the framework of automata theory, for example, von Neumann. However, the data of experimental observations do not confirm the validity of such models. Self-assembly processes do not fit into the lumped control scheme.
Experimental data allow us to assert that in the process of self-assembly there is no control element and no sign system is found in any form that describes the sequence of assembly acts or the order of arrangement of elements in the structure of self-assembly products. The specificity of the self-assembly phenomenon lies in the fact that the process is undoubtedly determined, but the mechanism of determination does not fit into a simple and understandable method of concentrated control.
Self-assembly is an implementation of the distributed control method, in which control functions are implemented in the internal structure of the elements involved in the process, and the control information that determines the process is distributed among all elements. Consequently, the carrier of determination in distributed control is specific sign systems that are fundamentally different from the simplest imperative linear languages, like computer languages or the DNA-protein system. The main task of the study of self-assembly is to determine the logic of the relationship of elements and the search for sign systems, carriers of distributed control.
Consider a hypothetical self-assembly scenario that meets the requirements of distributed control implementation. Some steps of the script are shown in Fig.3.
Figure 3 - Hypothetical scenario of elements interaction
Let us assume that in the assembly of the simplest structure, a tube, molecules of two types, a sphere and an amphora, are involved. We consider only the logical aspect of self-assembly and do not yet involve the physicochemical basis of interaction in the description. The ball and amphora &mdash are abstractions endowed with the ability to some postulated montage activity. The abstraction "combination lock" is introduced into the composition of the element. The assembly act is possible only if the lock codes match. The amphora and the ball have different combination locks K1 and K2, so two balls are linked at the first assembly step. As a result, a sub-unit with a new combination lock K2 is formed. Further, an amphora with a K2 code lock is docked to the sub-aggregate and a “tooth” sub-aggregate with a K3 code lock is formed. Further, disks are built from the teeth as sectors, and the disks are assembled into a tube. In order to construct such a scenario, it is necessary to postulate a procedure for an elementary assembly act.
We define the elementary act of assembly as a procedure consisting of four steps:
.activation of the code lock;
.search and convergence of two elements with matching lock codes;
.activation of locks
.deactivation of their activity, the formation of a new combination lock to continue the process.
Thus, at each assembly step, the assembly acts are determined by the states of the code locks, and the execution of the assembly act ends with the generation of a new code and a new lock.
To date, there are mathematical tools that can describe the logical aspect of self-assembly processes. Stream production systems meet the requirements for sign systems that support distributed control and can act as determinants of the self-assembly process at the logical level. The next next task is a joint work with physical chemists and biologists on the construction of flow production systems that simulate at the logical level real scenarios of self-assembly of specific objects. This will be followed by a search for elements of flow production systems in the physical and chemical structure of the elements of self-assembly participants. The greatest readiness for such programs is in the area of plant virus research. .
If someone thinks that a student of Donetsk University N.V. Rebrov wrote nonsense here, I quote the material that I read 20 years ago and which I cited in my book "Geometry of Life" .
There is a very important observation about the "auto-assembly" of organic structures by the Soviet Academician V.A. Engelhardt(1894-1984).
Here is what he writes about this phenomenon in the article “On some attributes of life: hierarchy, integration, “recognition”.(The article was published in the collection: "Philosophy, natural science, modernity", Moscow, "Thought", 1981).
“The phenomena of “recognition” and at the same time integration in a particularly distinct, almost visually perceptible form (if you resort to the help of an electron microscope) are expressed in the processes of the so-called self-assembly of supramolecular structures, such as viruses and phages, ribosomes or enzyme particles with a complex structure . A large number of processes of this kind have already been studied in detail. They essentially boil down to the fact that if a complex, multicomponent object is artificially decomposed into its component parts by one or another sparing methods, isolated from each other, and then mixed in appropriate proportions and favorable conditions are created, then they will spontaneously reassemble into their original integrity. Its usefulness is easily and with the utmost convincingness proved by the fact that not only its original morphological structure is restored, but also its specific biological properties, for example, catalytic activity in enzymes, infectious properties in viruses, etc.”
As you all, friends, understand, the course of the described processes "recognition" And self-assembly molecular structures into something "whole" and at the same time alive, animated(!), cannot be represented without processes information and energy interaction of the microcosm with the macrocosm. How such a process of information-energy interaction between the macro- and microworld proceeds was quite clearly described by the Soviet scientist, Professor Alexander Leonidovich Chizhevsky (1897-1964), the creator of the new science - " Heliobiology".
“The process of development of the organic world is not an independent, autochthonous, self-contained process, but is the result of the action of terrestrial and cosmic factors, of which the latter are the most important, since they determine the state of the earth's environment.At every given moment, the organic world is under the influence of the cosmic environment and most sensitively reflects in itself, in its functions, the changes or fluctuations that take place in the cosmic environment. We can easily imagine this dependence if we remember that even a slight change in the temperature of our Sun would have to lead to the most fabulous, incredible changes in the entire organic world. And there are a lot of such important factors as temperature: the space environment brings to us hundreds of different, constantly changing and fluctuating forces from time to time. Some electromagnetic radiation coming from the Sun and stars can be divided into a very large number of categories, differing from one another in wavelength, amount of energy, degree of permeability and many other properties ... "
It only remains for me to add: in the same way as one is born in Nature according to the principle "self-assembly" various viruses and phages, just like the principle of "self-assembly" in the ocean world ether, which the ancient sages rightly considered cradle of life and the medium of propagation of heat and light, all life in general was born. In considering this information, I would recommend taking into account the fact that spontaneous generation complex forms of life on earth occurs occasionally and these evolutionary processes, apparently, are associated with cataclysms of a global scale, for example, such as the change of the Earth's poles or the fall of giant asteroids to the Earth. In nature, nothing happens by chance, everything is natural, therefore, any global process must be related to something else. global process. And when something perishes on a planetary or even cosmic scale, something else is born at the same time.
In recent years, the concept of "self-organization" has been widely used to describe and explain similar phenomena in physical, chemical, biological, and even economic and sociological systems. It would seem that, contrary to generally accepted thermodynamic laws, in a distributed dynamic system consisting of its inherent simple elements, order arises - complex structures, complex behavior, or complex spatio-temporal phenomena. At the same time, the properties of the emerging structures are fundamentally different from the properties of the initial elements of the system. And the most surprising thing is that self-organization in the system appears spontaneously from a homogeneous state.
Self-organization is a phenomenon of spontaneous formation of a structure in systems that are different in their physical nature. The spontaneous emergence of a structure means the appearance of an ordered state in an initially random distribution of system components without visible external influence. Ordered states in the general case can be a spatially non-uniform distribution of the material components of the system that persists in time; undamped fluctuations in the concentrations of system components when they oscillate between two or more values; more complex forms of ordered collective behavior of components. The formation of a structure is equally inherent in both physical devices such as lasers, and chemical reaction media and biological tissues, communities of living organisms, geological and meteorological processes, and social phenomena of human society. Self-organization mechanisms turn out to be different for systems of different nature, but nevertheless, they all have some common structural and dynamic characteristics.
Systems that are different in nature can correspond to different, often sharply different levels of complexity of self-organization. This complexity is determined by the nature of the self-organizing system - the complexity of its structure and behavior, the dynamic mechanisms of interaction between components. Thus, the much more complex behavior of collective insects (bees, termites, ants) in comparison with bacteria and viruses underlies much more complex processes of self-organization of behavior in the community of collective insects. At the same time, specific manifestations of self-organization processes at relatively simple levels of its complexity can act as an integral part of phenomena at a more complex level.
Vivid and consistent examples of self-organization have been found among physical systems. The concept of self-organization has also spread to chemical phenomena, where, along with it, the term "self-assembly" is widely used. And in biology, self-organization during the second half of the 20th century became the central concept in describing the dynamics of biological systems, from intracellular processes to the evolution of ecosystems. Thus, self-organization is an interdisciplinary phenomenon and belongs to the field of knowledge, which is usually called cybernetics or more narrowly synergy.
Any particular process of self-organization is based on some dualism. On the one hand, the self-organization of the system is carried out by specific physical, chemical or some other mechanisms. On the other hand, in order for a system to be self-organizing, it is necessary to fulfill the cybernetic conditions common to all self-organizing systems - the general principles of self-organization.
- 1. Processes of self-organization arise in distributed dynamic systems. A distributed system should be a collection of a large number of individual components, elements that make up the system. These may include individual molecules in chemical reaction-diffusion systems, individuals in a school of fish, individuals in a crowd gathered in a square. These components must interact with each other, i.e. the system must be dynamic, functioning on the basis of dynamic mechanisms.
- 2. An important feature of self-organization processes is that they are carried out in open systems. In a thermodynamically closed system, evolution in time leads to an equilibrium state with the maximum value of the entropy of the system. And, according to Boltzmann, this is the state with the maximum degree of chaos.
- 3. Positive and negative feedbacks should appear in the system. The processes occurring in a dynamic system tend to change the initial relationships between the system components involved in these processes. This can be conditionally called changes in the output of the system. At the same time, these components are the initial ones for the processes occurring in the system; they are also the parameters at the entrance to the system. If changes in the output of the system affect the input parameters in such a way that the changes in the output are amplified, this is called positive feedback. Under negative feedback the situation when the dynamic processes in the system maintain a constant output state is implied. In the general case, dynamic systems with positive and negative feedbacks are modeled by nonlinear differential equations. This is a reflection of the non-linear nature of systems capable of self-organization, which is apparently the main property of a system that determines its ability to self-organize.
The concept of "self-assembly" has a chemical origin. It was introduced in 1987 by the French chemist J.-M. Len in order to single out among the numerous phenomena of self-organization the processes of spontaneous structure formation in systems that are in a state of thermodynamic equilibrium. Indeed, a large number of such processes of structure formation are known under equilibrium, or rather close to equilibrium, conditions. Among them are, for example, "helix-coil" transitions in polymer molecules, the formation of supramolecular structures of amphiphilic molecules (micelles, liposomes, bilayers), etc., up to crystallization. Basically, the term "self-assembly" is used in relation to molecular systems. Nevertheless, processes related to self-assembly were also found in the case of other micrometer-sized formations.
self-assembly called a process in which a spontaneously ordered whole (aggregate) is formed from individual components or components of a mixture due to the minimization of their total energy. In nature, the final conformation of a huge number of macromolecules (such as proteins, micelles, liposomes and colloids) is formed by self-assembly during the folding process. There are many examples of natural self-assembly, spontaneously occurring under the influence of natural forces. Such natural self-assemblies are observed at all levels (from molecular to macromolecular) and in various systems of living matter.
Self-assembly in nanotechnology covers a wide range of concepts and ways of complicating the structure, from growing crystals to creating perfect biological organisms. With the help of natural mechanisms in such self-assemblies, it is possible to form and create various nanostructures and further larger systems and materials with the required physical and chemical properties. Enlarged heterogeneous aggregates should be suitable for performing various complex functions or creating new forms of materials with unusual properties.
The implementation of guided self-assembly of the required artificial nanostructures from molecular "building" blocks is the main task of nanotechnology. Of course, to solve it, it is necessary to use information about the intermolecular interaction between molecular "building" blocks, the spatial arrangement of nanostructures, the results of computer molecular modeling, and bionics data. By bionics is meant the production of artificial objects based on the structures and functions of biological substances that imitate natural systems.
Self-assembly is the main process (or driving force) that led from inanimate matter to the evolution of the biological world. Understanding, inducing and guiding self-assembly is the key to a gradual transition to bottom-up nanotechnology. If you know the principles of self-assembly, you can understand the role of various forces of intermolecular interaction that govern this self-assembly. To induce the process of the required self-assembly and control it, it is also necessary to be able to model and predict the course of the self-assembly process under various conditions.
The success of self-assembly is determined by five factors:
- 1. The presence of molecular "building" blocks. Of greatest interest for nanotechnology are self-assemblies of molecules of large sizes, in the range from 1 to 100 nm. At the same time, the larger and more well-structured are the initial molecular "building" blocks, the higher the level of technical control over the rest of the molecules and their interactions, which greatly facilitates the process of self-assembly. As the most versatile and promising categories of molecular "building" blocks, diamondoids can be considered - hydrocarbons in which carbon atoms form a tetrahedral spatial lattice, exactly the same as in diamond (adamantanes, diamantanes and triamantanes).
- 2. Intermolecular interactions. Usually, the forces that ensure self-assembly are determined by weak non-covalent intermolecular bonds: electrostatic and hydrogen bonds, van der Waals, polar, hydrophobic and hydrophilic interactions. The compatibility of individual parts and the stability of the entire self-assembly complex is provided by a large number of such weak interactions for the conformation of each molecular site. An example of a stable self-assembly built with weak interactions is the structure of proteins.
- 3. process reversibility. Existing as well as proposed self-assemblies in nanotechnology are controlled but spontaneous processes during which molecular building blocks are combined into the required ordered assemblies or complexes. For such a process to be spontaneous, it must be carried out in a reversible way.
- 4. Ensuring the mobility of molecules. Due to the dynamic nature of the self-assembly process, a liquid medium is required to carry it out. The environment that can be used may include: liquids, gases, fluids in a supercritical state, interphase boundaries between crystals and liquids from the liquid phase, etc. In all these cases, during self-assembly, dynamic exchange processes must occur in the direction of achieving a minimum energy value systems.
- 5. Process environment. Self-assembly is significantly influenced by the environment. The resulting molecular aggregate is an ordered set of particles that has the most thermodynamically stable conformation. Self-assembly occurs in liquid and gaseous media (including dense gas-supercritical fluid media), near the interface between a crystal and a fluid, or at an interface between a gas and a liquid.
At each stage of the assembly, at least one component must diffuse freely in the solvent to find a specific binding site intended only for it after examining all possible positions and orientations. This requires that the component be soluble, have a surface that is complementary to the surface of its specific binding site, and that all other surfaces of the preform and component be non-complementary to prevent their stable binding. These parameters complement the functional requirements: for the formation of complex structures using self-assembly, materials and working environments in natural conditions are most suitable. This process has been successfully used in supramolecular chemistry and is also widely used to control molecular crystallization.
Consider the self-assembly methodology. There are two types of it, which are based on two processes occurring, firstly, at the interface between the liquid and solid phases and, secondly, inside the fluid phase. The fluid phase can be taken as a liquid, steam, or dense gas (in the supercritical state).
There are a number of laboratory self-assembly methods that use a fluid medium as an external medium for the association of molecules, and a solid surface as a basis for nucleation and growth.
The fixation of molecules as seeds for assembly on solid substrates used for self-assembly can be carried out by the formation of covalent or non-covalent bonds between the molecule and the surface. The first cause irreversible and, therefore, stable fixation at all stages of assembly. Fixation with the help of the latter is a reversible process, at the beginning of which it is unstable, but becomes stable with the appropriate development of the self-assembly process.
The most commonly used covalent bond for fixation is the sulfide-noble metal bond. One such example is the covalent bond between thiol-containing molecules (such as alkanethiol chains or proteins containing cystine in the structure) and gold. Typical non-covalent bonds used for fixation include the following three types of binding: 1) due to the energy of affinity for antibodies; 2) due to affinity energy using the biotin-streptavidin system and its modification; 3) complexation with fixed metal ions.
The self-assembly of a monolayer is of great practical importance. By definition, a self-assembled monolayer is a one molecule thick two-dimensional film that forms covalent bonds with a solid surface. Self-assembly of a monolayer is widely used in nanotechnology, including nanolithography, in modifying the adhesive properties and wetting characteristics of surfaces, in the development of chemical and biological sensors, insulating layers in microelectronic circuits and in the manufacture of nanodevices, etc.
Various methods for obtaining self-assembling monolayers (SCM) of proteins:
Let us consider various ways of self-assembly of a protein monolayer (Fig. 6.14).
- 1. physical adsorption. This technique is based on the adsorption of proteins on solid surfaces such as carbon electrode, metal oxide or silicon oxide. The adsorbed proteins form a self-assembling monolayer with randomly oriented proteins. The control of orientation characteristics can be improved by modifying the protein and the surface itself, as shown in Fig. 6.14a.
- 2. Incorporation of polyelectrolytes or conductive polymers, which can serve as a matrix, the surface of which captures, fixes and adsorbs proteins. This process is shown in Fig. 6.146.
- 3. Incorporation of alkanethiol chains into a self-assembling monolayer creates a membrane-like monolayer on the noble metal, while proteins can be physically adsorbed (a); inclusion of proteins in polyelectrolytes or conductive polymers (b); interspersed in SCM (c); joining the CCM with a non-oriented location ( G); connection to the SMS with oriented location (b); direct site-specific attachment to the gold surface (e).
arranged without any particular orientation. If chains of different lengths are used (creating dents and pits), then this will determine a certain topography of the self-assembling monolayer, which, in turn, can orient proteins (Fig. 6.14c).
- 4. Non-oriented attachment to a self-assembling monolayer. In this case, the chains that form a self-assembling monolayer have functional groups at the ends that react in a non-specific way with different parts of the protein. For this reason, the orientation of proteins is random, as shown in Fig. 6.14.
- 5. Oriented attachment to a self-assembling monolayer. The assembly principles are the same as in the previous case, but here the functional group specifically interacts only with a certain domain or section of a given domain, and, therefore, a well-defined orientation is carried out. To this end, the structure of proteins can be chemically or genetically modified. This self-assembly method is shown in Fig. 6.14d.
- 6. Direct selective addition to gold. This happens when cystine, which has unique properties, binds to the gold surface. In this case, the orientation is completely controlled. This type of connection is shown in Fig. 6.14e.
Strain-guided self-assembly is used in the manufacture and connection of wires and switches. A surface with a lithographically specified relief is impregnated with a deposited substance of a controlled composition under conditions of deformation. A functional group can be introduced into the substrate, which is usually associated with the functionality of the surface. This self-assembly method can be used, for example, in the creation of semiconductor devices, where it is required to fix the system components on a solid substrate in order to fully control the progress of the self-assembly process and its completion.
Diagram of DNA-guided assembly
DNA can be used both for node-selective fixation and as a binder, resulting in a lattice framework for self-assembly of nanostructures. Synthesis of a conjugate of nucleic acid and protein using specific interactions between two complementary strands of DNA, antigen and antibody, between BIO and CTB can determine effective mechanisms that determine the direction of attachment of nanostructural modules (Fig. 6.15).
Recent advances in genetic engineering, in methods of manipulating DNA sequences fixed on the surface of gold, like doping, further increase control over the self-assembly process. A similar method can be used in the case of molecules of inorganic substances reaching the size of nanocrystals. DNA can also be used for synthesis involving templates. An example of such a synthesis is the fabrication of silver nanowires using DNA as a base.
An effective way to discover promising compounds and self-assemblies is to apply the achievements of dynamic combinatorial chemistry, which is a bottom-up evolutionary approach to nanotechnology. To develop the structure of dynamic combinatorial chemistry, it is necessary to assemble a dynamic combinatorial library of intermediate components that, when templates are added, form the required molecular assembly. In dynamic combinatorial chemistry, an important component is the mechanism of molecular recognition. An addition is the knowledge of the features of creating "guest-host" complexes.
Currently, combinatorial chemistry is used as a method of theoretical research in establishing the structural basis of the function of enzymes and identifying new enzyme inhibitors. It is believed that with its help it is possible to potentially quickly reach new self-assemblies in nanotechnology, as well as the discovery of new drugs, supramolecular assemblies, and catalysts.
There are two types of combinatorial chemistry: traditional and dynamic (Fig. 6.16). The main difference between the two is that in dynamic chemistry the molecular building blocks are held together by weak but reversible non-covalent bonds, while in traditional combinatorial chemistry the interactions are driven primarily by strong and irreversible covalent bonds.
In traditional combinatorial chemistry, a static mixture of aggregates of a fixed composition is formed, and the introduced “template” (ligand) selects the best binder without increasing its content. In dynamic combinatorial chemistry, one proceeds from a dynamic mixture, in which, after the addition of a "template", the composition and distribution of block concentrations change, and the best binder in relation to the "template" will be the only predominant product.
In combinatorial chemistry, a “template” (or ligand) is considered to be a molecule, ion, or macromolecule that reacts with other components and changes the distribution of the concentrations of the products of the system during continuously occurring reactions to form the required aggregate, macromolecule, or intermediate product. An example of a "template" is a DNA molecule that acts as a model for the synthesis of an RNA-type macromolecule.
Self-assembly in dynamic combinatorial chemistry enables new approaches to molecular assembly. In recent years, many interesting improvements have been made in this area. In particular, the so-called molecular docking, a procedure for searching for optimal docking sites for small molecules of a ligand (biologically active substance) to a protein macromolecule, has received great development.
A dynamic combinatorial library (DCL) is a set of intermediate substances that can be in dynamic equilibrium with building blocks. To describe the composition of the DCS, the term "chemistry set" is usually used, which consists of two or more library components, building blocks or reagents. “Building” blocks with properties suitable for the formation of self-assembling objects are selected from the dynamic combinatorial library, and self-assembly is carried out in the presence of a “template”.
DCS components interact through the formation of weak non-covalent bonds. In principle, it is possible to create any reversible assemblies from these components. Since all interactions between the components are reversible and equilibrium, DCS is dynamic in nature. Thus, DCS is able to easily respond to various factors of external influence. In particular, the number of certain DCB aggregates may vary with changing thermodynamic conditions and depending on the nature of the "template" added to the system. In the equilibrium state, before the addition of the "template", DCS components have many opportunities to interact with each other through weak non-covalent bonds with the formation of various aggregates. After the “template” is added to the DCS system, the content of intermediate substances is redistributed. As a result, only the concentration of those aggregates or assemblies that best fit the “template” will increase and become stable.
An increase in the concentration of a certain intermediate product can only occur as a result of a reversible shift of the remaining reactions in the direction of the formation of this product, if only this is dictated by equilibrium conditions (achieving a minimum of energy and a maximum of entropy). Consequently, the system seeks to provide the assembly with the most stable bonds to the “template”, while the concentration of unstable assemblies decreases. At the same time, DCS components can spontaneously interact with each other, producing a large number of various aggregates with different shapes and properties.
There are many factors that affect the effectiveness of DCS. These include:
1. The nature of the components and "templates" of DCS. It is essential that the selected components have suitable functional groups. The greater the diversity of these groups in the components, the greater the variability that can be achieved in the development of systems (see Figure 6.17). In addition, the properties of these groups must be compatible with the properties of the "template".
- 2. Types of intermolecular interactions in DCS. In order to be able to predict the possibility of the formation of molecular aggregates using computational chemistry, it is necessary to know a priori about intermolecular interactions between components and the mechanism of association of a component with a “template”. In DCS, intermolecular interactions must be non-covalent, which leads to the reversibility of transformations occurring between DCS components. Such interactions contribute to the rapid establishment of equilibrium, so that all possible possibilities for the formation of molecular aggregates can be tested.
- 3. Thermodynamic conditions. The solubility of components, templates, and resulting molecular aggregates in a solvent (DCB medium) can strongly depend on equilibrium thermodynamic conditions. To increase the efficiency of DCS, the solubility of the components in the medium should not differ significantly from the solubility of the "template". In the aquatic environment, the lack of solubility of the "template" is a problem mainly when using a protein as its quality, nucleic acids can also create a similar problem. The formation of an insoluble molecular aggregate shifts the equilibrium in the direction of the formation of this aggregate as a reaction product. The conditions for the reactions presented in DCS should be as mild as possible in order to minimize the likelihood of incompatibility, inevitable in the processes of exchange and recognition.
- 4. Analysis methods. In DCS, under certain circumstances, it must be possible to terminate the ongoing reactions in order to be able to move the system from a dynamic to a static state. Termination of reactions allows the system to be “disconnected” from synthesis after the addition of a “template” and the formation of the best possible crosslinking reagent. In this case, the system comes to an equilibrium state and the distribution of molecular aggregates is kept constant for the possibility of analysis.
Sometimes a simplification of the self-assembly process can be achieved by analysis at the recognition stage. Molecular recognition is a specific identification by the interaction of one molecule with another.
A feature of the recognition of DCS molecules is the choice of the receptor most suitable for a given "template". This contributes to the development of an evolutionary approach to obtain and selectively select the most suitable receptors, similar to the evolutionary development of nature. Directed evolution of high affinity ligands for biomolecules in a recent field of combinatorial chemistry called dynamic variability, can be widely used in self-assembly.
There are two fundamental approaches to the process of molecular recognition: shaping and molding (see Fig. 6.18).
When "shaping" the created molecular aggregate from the library of compounds takes the form
Illustration of shaping and shaping in molecular recognition
emptiness bounded by the "template". The free space inside the "template" performs the function of a mold and a place where the library components are connected and aggregates are formed. When "forming" there is a direct connection of the dynamic library components with the help of "templates".
A huge number of molecules are used for self-assembly, receptor formation, and molecular recognition. Such "recognizing" molecules may contain receptors for recognition of acidic carboxyl, peptide, carbohydrate and other groups.
Molecular receptors are conceptually the simplest objects of supramolecular chemistry, although their structure is by no means always simple. Their function is to “find” the desired substrate among similar ones and selectively, i.e., selectively bind it. Selectivity of molecular recognition is achieved if, along with the complementarity of the receptor and the substrate, there is a strong total binding between them, which arises due to the multiple interaction of several binding centers. A necessary condition for such an interaction is a large area of contact between the receptor and the substrate.
Special methods and reagents are available for constructing cyclic, containerized, or linear self-assembling structures (or complexes) as receptors and for identifying molecules. For example, a strategy for building a cyclic structure is to use triple and complementary hydrogen bonds between the donor-donor-acceptor group of one molecule and the acceptor-acceptor-donor group of another molecule.
"Container" supramolecular chemistry techniques can also be used to design macromolecules that are susceptible to molecular recognition and the formation of specific bonds. In these methods, the inner surface of the designed molecule (the "host" or receptor) interacts with the surface of the "guest" or ligand, and the energy of the weak bonds formed between them determines the strength of the specific binding and the possibility of recognizing molecules.
After the completion of the self-assembly of the components, the resulting "host" takes on an individual spatial conformation, often with a void or a gap for the complete or partial inclusion of the "guest" molecule in it. Although the control over the development of technology and the specificity of recognition in these methods are not as significant as in the dynamic combinatorial library, in many cases there are fewer restrictions and difficulties in development than in dynamic combinatorial library systems.
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Figure 1. The molecular structure of a polyhedron obtained by self-assembly from 144 molecules "border="0"> deciphered by X-ray crystallography
A group of chemists from Japan managed to break the self-assembly record of molecular geometric shapes set by them. Scientists were able to choose the conditions and components in such a way that a self-assembly reaction of a molecular polyhedron, similar to viral capsids (protein coats), took place in the solution. The new record holder consisted of 144 molecules. This discovery has enormous application potential, as smaller structures have long been used for catalysis, hypersensitivity sensors, energy storage, explosives stabilization, and more.
If you look at experimental chemistry philosophically, it is all essentially self-assembly. The chemist only adds some reagents to others, and they interact in solution on their own: as a rule, nothing but diffusion and electrostatics pushes them towards each other. Crystals grow in the same way: one molecule “sticks” to another, “choosing” the most energetically favorable conformation.
In principle, this happens in a living cell. Molecules, floating in the cytoplasm, assemble themselves into structures, then these structures catalyze the self-assembly of other structures, up to a multicellular organism. All this looks like a huge working factory without a single worker, foreman, director or cleaner. Everything works according to (bio)chemical laws without anyone's conscious supervision or control - this is the result of evolution, gradual complication, the survival of working systems and the death of non-working ones.
Research into the laws of self-assembly of molecules began with attempts to copy natural processes. However, biological objects are such that it is sometimes difficult for the human brain to even imagine their shape. This presents a serious problem for biochemical research. So gradually, in the early 90s, the idea arose: why, in fact, it is necessary to study only natural self-assembly? Is it possible to approach from the other side? Choose models that are easier to research and try to understand nature based on them. That is, first collect the knowledge scattered under the burning lantern, and only then go to the extinguished lanterns. Well, what could be simpler than geometric shapes? This idea, as often happens, arose independently in different scientific teams - the group of Peter Stang (Peter J. Stang) from the USA and the group of Makoto Fujita (Makoto Fujita) from Japan.
Almost immediately it became clear that one could not stop at two-dimensional structures and try to assemble three-dimensional structures in a similar way - molecular "cages" (cages); rice. 3. To obtain three-dimensional figures, donors and/or acceptors with three or more active endings are needed.
The reactions turned out to have a somewhat unexpected, and even counterintuitive, property: if you mix several different “blue” molecules with “red” ones, they still “choose” from the solution those that give the most ordered structures without mixing with each other. Thus, in fact, not only self-assembly, but also self-sorting is carried out (Fig. 4). This is explained by the fact that the most ordered structures in combination turned out to be the most energetically favorable.
At first glance, the field of research on the self-assembly of molecular geometric shapes may seem very narrow, representing no more than academic interest. There are really enough such areas that someday will be useful (or not useful), but in the case under discussion, the situation is completely different. Both the structures and the methods of obtaining them (as well as the discovered regularities) very quickly found a huge number of immediate and distant applications. As expected, these studies have made it easier to understand how the self-assembly of biological structures (eg, viral capsids) works.
Self-assembly methods have formed the basis of a huge field of research on metal-organic coordination polymers (Metal-organic frameworks, MOFs). Structures obtained by such methods are used as hypersensitive sensors, since when interacting with certain substances, they change their physical properties. With the help of molecular "cells" organic reactions are accelerated, using internal cavities to bring reactants closer to each other (as enzymes do in nature). They also stabilize explosive or self-igniting substances, such as white phosphorus. Drugs are inserted into some types of molecular "cells" and brought to target organs, bypassing healthy ones. And this is not a complete list.
Of course, academic research in such a useful area has not stopped. In particular, one of the curious questions asked by self-assembly researchers is what is the largest number of molecules that can "self-assemble" into an ordered structure without any outside help? In nature, hundreds of components (for example, the same viral capsids) can perform such a trick. Will chemists be able to compete with nature?
The penultimate record was set in Fujita's group. In early 2016, by carefully calculating the topology of the desired structure and planning the geometry of the molecular "constructor pieces", they were able to (self) assemble a structure belonging to the class of Archimedean solids from 90 particles: 30 tetravalent palladium acceptors and 60 bipyridine donors (second from right in Fig. 5).
The barrier of one hundred components had not yet been overcome at that time, and some believed that it was insurmountable. Ignoring the predictions of skeptics, in the new study, scientists swung at the following Archimedean polyhedron, of 180 particles: 60 palladium acceptors and 120 pyridine donors (the structure on the far right in Fig. 5).
Having made the appropriate calculations, chemists synthesized molecular building blocks for it, made a solution of the ingredients in the ratio of one acceptor to two donors, and followed the reaction using NMR spectroscopy. When all the initial reagents reacted, it was possible to isolate crystals from the solution and characterize their molecular structure by X-ray diffraction analysis. To the surprise of the experimenters, they faced a polyhedron with a structure far from what was expected (Fig. 6, left).
Just like the previous record holder, it consisted of 30 acceptors and 60 donors (“aha!” - exclaimed skeptics), only it did not belong to Archimedean polyhedra, but was close to another class of figures - Goldberg polyhedra (see Goldberg polyhedron).
Goldberg polyhedra are geometric figures discovered by mathematician Michael Goldberg in 1937. Classical Goldberg polyhedra consist of pentagons and hexagons connected to each other according to certain rules (by the way, the truncated icosahedron, familiar to many in the shape of a soccer ball, is an example of a Goldberg polyhedron). Despite the fact that in the work under discussion the polyhedra consist of triangles and squares, they are related to the Goldberg polyhedra, which is proved using graph theory.
The scientists made additional calculations, from which it followed that this structure is metastable and that there is a more energetically stable polyhedron of 48 acceptors and 96 donors, which can be obtained from the same initial molecules. It remained “only” to find suitable conditions for its production, isolation and characterization. After numerous attempts, at different temperatures and using different solvents, crystals were obtained, which under the microscope visually differed from the previous ones. They were selected with tweezers from the previously characterized ones, and X-ray diffraction analysis confirmed that a new champion consisting of 144 molecules was obtained by self-assembly (Fig. 6, right).
Given the history of successful searches for applications for smaller analogues, the authors hope that there will be interesting applications for newly discovered molecules, as well as the methods that have been developed for them. They are not going to stop there and intend to get even larger structures from more components.
Sources:
1) Rajesh Chakrabarty, Partha S. Mukherjee, Peter J. Stang. Supramolecular Coordination: Self-Assembly of Finite Two- and Three-Dimensional Ensembles // Chemical Reviews. 2011. V. 111, P. 6810–6918. DOI: 10.1021/cr200077m.
2) Daishi Fujita, Yoshihiro Ueda, Sota Sato, Nobuhiro Mizuno, Takashi Kumasaka, Makoto Fujita. Self-assembly tetra ofvalent Goldberg polyhedral from 144 small components // Nature. 2016. V. 510, P. 563–567. DOI: 10.1038/nature20771.
Grigory Molev
Nanoparticle is a particle smaller than 100 microns. The modern trend towards miniaturization has shown that a substance can have completely new properties if one takes a very small particle of this substance. Particles ranging in size from 1 to 100 nanometers are commonly referred to as "nanoparticles". For example, it turned out that nanoparticles of some materials have very good catalytic and adsorption properties. Other materials show amazing optical properties, such as ultra-thin films of organic materials used to make solar cells. Such batteries, although they have a relatively low quantum efficiency, are cheaper and can be mechanically flexible. It is possible to achieve the interaction of artificial nanoparticles with natural nanosized objects - proteins, nucleic acids, etc. Carefully purified nanoparticles can self-align into certain structures. Such a structure contains strictly ordered nanoparticles and also often exhibits unusual properties. Nanoobjects are divided into 3 main classes: three-dimensional particles obtained by explosion of conductors, plasma synthesis; two-dimensional objects - films obtained by molecular deposition, CVD, ALD, ion deposition; one-dimensional objects - whiskers (these objects are obtained by molecular layering, the introduction of substances into cylindrical micropores). At the moment, only the microlithography method has received extensive use, which makes it possible to obtain flat island objects with a size of 50 nm or more on the surface of matrices; it is used in electronics; the CVD and ALD method is mainly used to create micron films. Other methods are mainly used for scientific purposes. In particular, the methods of ionic and molecular deposition should be noted, since they can be used to create real monolayers. Nanotechnology- an interdisciplinary field of fundamental and applied science and technology, dealing with a combination of theoretical justification, practical methods of research, analysis and synthesis, as well as methods for the production and use of products with a given atomic structure by controlled manipulation of individual atoms and molecules . Nanomaterials- materials developed on the basis of nanoparticles with unique characteristics arising from the microscopic dimensions of their constituents. Carbon nanotubes are extended cylindrical structures with a diameter of one to several tens of nanometers and a length of up to several centimeters, consisting of one or more hexagonal graphite planes rolled into a tube and usually ending in a hemispherical head. Fullerenes are molecular compounds belonging to the class of allotropic forms of carbon. Graphene is a monolayer of carbon atoms obtained in October 2004 at the University of Manchester. Graphene can be used as a molecular detector. Nanolithography the most important method for creating devices with nanometer dimensions. This method can be used to create electronic circuits, high capacity memory circuits, sensors. Nanomedicine- tracking, fixing, designing and controlling human biological systems at the molecular level, using nanodevices and nanostructures. Nanobioelectronics) is a section of electronics and nanotechnologies that uses biomaterials and the principles of information processing by biological objects in computer technology to create electronic devices. Molecular self-assembly- Creation of arbitrary DNA sequences that can be used to create the required proteins or amino acids.
) — the process of formation of an ordered supramolecular structure or medium, in which only the components (elements) of the original structure take part in an almost unchanged form, additively constituting or “collecting”, as parts of the whole, the resulting complex structure.
Description
Self-assembly is one of the typical bottom-up methods for obtaining nanostructures (nanomaterials). The main task that stands in its implementation is the need to influence the parameters of the system in such a way and set the properties of individual particles in such a way that they organize themselves with the formation of the desired structure. Self-assembly is at the heart of many processes where the "instructions" how to assemble large objects are "encoded" in the structural features of individual molecules. Self-assembly should be distinguished from self-assembly, which can be used as a mechanism for creating complex "patterns", processes and structures at a higher hierarchical level of organization than that observed in the original system (see figure). The differences are in the numerous and multivariate interactions of the components at low levels, at which there are their own, local, laws of interaction that are different from the collective laws of behavior of the ordering system itself. The processes of self-organization are characterized by interaction energies of different scales, as well as the existence of restrictions on the degrees of freedom of the system at several different levels of its organization. Thus, the self-assembly process is a simpler phenomenon. Nevertheless, one should not go to extremes and assume, for example, that the process of single crystal growth is the self-assembly of atoms (which, in principle, corresponds to the definition), although, for example, the self-assembly of larger objects - microspheres of the same size, forming the densest spherical packing, which leads to the formation of the so-called (three-dimensional diffraction grating of microspheres), is a typical example of self-assembly. Self-assembly can include the formation (for example, thiol molecules on a smooth gold film), the formation of films, etc.
Illustrations
author
- Gudilin Evgeny Alekseevich
Sources
- Philosophy of nanosynthesis // Nanometer, 2007. - www.nanometer.ru/2007/12/15/samosborka_5415.html (date of access: 10/13/2009).
- Self-assembly // Wikipedia, the free Encyclopedia. - http://en.wikipedia.org/wiki/Self-assembly (accessed 07/31/2010).
