Systems chemistry

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Systems chemistry is the science of studying networks of interacting molecules, to create new functions from a set (or library) of molecules with different hierarchical levels and emergent properties. [1] [2]

Contents

Systems chemistry is also related to the origin of life (abiogenesis). [3]

Relations to systems biology

Systems chemistry is a relatively young sub-discipline of chemistry, where the focus does not lie on the individual chemical components but rather on the overall network of interacting molecules and on their emergent properties. Hence, it combines the classical knowledge of chemistry (structure, reactions and interactions of molecules) together with a systems approach inspired by systems biology and systems science.

Examples

Dynamic combinatorial chemistry has been used as a method to develop ligands for biomolecules and receptors for small molecules. [4]

Ligands that can recognize biomolecules are being identified by preparing libraries of potential ligands in the presence of a target biomacromolecule. This is relevant for application as biosensors for fast monitoring of imbalances and illnesses and therapeutic agents. [5]

Individual components of certain chemical system will self-assemble to form receptors which are complementary to target molecule. In principle, the preferred library members will be selected and amplified based on the strongest interactions between the template and products. [6]

Molecular networks and equilibrium

A fundamental difference exists between chemistry as it is performed in most laboratories and chemistry as it occurs in life. Laboratory processes are mostly designed such that the (closed) system goes thermodynamically downhill; i.e. the product state is of lower Gibbs free energy, yielding stable molecules that can be isolated and stored. Yet the chemistry of life operates in a very different way: most molecules from which living systems are constituted are turned over continuously and are not necessarily thermodynamically stable. Nevertheless, living systems can be stable, but in a homeostatic sense. Such homeostatic (open) systems are far-from-equilibrium and are dissipative: they need energy to maintain themselves. In dissipative controlled systems the continuous supply of energy allows a continuous transition between different supramolecular states, where systems with unexpected properties may be discovered. One of the grand challenges of Systems Chemistry is to unveil complex reactions networks, where molecules continuously consume energy to perform specific functions.

History

While multicomponent reactions have been studied for centuries, the idea of deliberately analyzing mixtures and reaction networks is more recent. The first mentions of systems chemistry as a field date from 2005. [7] [8] Early adopters focused on prebiotic chemistry combined with supramolecular chemistry, before it was generalized to the study of emergent properties and functions of any complex molecular systems. A 2017 review in the field of systems chemistry [9] described the state of the art as out-of-equilibrium self-assembly, fuelled molecular motion, chemical networks in compartments and oscillating reactions.

Related Research Articles

<span class="mw-page-title-main">Hückel's rule</span> Method of determining aromaticity in organic molecules

In organic chemistry, Hückel's rule predicts that a planar ring molecule will have aromatic properties if it has 4n + 2 π electrons, where n is a non-negative integer. The quantum mechanical basis for its formulation was first worked out by physical chemist Erich Hückel in 1931. The succinct expression as the 4n + 2 rule has been attributed to W. v. E. Doering (1951), although several authors were using this form at around the same time.

Supramolecular chemistry refers to the branch of chemistry concerning chemical systems composed of a discrete number of molecules. The strength of the forces responsible for spatial organization of the system range from weak intermolecular forces, electrostatic charge, or hydrogen bonding to strong covalent bonding, provided that the electronic coupling strength remains small relative to the energy parameters of the component. While traditional chemistry concentrates on the covalent bond, supramolecular chemistry examines the weaker and reversible non-covalent interactions between molecules. These forces include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi–pi interactions and electrostatic effects.

<span class="mw-page-title-main">Host–guest chemistry</span> Supramolecular structures held together other than by covalent bonds

In supramolecular chemistry, host–guest chemistry describes complexes that are composed of two or more molecules or ions that are held together in unique structural relationships by forces other than those of full covalent bonds. Host–guest chemistry encompasses the idea of molecular recognition and interactions through non-covalent bonding. Non-covalent bonding is critical in maintaining the 3D structure of large molecules, such as proteins and is involved in many biological processes in which large molecules bind specifically but transiently to one another.

<span class="mw-page-title-main">Supramolecular assembly</span> Complex of molecules non-covalently bound together

In chemistry, a supramolecular assembly is a complex of molecules held together by noncovalent bonds. While a supramolecular assembly can be simply composed of two molecules, or a defined number of stoichiometrically interacting molecules within a quaternary complex, it is more often used to denote larger complexes composed of indefinite numbers of molecules that form sphere-, rod-, or sheet-like species. Colloids, liquid crystals, biomolecular condensates, micelles, liposomes and biological membranes are examples of supramolecular assemblies, and their realm of study is known as supramolecular chemistry. The dimensions of supramolecular assemblies can range from nanometers to micrometers. Thus they allow access to nanoscale objects using a bottom-up approach in far fewer steps than a single molecule of similar dimensions.

In chemical synthesis, click chemistry is a class of simple, atom-economy reactions commonly used for joining two molecular entities of choice. Click chemistry is not a single specific reaction, but describes a way of generating products that follow examples in nature, which also generates substances by joining small modular units. In many applications, click reactions join a biomolecule and a reporter molecule. Click chemistry is not limited to biological conditions: the concept of a "click" reaction has been used in chemoproteomic, pharmacological, biomimetic and molecular machinery applications. However, they have been made notably useful in the detection, localization and qualification of biomolecules.


Dynamic covalent chemistry (DCvC) is a synthetic strategy employed by chemists to make complex molecular and supramolecular assemblies from discrete molecular building blocks. DCvC has allowed access to complex assemblies such as covalent organic frameworks, molecular knots, polymers, and novel macrocycles. Not to be confused with dynamic combinatorial chemistry, DCvC concerns only covalent bonding interactions. As such, it only encompasses a subset of supramolecular chemistries.

In organic chemistry, a cycloalkyne is the cyclic analog of an alkyne. A cycloalkyne consists of a closed ring of carbon atoms containing one or more triple bonds. Cycloalkynes have a general formula CnH2n−4. Because of the linear nature of the C−C≡C−C alkyne unit, cycloalkynes can be highly strained and can only exist when the number of carbon atoms in the ring is great enough to provide the flexibility necessary to accommodate this geometry. Large alkyne-containing carbocycles may be virtually unstrained, while the smallest constituents of this class of molecules may experience so much strain that they have yet to be observed experimentally. Cyclooctyne is the smallest cycloalkyne capable of being isolated and stored as a stable compound. Despite this, smaller cycloalkynes can be produced and trapped through reactions with other organic molecules or through complexation to transition metals.

In chemistry, mechanically interlocked molecular architectures (MIMAs) are molecules that are connected as a consequence of their topology. This connection of molecules is analogous to keys on a keychain loop. The keys are not directly connected to the keychain loop but they cannot be separated without breaking the loop. On the molecular level, the interlocked molecules cannot be separated without the breaking of the covalent bonds that comprise the conjoined molecules; this is referred to as a mechanical bond. Examples of mechanically interlocked molecular architectures include catenanes, rotaxanes, molecular knots, and molecular Borromean rings. Work in this area was recognized with the 2016 Nobel Prize in Chemistry to Bernard L. Feringa, Jean-Pierre Sauvage, and J. Fraser Stoddart.

<span class="mw-page-title-main">Cation–π interaction</span>

Cation–π interaction is a noncovalent molecular interaction between the face of an electron-rich π system (e.g. benzene, ethylene, acetylene) and an adjacent cation (e.g. Li+, Na+). This interaction is an example of noncovalent bonding between a monopole (cation) and a quadrupole (π system). Bonding energies are significant, with solution-phase values falling within the same order of magnitude as hydrogen bonds and salt bridges. Similar to these other non-covalent bonds, cation–π interactions play an important role in nature, particularly in protein structure, molecular recognition and enzyme catalysis. The effect has also been observed and put to use in synthetic systems.

<span class="mw-page-title-main">Crystal engineering</span>

Crystal engineering studies the design and synthesis of solid-state structures with desired properties through deliberate control of intermolecular interactions. It is an interdisciplinary academic field, bridging solid-state and supramolecular chemistry.

<span class="mw-page-title-main">Hydroamination</span> Addition of an N–H group across a C=C or C≡C bond

In organic chemistry, hydroamination is the addition of an N−H bond of an amine across a carbon-carbon multiple bond of an alkene, alkyne, diene, or allene. In the ideal case, hydroamination is atom economical and green. Amines are common in fine-chemical, pharmaceutical, and agricultural industries. Hydroamination can be used intramolecularly to create heterocycles or intermolecularly with a separate amine and unsaturated compound. The development of catalysts for hydroamination remains an active area, especially for alkenes. Although practical hydroamination reactions can be effected for dienes and electrophilic alkenes, the term hydroamination often implies reactions metal-catalyzed processes.

<span class="mw-page-title-main">Molecular sensor</span>

A molecular sensor or chemosensor is a molecular structure that is used for sensing of an analyte to produce a detectable change or a signal. The action of a chemosensor, relies on an interaction occurring at the molecular level, usually involves the continuous monitoring of the activity of a chemical species in a given matrix such as solution, air, blood, tissue, waste effluents, drinking water, etc. The application of chemosensors is referred to as chemosensing, which is a form of molecular recognition. All chemosensors are designed to contain a signalling moiety and a recognition moiety, that is connected either directly to each other or through a some kind of connector or a spacer. The signalling is often optically based electromagnetic radiation, giving rise to changes in either the ultraviolet and visible absorption or the emission properties of the sensors. Chemosensors may also be electrochemically based. Small molecule sensors are related to chemosensors. These are traditionally, however, considered as being structurally simple molecules and reflect the need to form chelating molecules for complexing ions in analytical chemistry. Chemosensors are synthetic analogues of biosensors, the difference being that biosensors incorporate biological receptors such as antibodies, aptamers or large biopolymers.

In chemistry, π-effects or π-interactions are a type of non-covalent interaction that involves π systems. Just like in an electrostatic interaction where a region of negative charge interacts with a positive charge, the electron-rich π system can interact with a metal, an anion, another molecule and even another π system. Non-covalent interactions involving π systems are pivotal to biological events such as protein-ligand recognition.

Jeremy Keith Morris Sanders is a British chemist and Emeritus Professor in the Department of Chemistry at the University of Cambridge. He is also Editor-in-Chief of Royal Society Open Science. He is known for his contributions to many fields including NMR spectroscopy and supramolecular chemistry. He served as the Pro-Vice-Chancellor for Institutional Affairs at the University of Cambridge, 2011–2015.

<span class="mw-page-title-main">Dynamic combinatorial chemistry</span>

Dynamic combinatorial chemistry (DCC); also known as constitutional dynamic chemistry (CDC) is a method to the generation of new molecules formed by reversible reaction of simple building blocks under thermodynamic control. The library of these reversibly interconverting building blocks is called a dynamic combinatorial library (DCL). All constituents in a DCL are in equilibrium, and their distribution is determined by their thermodynamic stability within the DCL. The interconversion of these building blocks may involve covalent or non-covalent interactions. When a DCL is exposed to an external influence, the equilibrium shifts and those components that interact with the external influence are stabilised and amplified, allowing more of the active compound to be formed.

<span class="mw-page-title-main">Weak-Link Approach</span>

The Weak-Link Approach (WLA) is a supramolecular coordination-based assembly methodology, first introduced in 1998 by the Mirkin Group at Northwestern University. This method takes advantage of hemilabile ligands -ligands that contain both strong and weak binding moieties- that can coordinate to metal centers and quantitatively assemble into a single condensed ‘closed’ structure. Unlike other supramolecular assembly methods, the WLA allows for the synthesis of supramolecular complexes that can be modulated from rigid ‘closed’ structures to flexible ‘open’ structures through reversible binding of allosteric effectors at the structural metal centers. The approach is general and has been applied to a variety of metal centers and ligand designs including those with utility in catalysis and allosteric regulation.

<span class="mw-page-title-main">Two-dimensional polymer</span>

A two-dimensional polymer (2DP) is a sheet-like monomolecular macromolecule consisting of laterally connected repeat units with end groups along all edges. This recent definition of 2DP is based on Hermann Staudinger's polymer concept from the 1920s. According to this, covalent long chain molecules ("Makromoleküle") do exist and are composed of a sequence of linearly connected repeat units and end groups at both termini.

<span class="mw-page-title-main">Supramolecular catalysis</span> Field of chemistry

Supramolecular catalysis is not a well-defined field but it generally refers to an application of supramolecular chemistry, especially molecular recognition and guest binding, toward catalysis. This field was originally inspired by enzymatic system which, unlike classical organic chemistry reactions, utilizes non-covalent interactions such as hydrogen bonding, cation-pi interaction, and hydrophobic forces to dramatically accelerate rate of reaction and/or allow highly selective reactions to occur. Because enzymes are structurally complex and difficult to modify, supramolecular catalysts offer a simpler model for studying factors involved in catalytic efficiency of the enzyme. Another goal that motivates this field is the development of efficient and practical catalysts that may or may not have an enzyme equivalent in nature.

Kim R. Dunbar is an American inorganic chemist and Distinguished Professor of Chemistry at Texas A&M University. Her research concerns inorganic and coordination chemistry, including molecular magnetism, metals in medicine, supramolecular chemistry Involving anions and anion-pi interactions, and multifunctional materials with organic radicals.

<span class="mw-page-title-main">Stephen L. Craig</span> American chemist and professor

Stephen L. Craig is the William T. Miller Professor of Chemistry at Duke University. He is the director of the Center for Molecularly Optimized Networks, a NSF Center for Chemical Innovation.

References

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  2. "Centre for Systems Chemistry". University of Groningen. 27 October 2011. Retrieved 26 October 2017.
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