Crystal engineering

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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. [1]

Contents

The main engineering strategies currently in use are hydrogen- and halogen bonding and coordination bonding. [2] These may be understood with key concepts such as the supramolecular synthon and the secondary building unit. [3]

An example of crystal engineering using hydrogen bonding reported by Wuest and coworkers in J. Am. Chem. Soc., 2007, 4306-4322. Crystal Engineering JACS 2007 vol129 page4306 commons.jpg
An example of crystal engineering using hydrogen bonding reported by Wuest and coworkers in J. Am. Chem. Soc. , 2007, 4306–4322.

History of term

The term 'crystal engineering' was first used in 1955 by R. Pepinsky [4] but the starting point is often credited to Gerhard Schmidt [5] in connection with photodimerization reactions in crystalline cinnamic acids. Since this initial use, the meaning of the term has broadened considerably to include many aspects of solid state supramolecular chemistry. A useful modern definition is that provided by Gautam Desiraju, who in 1988 defined crystal engineering as "the understanding of intermolecular interactions in the context of crystal packing and the utilization of such understanding in the design of new solids with desired physical and chemical properties." [6] Since many of the bulk properties of molecular materials are dictated by the manner in which the molecules are ordered in the solid state, it is clear that an ability to control this ordering would afford control over these properties.

Non-covalent control of structure

Br***O halogen bonds observed in crystal structure of 3D silsesquioxanes. Silsesquixane halogen bond.tif
Br···O halogen bonds observed in crystal structure of 3D silsesquioxanes.

Crystal engineering relies on noncovalent bonding to achieve the organization of molecules and ions in the solid state. Much of the initial work on purely organic systems focused on the use of hydrogen bonds, although coordination and halogen bonds provide additional control in crystal design. [8]

Molecular self-assembly is at the heart of crystal engineering, and it typically involves an interaction between complementary hydrogen bonding faces or a metal and a ligand. "Supramolecular synthons" are building blocks that are common to many structures and hence can be used to order specific groups in the solid state. [9]

Design of multi-component crystals

A five component crystal was designed by Desiraju and co workers by a rational retrosynthetic strategy (IUCrJ, 2016, 3, 96-101). Five component crystal.jpg
A five component crystal was designed by Desiraju and co workers by a rational retrosynthetic strategy (IUCrJ, 2016, 3, 96–101).

The intentional synthesis of cocrystals is most often achieved with strong heteromolecular interactions. The main relevance of multi-component crystals is focused upon designing pharmaceutical cocrystals. [10] Pharmaceutical cocrystals are generally composed of one API (Active Pharmaceutical Ingredient) with other molecular substances that are considered safe according to the guidelines provided by WHO (World Health Organization). Various properties (such as solubility, bioavailability, permeability) of an API can be modulated through the formation of pharmaceutical cocrystals.

In two dimensions

2D architectures (i.e., molecularly thick architectures) is a branch of crystal engineering. [11] The formation (often referred as molecular self-assembly depending on its deposition process) of such architectures lies in the use of solid interfaces to create adsorbed monolayers. Such monolayers may feature spatial crystallinity. [12] [13] However the dynamic and wide range of monolayer morphologies ranging from amorphous to network structures have made of the term (2D) supramolecular engineering a more accurate term. Specifically, supramolecular engineering refers to "(The) design (of) molecular units in such way that a predictable structure is obtained" [14] or as "the design, synthesis and self-assembly of well defined molecular modules into tailor-made supramolecular architectures". [15]

scanning probe microscopic techniques enable visualization of two dimensional assemblies.

Polymorphism

Polymorphism, the phenomenon wherein the same chemical compound exists in more than one crystal forms, is relevant commercially because polymorphic forms of drugs may be entitled to independent patent protection. The importance of crystal engineering to the pharmaceutical industry is expected to grow exponentially. [16]

Polymorphism arises due to the competition between kinetic and thermodynamic factors during crystallization. While long-range strong intermolecular interactions dictate the formation of kinetic crystals, the close packing of molecules generally drives the thermodynamic outcome. Understanding this dichotomy between the kinetics and thermodynamics constitutes the focus of research related to the polymorphism.

The pathways to kinetically favoured and thermodynamically favoured crystals. Kinetics and thermodynamics.tif
The pathways to kinetically favoured and thermodynamically favoured crystals.

In organic molecules, three types of polymorphism are mainly observed. Packing polymorphism arises when molecules pack in different ways to give different structures. Conformational polymorphism, on the other hand is mostly seen in flexible molecules where molecules have multiple conformational possibilities within a small energy window. As a result, multiple crystal structures can be obtained with the same molecule but in different conformations. The rarest form of polymorphism arises from the differences in the primary synthon and this type of polymorphism is called as synthon polymorphism.

Crystal structure prediction

Crystal structure prediction (CSP) is a computational approach to generate energetically feasible crystal structures (with corresponding space group and positional parameters) from a given molecular structure. The CSP exercise is considered most challenging as "experimental" crystal structures are very often kinetic structures and therefore are very difficult to predict. In this regard, many protocols have been proposed and are tested through several blind tests organized by CCDC since 2002. A major advance in the CSP happened in 2007 while a hybrid method based on tailor made force fields and density functional theory (DFT) was introduced. In the first step, this method employs tailor made force fields to decide upon the ranking of the structures followed by a dispersion corrected DFT method to calculate the lattice energies precisely. [17]

Apart from the ability of predicting crystal structures, CSP also gives computed energy landscapes of crystal structures where many structures lie within a narrow energy window. [18] This kind of computed landscapes lend insights into the study on polymorphism, design of new structures and also help to design crystallization experiments.

Property design

A resorcinol based templating strategy described by Macgillivray and co workers to illustrate the control of photodimerization outcome, J. Am. Chem. Soc., 2000, 122, 7817-7818. LRM photodimer.gif
A resorcinol based templating strategy described by Macgillivray and co workers to illustrate the control of photodimerization outcome, J. Am.Chem. Soc., 2000, 122, 7817-7818.

The design of crystal structures with desired properties is the ultimate goal of crystal engineering. Crystal engineering principles have been applied to the design of non-linear optical materials, especially those with second harmonic generation (SHG) properties. Using supramolecular synthons, supramolecular gels have been designed. [19] [20]

Mechanical properties of crystalline materials

Four mechanical properties of crystalline materials: shear strength, plasticity, elasticity, and brittleness. Information adapted from Saha et al. 2018. Mechanical Properties of Crystalline Materials.png
Four mechanical properties of crystalline materials: shear strength, plasticity, elasticity, and brittleness. Information adapted from Saha et al. 2018.
Designing a material with targeted mechanical properties requires command over complex structures across a range of length scales. Complexity and Scale of Structures within Crystalline Materials.png
Designing a material with targeted mechanical properties requires command over complex structures across a range of length scales.

Designing a crystalline material with targeted properties requires an understanding of the material's molecular and crystal features in relation to its mechanical properties. [22] Four mechanical properties are of interest for crystalline materials: plasticity, elasticity, brittleness, and shear strength). [21]

Intermolecular interactions

Manipulation of the intermolecular interaction network is a means for controlling bulk properties. [23] During crystallization, intermolecular interactions form according to an electrostatic hierarchy. [24] Strong hydrogen bonds are the primary director for crystal organization. [25] [24] [26]

Crystal architecture

Typically, the strongest intermolecular interactions form the molecular layers or columns and the weakest intermolecular interactions form the slip plane. [27] For example, long chains or layers of acetaminophen molecules form due to the hydrogen bond donors and acceptors that flank the benzene ring. The weaker interactions between the chains or layers of acetaminophen required less energy to break than the hydrogen bonds. As a result, a slip plane is formed.

A. Slip planes associated with layered or columnar architectural features in crystalline materials. Red dotted and black dashed lines represent the direction of the weakest and strongest intermolecular interactions, respectively, which influences the slip plane. B. Example of the strongest (hydrogen bonds) and weakest (van der Waals) interactions in acetaminophen structure that influences the crystal structure. Crystal Architecture and Intermolecular Interactions.png
A. Slip planes associated with layered or columnar architectural features in crystalline materials. Red dotted and black dashed lines represent the direction of the weakest and strongest intermolecular interactions, respectively, which influences the slip plane. B. Example of the strongest (hydrogen bonds) and weakest (van der Waals) interactions in acetaminophen structure that influences the crystal structure.

A supramolecular synthon is a pair of molecules that form relatively strong intermolecular interactions in the early phases of crystallization; these molecule pairs are the basic structural motif found in a crystal lattice. [28] [29] [30]

Defects or imperfections

Lattice defects, such as point defects, tilt boundaries, or dislocations, create imperfections in crystal architecture and topology. Any disruption to the crystal structure alters the mechanism or degree of molecular movement, thereby changing the mechanical properties of the material. [31] Examples of point imperfections include vacancies, substitutional impurities, interstitial impurities, Frenkel’s defects, and Schottky’s defects. [32] Examples of line imperfections include edge and screw dislocations. [32]

Assessing Crystal Structure

Crystallographic methods, such as X-ray diffraction, are used to elucidate the crystal structure of a material by quantifying distances between atoms. [32] The X-ray diffraction technique relies on a particular crystal structure creating a unique pattern after X-rays are diffracted through the crystal lattice. Microscopic methods, such as optical, electron, field ion, and scanning tunneling microscopy, can be used to visualize the microstructure, imperfections, or dislocations of a material. [32] Ultimately, these methods elaborate on the growth and assembly of crystallites during crystallization, which can be used to rationalize the movement of crystallites in response to an applied load. [33] Calorimetric methods, such as differential scanning calorimetry, use induce phase transitions in order to quantify the associated changes in enthalpy, entropy, and Gibb's free energy. [34] The melting and fusion phase transitions are dependent on the lattice energy of the crystalline material, which can be used to determine percent crystallinity of the sample. Raman spectroscopy is a method that uses light scattering to interact with bonds in a sample. [35] This technique provides information about chemical bonds, intermolecular interactions, and crystallinity.

Assessing mechanical properties

Nanoindentation is a standard and widely-accepted method for measuring mechanical properties within the crystal engineering field. [21] [36] The method quantifies hardness, elasticity, packing anisotropy, and polymorphism of a crystalline material. [21] [37] [38] [39] [40] Hirshfeld surfaces are visual models of electron density at a specific isosurface that aid in visualizing and quantifying intermolecular interactions. [41] An advantage to using Hirshfeld surfaces in crystal engineering is that these surface maps are embedded with information about a molecular and its neighbors. [41] The insight into molecular neighbors can be applied to assessment or prediction of molecular properties. [37] An emerging method for topography and slip plane analysis using energy frameworks, which are models of crystal packing that depict interaction energies as pillars or beams. [25] [37] [40]

See also

Related Research Articles

<span class="mw-page-title-main">Hydrogen bond</span> Intermolecular attraction between a hydrogen-donor pair and an acceptor

In chemistry, a hydrogen bond is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac). Such an interacting system is generally denoted Dn−H···Ac, where the solid line denotes a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond. The most frequent donor and acceptor atoms are the period 2 elements nitrogen (N), oxygen (O), and fluorine (F).

An intermolecular force (IMF) is the force that mediates interaction between molecules, including the electromagnetic forces of attraction or repulsion which act between atoms and other types of neighbouring particles, e.g. atoms or ions. Intermolecular forces are weak relative to intramolecular forces – the forces which hold a molecule together. For example, the covalent bond, involving sharing electron pairs between atoms, is much stronger than the forces present between neighboring molecules. Both sets of forces are essential parts of force fields frequently used in molecular mechanics.

<span class="mw-page-title-main">Polymer</span> Substance composed of macromolecules with repeating structural units

A polymer is a substance or material consisting of very large molecules called macromolecules, composed of many repeating subunits. Due to their broad spectrum of properties, both synthetic and natural polymers play essential and ubiquitous roles in everyday life. Polymers range from familiar synthetic plastics such as polystyrene to natural biopolymers such as DNA and proteins that are fundamental to biological structure and function. Polymers, both natural and synthetic, are created via polymerization of many small molecules, known as monomers. Their consequently large molecular mass, relative to small molecule compounds, produces unique physical properties including toughness, high elasticity, viscoelasticity, and a tendency to form amorphous and semicrystalline structures rather than crystals.

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 chemistry, a non-covalent interaction differs from a covalent bond in that it does not involve the sharing of electrons, but rather involves more dispersed variations of electromagnetic interactions between molecules or within a molecule. The chemical energy released in the formation of non-covalent interactions is typically on the order of 1–5 kcal/mol. Non-covalent interactions can be classified into different categories, such as electrostatic, π-effects, van der Waals forces, and hydrophobic effects.

In materials science, polymorphism describes the existence of a solid material in more than one form or crystal structure. Polymorphism is a form of isomerism. Any crystalline material can exhibit the phenomenon. Allotropy refers to polymorphism for chemical elements. Polymorphism is of practical relevance to pharmaceuticals, agrochemicals, pigments, dyestuffs, foods, and explosives. According to IUPAC, a polymorphic transition is "A reversible transition of a solid crystalline phase at a certain temperature and pressure to another phase of the same chemical composition with a different crystal structure." According to McCrone, polymorphs are "different in crystal structure but identical in the liquid or vapor states." Materials with two polymorphs are called dimorphic, with three polymorphs, trimorphic, etc.

<span class="mw-page-title-main">Molecular solid</span> Solid consisting of discrete molecules

A molecular solid is a solid consisting of discrete molecules. The cohesive forces that bind the molecules together are van der Waals forces, dipole-dipole interactions, quadrupole interactions, π-π interactions, hydrogen bonding, halogen bonding, London dispersion forces, and in some molecular solids, coulombic interactions. Van der Waals, dipole interactions, quadrupole interactions, π-π interactions, hydrogen bonding, and halogen bonding are typically much weaker than the forces holding together other solids: metallic, ionic, and network solids. Intermolecular interactions, typically do not involve delocalized electrons, unlike metallic and certain covalent bonds. Exceptions are charge-transfer complexes such as the tetrathiafulvane-tetracyanoquinodimethane (TTF-TCNQ), a radical ion salt. These differences in the strength of force and electronic characteristics from other types of solids give rise to the unique mechanical, electronic, and thermal properties of molecular solids.

The term "polymer" refers to large molecules whose structure is composed of multiple repeating units and the prefix "supra" meaning "beyond the limits of". Supramolecular polymers are a new category of polymers that can potentially be used for material applications beyond the limits of conventional polymers. By definition, supramolecular polymers are polymeric arrays of monomeric units that are connected by reversible and highly directional secondary interactions–that is, non-covalent bonds. These non-covalent interactions include van der Waals interactions, hydrogen bonding, Coulomb or ionic interactions, π-π stacking, metal coordination, halogen bonding, chalcogen bonding, and host–guest interaction. The direction and strength of the interactions are precisely tuned so that the array of molecules behaves as a polymer in dilute and concentrated solution, as well as in the bulk.

<span class="mw-page-title-main">Molecular self-assembly</span> Movement of molecules into a defined arrangement without outside influence

In chemistry and materials science, molecular self-assembly is the process by which molecules adopt a defined arrangement without guidance or management from an outside source. There are two types of self-assembly: intermolecular and intramolecular. Commonly, the term molecular self-assembly refers to the former, while the latter is more commonly called folding.

A halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. Like a hydrogen bond, the result is not a formal chemical bond, but rather a strong electrostatic attraction. Mathematically, the interaction can be decomposed in two terms: one describing an electrostatic, orbital-mixing charge-transfer and another describing electron-cloud dispersion. Halogen bonds find application in supramolecular chemistry; drug design and biochemistry; crystal engineering and liquid crystals; and organic catalysis.

<span class="mw-page-title-main">Gautam Radhakrishna Desiraju</span> Indian chemist (born 1952)

Gautam Radhakrishna Desiraju is an Indian structural chemist, educationist and an honorary professor at the Indian Institute of Science. He worked on crystal engineering and weak hydrogen bonding and co-authored a textbook in crystal engineering (2011). He subsequently wrote a book entitled "Bharat: India 2.0" (2022) in which he claims that India is a 5000 year civilization that does not need a constitution. He espouses ideas of intrinsic Indian sacredness, righteousness, and the belief that scientists should not take part in political discussions and has been an outspoken critic of academics who speak against government policies particularly those of the ruling right-wing BJP party.

In materials science, cocrystals are "solids that are crystalline, single-phase materials composed of two or more different molecular or ionic compounds generally in a stoichiometric ratio which are neither solvates nor simple salts." A broader definition is that cocrystals "consist of two or more components that form a unique crystalline structure having unique properties." Several subclassifications of cocrystals exist.

Nuclear magnetic resonance crystallography is a method which utilizes primarily NMR spectroscopy to determine the structure of solid materials on the atomic scale. Thus, solid-state NMR spectroscopy would be used primarily, possibly supplemented by quantum chemistry calculations, powder diffraction etc. If suitable crystals can be grown, any crystallographic method would generally be preferred to determine the crystal structure comprising in case of organic compounds the molecular structures and molecular packing. The main interest in NMR crystallography is in microcrystalline materials which are amenable to this method but not to X-ray, neutron and electron diffraction. This is largely because interactions of comparably short range are measured in NMR crystallography.

<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.

Giuseppe Resnati is an Italian chemist with interests in supramolecular chemistry and fluorine chemistry. He has a particular focus on self-assembly processes driven by halogen bonds and chalcogen bonds.

A chalcogen bond (ChB) is an attractive interaction in the family of σ-hole interactions, along with halogen bonds. Electrostatic, charge-transfer (CT) and dispersion terms have been identified as contributing to this type of interaction. In terms of CT contribution, this family of attractive interactions has been modeled as an electron donor ) interacting with the σ* orbital of a C-X bond of the bond donor. In terms of electrostatic interactions, the molecular electrostatic potential (MEP) maps is often invoked to visualize the electron density of the donor and an electrophilic region on the acceptor, where the potential is depleted, referred to as a σ-hole. ChBs, much like hydrogen and halogen bonds, have been invoked in various non-covalent interactions, such as protein folding, crystal engineering, self-assembly, catalysis, transport, sensing, templation, and drug design.

<span class="mw-page-title-main">Margaret C. Etter</span> American chemist and crystallographer

Margaret Cairns Etter, known informally as Peggy Etter, was an American chemist who contributed to the development of solid state chemistry for crystalline organic compounds. She is known for her work characterizing and classifying contacts by hydrogen bonds in organic compounds. Her "enlightened imagination, innovative creativity, and unfailing enthusiasm" is recognised as having a "transformative effect" in many areas of organic chemistry.

<span class="mw-page-title-main">Hydrogen-bonded organic framework</span>

Hydrogen-bonded organic frameworks (HOFs) are a class of two- or three-dimensional materials formed by hydrogen bonds among molecular monomer units to afford porosity and structural flexibility. There are diverse hydrogen bonding pair choices that could be used in HOFs construction, including identical or nonidentical hydrogen bonding donors and acceptors. For organic groups acting as hydrogen bonding units, species like carboxylic acid, amide, 2,4-diaminotriazine, and imidazole, etc., are commonly used for the formation of hydrogen bonding interaction. Compared with other organic frameworks, like COF and MOF, the binding force of HOFs is relatively weaker and the activation of HOFs is more difficult than other frameworks, while the reversibility of hydrogen bonds guarantees a high crystallinity of the materials. Though the stability and pore size expansion of HOFs has potential problems, HOFs still show strong potential for applications in different areas.

References

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