Structural chemistry

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Structural chemistry is a part of chemistry and deals with spatial structures of molecules (in the gaseous, liquid or solid state) and solids (with extended structures that cannot be subdivided into molecules). For structure elucidation [1] a range of different methods is used. One has to distinguish between methods that elucidate solely the connectivity between atoms (constitution) and such that provide precise three dimensional information such as atom coordinates, bond lengths and angles and torsional angles.

Contents

Determination methods

The determination of chemical structure include (mainly):

To identify connectivity and the presence of functional groups a variety of methods of molecular spectroscopy and solid state spectroscopy can be used.

Gaseous state

Electron diffraction

Gas electron diffraction focuses on determining the geometrical arrangement of atoms in a gaseous molecule. It does this by interpreting the electron diffraction patterns that result when a molecule is intersected by a beam of electrons. Studies have used gas electron diffraction to obtain equilibrium and vibrationally averaged structures of gases. [8] Gas electron diffraction is also crucial for acquiring data on both stable and unstable free molecules, radicals, and ions, providing essential structural information. [9] For instance, the structure of gaseous fluorofullerene C60F36 was determined using electron diffraction supplemented with quantum chemical calculations. [10]

Microwave spectroscopy

Microwave rotational spectroscopy measures the energies of rotational transitions through microwave radiation for a gasous molecule. The electric dipole moment of the molecules interacts with the electromagnetic field of the exciting microwave photon, which facilitates the measurement of these transitions. [11] It employs chirped-pulse Fourier transform microwave (FTMW) spectroscopy to determine the rotational constants of compounds. [3] This method has long been regarded as robust for the precise determination of structures, with the ability to discern different conformational states of molecules. [12] Its accuracy is highlighted by its application in providing molecular structure in the gas phase, with rotational transitions being particularly informative when ΔJ = ±1. [13]

Liquid state

NMR Spectroscopy

Liquid-state NMR spectroscopy has become a principal method for molecular structure elucidation in liquids. [4] It is a flexible method that accommodates a wide array of applications, including structure determination, in situ monitoring, and analysis of mixtures. [14] Techniques like SHARPER (Sensitive, Homogeneous And Resolved PEaks in Real time) have further enhanced the sensitivity of NMR, particularly in reaction monitoring by removing J splittings, which creates very narrow signals that are crucial for accurate analysis. [4] NMR spectroscopy also enables the determination of 3D structures of molecules in the liquid state by measuring interproton distances through Nuclear Overhauser Effect (NOE) experiments. [15]

Solid state

X-ray Diffraction

X-ray diffraction is a powerful technique for determining the atomic and molecular structure of crystalline solids. [5] It relies on the interaction of X-rays with the electron density of the crystal lattice, producing diffraction patterns that can be used to deduce the arrangement of atoms. [5] This method has been instrumental in elucidating the structures of a wide range of materials, including organic compounds, inorganic compounds, and proteins.

Using X-ray diffraction to determine the structure of membrane protein Using X-ray diffractometer to solve the 3D structure of membrane proteins of the flagellar system (41795117862).jpg
Using X-ray diffraction to determine the structure of membrane protein

Electron diffraction

Electron diffraction involves firing a beam of electrons at a crystalline sample. [6] Similar to X-ray diffraction, it produces diffraction patterns that can be used to determine the structure of the sample. [6] Electron diffraction is particularly useful for the study of small organic molecules and complex organic compounds.

Neutron diffraction

Neutron diffraction is a technique that employs a beam of neutrons instead of X-rays or electrons. [7] Neutrons interact with atomic nuclei and are sensitive to the positions of light atoms, such as hydrogen. [7] This method is vital for understanding the structure of materials where hydrogen plays a significant role, such as in hydrogen-bonded systems.

Importance and contributions

Structural chemistry is pivotal in understanding the fundamental nature of matter and the properties of materials. Structural chemists play a crucial role in various scientific and industrial fields. [16] The prospective of structural chemistry lies in its ability to address real-world challenges, fuel scientific innovation, and contribute to advancements in various fields. Collaboration, technological advancements, and a multidisciplinary approach will continue to shape the future of structural chemistry, paving the way for groundbreaking discoveries and applications.

Contributions

Drug Discovery and Design

Structural chemists contribute significantly to drug discovery by elucidating the three-dimensional structures of biological molecules, enabling the design of targeted drugs with higher efficacy and fewer side effects. [17]

Materials Science

Understanding the atomic and molecular arrangements in materials helps in developing new materials with specific properties, leading to innovations in electronics, energy storage, and nanotechnology. [18]

Catalysis

Structural chemistry provides insights into the active sites of catalysts, enabling the design of efficient catalysts for chemical reactions, including those used in sustainable energy technologies. [19]

Biological Research

Structural biologists use techniques like X-ray crystallography and NMR spectroscopy to determine the structures of biomolecules, contributing to our understanding of biological processes and diseases. [20]

Environmental Science

Structural chemistry aids in analyzing pollutants, understanding their behavior, and developing methods to mitigate environmental impact. [21]

Challenges

Complexity of Systems

As researchers delve into more complex materials and biological systems, determining their structures accurately becomes challenging due to the intricate interactions and large molecular sizes involved. Recent study has found unprecedented applications in the biological context and for the first time enables scientists to address complex questions in biology on the level of molecules, cells, tissues and entire organs, as well as to begin to address important challenges imposed by cardiovascular diseases, cancer, and in digestive and reproductive biology. [22]

Technological Limitations

The development of advanced experimental techniques and computational methods is essential. High-resolution techniques like cryo-electron microscopy and advancements in computational simulations are addressing some challenges. [23]

Data Analysis

Handling vast amounts of structural data requires sophisticated algorithms and data analysis techniques to extract meaningful information, posing challenges in data interpretation and storage. [24] However, with the advent of deep learning, a branch of machine learning and artificial intelligence, and it has become possible to analyze large datasets with greater accuracy and efficiency. [24] However, method also has its own limitations, such as the lack of training data, imbalanced data, and overfitting. [24]

Future directions

Combining various experimental and computational techniques can provide comprehensive insights into complex structures. Integrating data from X-ray crystallography, NMR spectroscopy, and computational modeling enhances accuracy and reliability. Continued progress in computational simulations, including quantum chemistry and molecular dynamics, will allow researchers to study larger and more complex systems, aiding in predicting and understanding novel structures. [18] [17] Open-access databases and collaborative efforts enable researchers worldwide to share structural data, accelerating scientific progress and fostering innovation. [24]

Structural chemistry can contribute to the design of eco-friendly materials and catalysts, promoting sustainable practices in the chemical industry. Structural chemistry can contribute to the design of eco-friendly materials and catalysts, promoting sustainable practices in the chemical industry. Recent development of metal-free nanostructured catalysts is one of the advancements in the field of structural chemistry that has the potential to drive organic transformations in a sustainable manner. [25]

See also

Related Research Articles

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

Inorganic chemistry deals with synthesis and behavior of inorganic and organometallic compounds. This field covers chemical compounds that are not carbon-based, which are the subjects of organic chemistry. The distinction between the two disciplines is far from absolute, as there is much overlap in the subdiscipline of organometallic chemistry. It has applications in every aspect of the chemical industry, including catalysis, materials science, pigments, surfactants, coatings, medications, fuels, and agriculture.

<span class="mw-page-title-main">Spectroscopy</span> Study involving matter and electromagnetic radiation

Spectroscopy is the field of study that measures and interprets electromagnetic spectra. In narrower contexts, spectroscopy is the precise study of color as generalized from visible light to all bands of the electromagnetic spectrum.

<span class="mw-page-title-main">Structural biology</span> Study of molecular structures in biology

Structural biology is a field that is many centuries old which, as defined by the Journal of Structural Biology, deals with structural analysis of living material at every level of organization. Early structural biologists throughout the 19th and early 20th centuries were primarily only able to study structures to the limit of the naked eye's visual acuity and through magnifying glasses and light microscopes.

<span class="mw-page-title-main">Surface science</span> Study of physical and chemical phenomena that occur at the interface of two phases

Surface science is the study of physical and chemical phenomena that occur at the interface of two phases, including solid–liquid interfaces, solid–gas interfaces, solid–vacuum interfaces, and liquid–gas interfaces. It includes the fields of surface chemistry and surface physics. Some related practical applications are classed as surface engineering. The science encompasses concepts such as heterogeneous catalysis, semiconductor device fabrication, fuel cells, self-assembled monolayers, and adhesives. Surface science is closely related to interface and colloid science. Interfacial chemistry and physics are common subjects for both. The methods are different. In addition, interface and colloid science studies macroscopic phenomena that occur in heterogeneous systems due to peculiarities of interfaces.

<span class="mw-page-title-main">Chemical structure</span> Organized way in which molecules are ordered and sorted

A chemical structure of a molecule is a spatial arrangement of its atoms and their chemical bonds. Its determination includes a chemist's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target molecule or other solid. Molecular geometry refers to the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together and can be represented using structural formulae and by molecular models; complete electronic structure descriptions include specifying the occupation of a molecule's molecular orbitals. Structure determination can be applied to a range of targets from very simple molecules to very complex ones.

<span class="mw-page-title-main">Molecular geometry</span> Study of the 3D shapes of molecules

Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that determine the position of each atom.

Gas electron diffraction (GED) is one of the applications of electron diffraction techniques. The target of this method is the determination of the structure of gaseous molecules, i.e., the geometrical arrangement of the atoms from which a molecule is built up. GED is one of two experimental methods to determine the structure of free molecules, undistorted by intermolecular forces, which are omnipresent in the solid and liquid state. The determination of accurate molecular structures by GED studies is fundamental for an understanding of structural chemistry.

<span class="mw-page-title-main">Elemental analysis</span> Process of analytical chemistry

Elemental analysis is a process where a sample of some material is analyzed for its elemental and sometimes isotopic composition. Elemental analysis can be qualitative, and it can be quantitative. Elemental analysis falls within the ambit of analytical chemistry, the instruments involved in deciphering the chemical nature of our world.

<span class="mw-page-title-main">Nuclear magnetic resonance spectroscopy</span> Laboratory technique

Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique based on re-orientation of atomic nuclei with non-zero nuclear spins in an external magnetic field. This re-orientation occurs with absorption of electromagnetic radiation in the radio frequency region from roughly 4 to 900 MHz, which depends on the isotopic nature of the nucleus and increased proportionally to the strength of the external magnetic field. Notably, the resonance frequency of each NMR-active nucleus depends on its chemical environment. As a result, NMR spectra provide information about individual functional groups present in the sample, as well as about connections between nearby nuclei in the same molecule. As the NMR spectra are unique or highly characteristic to individual compounds and functional groups, NMR spectroscopy is one of the most important methods to identify molecular structures, particularly of organic compounds.

Hydrogen–deuterium exchange is a chemical reaction in which a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa. It can be applied most easily to exchangeable protons and deuterons, where such a transformation occurs in the presence of a suitable deuterium source, without any catalyst. The use of acid, base or metal catalysts, coupled with conditions of increased temperature and pressure, can facilitate the exchange of non-exchangeable hydrogen atoms, so long as the substrate is robust to the conditions and reagents employed. This often results in perdeuteration: hydrogen-deuterium exchange of all non-exchangeable hydrogen atoms in a molecule.

<span class="mw-page-title-main">Molecular biophysics</span> Interdisciplinary research area

Molecular biophysics is a rapidly evolving interdisciplinary area of research that combines concepts in physics, chemistry, engineering, mathematics and biology. It seeks to understand biomolecular systems and explain biological function in terms of molecular structure, structural organization, and dynamic behaviour at various levels of complexity. This discipline covers topics such as the measurement of molecular forces, molecular associations, allosteric interactions, Brownian motion, and cable theory. Additional areas of study can be found on Outline of Biophysics. The discipline has required development of specialized equipment and procedures capable of imaging and manipulating minute living structures, as well as novel experimental approaches.

Physical organic chemistry, a term coined by Louis Hammett in 1940, refers to a discipline of organic chemistry that focuses on the relationship between chemical structures and reactivity, in particular, applying experimental tools of physical chemistry to the study of organic molecules. Specific focal points of study include the rates of organic reactions, the relative chemical stabilities of the starting materials, reactive intermediates, transition states, and products of chemical reactions, and non-covalent aspects of solvation and molecular interactions that influence chemical reactivity. Such studies provide theoretical and practical frameworks to understand how changes in structure in solution or solid-state contexts impact reaction mechanism and rate for each organic reaction of interest.

Carbohydrate NMR spectroscopy is the application of nuclear magnetic resonance (NMR) spectroscopy to structural and conformational analysis of carbohydrates. This method allows the scientists to elucidate structure of monosaccharides, oligosaccharides, polysaccharides, glycoconjugates and other carbohydrate derivatives from synthetic and natural sources. Among structural properties that could be determined by NMR are primary structure, saccharide conformation, stoichiometry of substituents, and ratio of individual saccharides in a mixture. Modern high field NMR instruments used for carbohydrate samples, typically 500 MHz or higher, are able to run a suite of 1D, 2D, and 3D experiments to determine a structure of carbohydrate compounds.

<span class="mw-page-title-main">Molecular models of DNA</span>

Molecular models of DNA structures are representations of the molecular geometry and topology of deoxyribonucleic acid (DNA) molecules using one of several means, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. These representations include closely packed spheres made of plastic, metal wires for skeletal models, graphic computations and animations by computers, artistic rendering. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.

<span class="mw-page-title-main">Nuclear magnetic resonance</span> Spectroscopic technique based on change of nuclear spin state

Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field and respond by producing an electromagnetic signal with a frequency characteristic of the magnetic field at the nucleus. This process occurs near resonance, when the oscillation frequency matches the intrinsic frequency of the nuclei, which depends on the strength of the static magnetic field, the chemical environment, and the magnetic properties of the isotope involved; in practical applications with static magnetic fields up to ca. 20 tesla, the frequency is similar to VHF and UHF television broadcasts (60–1000 MHz). NMR results from specific magnetic properties of certain atomic nuclei. Nuclear magnetic resonance spectroscopy is widely used to determine the structure of organic molecules in solution and study molecular physics and crystals as well as non-crystalline materials. NMR is also routinely used in advanced medical imaging techniques, such as in magnetic resonance imaging (MRI). The original application of NMR to condensed matter physics is nowadays mostly devoted to strongly correlated electron systems. It reveals large many-body couplings by fast broadband detection and it should not to be confused with solid state NMR, which aims at removing the effect of the same couplings by Magic Angle Spinning techniques.

<span class="mw-page-title-main">Instrumental chemistry</span> Study of analytes using scientific instruments

Instrumental analysis is a field of analytical chemistry that investigates analytes using scientific instruments.

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.

The following outline is provided as an overview of and topical guide to biophysics:

<span class="mw-page-title-main">Macromolecular assembly</span>

The term macromolecular assembly (MA) refers to massive chemical structures such as viruses and non-biologic nanoparticles, cellular organelles and membranes and ribosomes, etc. that are complex mixtures of polypeptide, polynucleotide, polysaccharide or other polymeric macromolecules. They are generally of more than one of these types, and the mixtures are defined spatially, and with regard to their underlying chemical composition and structure. Macromolecules are found in living and nonliving things, and are composed of many hundreds or thousands of atoms held together by covalent bonds; they are often characterized by repeating units. Assemblies of these can likewise be biologic or non-biologic, though the MA term is more commonly applied in biology, and the term supramolecular assembly is more often applied in non-biologic contexts. MAs of macromolecules are held in their defined forms by non-covalent intermolecular interactions, and can be in either non-repeating structures, or in repeating linear, circular, spiral, or other patterns. The process by which MAs are formed has been termed molecular self-assembly, a term especially applied in non-biologic contexts. A wide variety of physical/biophysical, chemical/biochemical, and computational methods exist for the study of MA; given the scale of MAs, efforts to elaborate their composition and structure and discern mechanisms underlying their functions are at the forefront of modern structure science.

Operando spectroscopy is an analytical methodology wherein the spectroscopic characterization of materials undergoing reaction is coupled simultaneously with measurement of catalytic activity and selectivity. The primary concern of this methodology is to establish structure-reactivity/selectivity relationships of catalysts and thereby yield information about mechanisms. Other uses include those in engineering improvements to existing catalytic materials and processes and in developing new ones.

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