From the middle of the 20th century there are fundamental changes in methods chemical research, which involve a wide arsenal of means of physics and mathematics. The classical problems of chemistry - the establishment of the composition and structure of substances - are increasingly successfully solved using the latest physical methods. An integral feature of theoretical and experimental chemistry has become the use of the latest high-speed computer science for quantum chemical calculations, identification of kinetic patterns, processing of spectroscopic data, calculation of the structure and properties of complex molecules.
Of the purely chemical methods developed in the 20th century, microchemical analysis should be noted, which makes it possible to carry out analytical operations with quantities of substances that are hundreds of times smaller than in the method of conventional chemical analysis. Chromatography has acquired great importance, serving not only for analytical purposes, but also for the separation of substances that are very similar in chemical properties on a laboratory and industrial scale. An important role is played by physicochemical analysis (PCA) as one of the methods for determining the chemical composition and nature of the interaction of components in solutions, melts, and other systems. In FHA, graphical methods are widely used (state diagrams and composition-property diagrams). The classification of the latter made it possible to clarify the concept of a chemical individual, the composition of which can be constant and variable. The class of non-stoichiometric compounds predicted by Kurnakov has gained great importance in materials science and a new field - solid state chemistry.
Luminescent analysis, the method of labeled atoms, X-ray structural analysis, electron diffraction, polarography, and other physicochemical methods of analysis are widely used in analytical chemistry. The use of radiochemical methods makes it possible to detect the presence of only a few atoms of a radioactive isotope (for example, in the synthesis of transuranium elements).
To establish the structure of chemical compounds, molecular spectroscopy is important, with the help of which distances between atoms, symmetry, the presence of functional groups, and other characteristics of a molecule are determined, and the mechanism of chemical reactions is also studied. The electronic energy structure of atoms and molecules, the magnitude of effective charges are determined by means of emission and absorption X-ray spectroscopy. The geometry of molecules is studied by X-ray structural analysis.
The discovery of the interaction between electrons and atomic nuclei (causing the hyperfine structure of their spectra), as well as between external and internal electrons, made it possible to create such methods for determining the structure of molecules as nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR), nuclear quadrupole resonance (NQR). ), gamma-resonance spectroscopy. special role in terms of breadth of application, NMR spectroscopy has acquired. Optical methods, such as spectropolarimetry, circular dichroism, and optical rotation dispersion, are becoming increasingly important in elucidating the spatial characteristics of molecules. The destruction of molecules in a vacuum under the influence of electron impact with the identification of fragments is used to determine their structure by mass spectroscopy. The arsenal of kinetic methods has been replenished with tools related to the use of EPR and NMR spectroscopy (chemical polarization of nuclei), the method of flash photolysis and radiolysis. This makes it possible to study ultrafast processes occurring in 10-9 seconds or less.
Molecular physics and thermodynamics are branches of physics that study macroscopic processes in bodies associated with a huge number of atoms and molecules contained in bodies. Examples of macroscopic systems are gases, liquids, solids, plasma. The sizes of atoms or molecules in comparison with the sizes of macrosystems are very small. They vary in the range from 10 -10 m (the size of a hydrogen atom) to 10 -7 m (the size of a virus protein molecule). The human senses do not allow to distinguish the size, shape, energy and momentum of individual molecules. However, a number of experiments indirectly, and in some cases directly, make it possible to do this. TO direct methods of observation molecules include methods of modern microscopy: electron, ion, holographic. Indirect methods of observation: Brownian motion, gas pressure on the walls of vessels, diffusion of gases and liquids, viscous friction, etc. All these phenomena can be explained if we assume that substances: a) consist of atoms and molecules, b) are in a state of continuous random motion and c) interaction forces act between them - attraction and repulsion.
To study macroscopic processes, two qualitatively different and mutually complementary methods are used: statistical (molecular-kinetic) And thermodynamic. The first underlies molecular physics, the second - thermodynamics.
Molecular physics- a branch of physics that studies the structure and properties of matter based on molecular kinetic concepts, based on the fact that all bodies consist of molecules that are in continuous chaotic motion and interact with each other according to certain laws. Here the macroscopic properties of bodies are considered as a manifestation of the total action of molecules. At the same time, in theory, they use statistical method, being interested not in the movement of individual molecules, but only in such average values that characterize the movement of a huge collection of particles. Hence its other name - statistical physics.
Thermodynamics- a branch of physics that studies the general properties of macroscopic systems in a state of thermodynamic equilibrium, and the processes of transition between these states. Thermodynamics does not consider the microprocesses that underlie these transformations. This thermodynamic, or phenomenological, the method differs from the statistical one.
Molecular-kinetic theory and thermodynamics mutually complement each other, forming a single whole, but differing in different research methods. Both methods should give the same results regarding the properties and state of a substance under similar conditions and, therefore, there should be a regular relationship between the parameters of a substance that describe its state in molecular-kinetic theory and in thermodynamics.
X-ray diffraction analysis: 1) According to the diffraction patterns obtained when an X-ray beam passes through the crystal, the interatomic distances are determined and the structure of the crystal is established; 2) Widely applied to determine the structure of protein and nucleic acid molecules; 3) The bond lengths and angles, which are precisely established for small molecules, are used as standard values, on the assumption that they remain the same in more complex polymer structures; 4) One of the steps in determining the structure of proteins and nucleic acids is the construction of molecular models of polymers that are consistent with X-ray data and retain standard bond lengths and bond angles.
Nuclear magnetic resonance: 1) At the base - absorption of electromagnetic waves in the radio frequency range by the nuclei of atoms having a magnetic moment; 2) The absorption of a quantum of energy occurs when the nuclei are in the strong magnetic field of the NMR spectrometer; 3) Nuclei with different chemical environments absorb energy in a slightly different magnetic field (or, at constant voltage, slightly different frequency radio frequency vibrations); 4) The result is NMR spectrum a substance in which magnetically asymmetric nuclei are characterized by certain signals - "chemical shifts" in relation to any standard ; 5) NMR spectra make it possible to determine the number of atoms of a given element in a compound and the number and nature of other atoms surrounding a given
Electron Paramagnetic Resonance (EPR): 1) The resonant absorption of radiation by electrons is used
Electron microscopy:1) They use an electron microscope that magnifies objects millions of times; 2) The first electron microscopes appeared in 1939; 3) With a resolution of ~0.4 nm, the electron microscope allows you to "see" the molecules of proteins and nucleic acids, as well as the details of the structure of cell organelles; 4) In 1950 were designed microtomes And knives , allowing to make ultrathin (20–200 nm) sections of tissues pre-embedded in plastic
Protein isolation and purification methods: Once a protein source has been chosen, the next step is to extract it from the tissue. If an extract containing a significant portion of the protein under study has been obtained, particles and non-protein material have been removed from it, protein purification can begin. concentration . It can be carried out by protein precipitation followed by dissolution of the precipitate in a smaller volume. Usually ammonium sulfate or acetone is used for this. The protein concentration in the initial solution should not be less than 1 mg/ml. Thermal denaturation . At the initial stage of purification, heat treatment is sometimes used to separate proteins. It is effective if the protein is relatively stable under heat conditions while the accompanying proteins are denatured. This varies the pH of the solution, the duration of treatment and temperature. For selection optimal conditions preliminarily conduct a series of small experiments. After the first stages of purification, the proteins are far from a homogeneous state. In the resulting mixture, proteins differ from each other in solubility, molecular weight, total charge of the molecule, relative stability, etc. Precipitation of proteins with organic solvents. This is one of the old methods. It plays an important role in the purification of proteins on an industrial scale. Most often, solvents such as ethanol and acetone are used, less often - isopropanol, methanol, dioxane. The main mechanism of the process: as the concentration of the organic solvent increases, the ability of water to solvate the charged hydrophilic molecules of the enzyme decreases. There is a decrease in the solubility of proteins to a level at which aggregation and precipitation begin. An important parameter affecting precipitation is the size of the protein molecule. The larger the molecule, the lower the concentration of the organic solvent causing protein precipitation. Gel filtration Using the gel filtration method, macromolecules can be quickly separated according to their size. The carrier for chromatography is a gel, which consists of a cross-linked three-dimensional molecular network, formed in the form of balls (granules) for easy filling of the columns. So sephadexes are cross-linked dextrans (α-1→6-glucans of microbial origin) with specified pore sizes. The dextran chains are cross-linked with three-carbon bridges using epichlorohydrin. The more crosslinks, the smaller the holes. The gel thus obtained plays the role of a molecular sieve. When a solution of a mixture of substances is passed through a column filled with swollen Sephadex granules, large particles larger than the pore size of Sephadex will move rapidly. Small molecules, such as salts, will move slowly as they penetrate into the granules as they move. electrophoresis
The physical principle of the electrophoresis method is as follows. A protein molecule in solution at any pH that differs from its isoelectric point has a certain average charge. This causes the protein to move in an electric field. The driving force is determined by the magnitude of the electric field strength E multiplied by the total charge of the particle z. This force is opposed by the viscosity of the medium, which is proportional to the viscosity coefficient η , particle radius r(Stokes radius) and speed v.; E z = 6πηrv.
Determination of the molecular weight of a protein. Mass spectrometry (mass spectroscopy, mass spectrography, mass spectral analysis, mass spectrometric analysis) is a method for studying a substance by determining the ratio of mass to charge. Proteins are capable of acquiring multiple positive and negative charges. Atoms of chemical elements have a specific mass. Thus, the exact determination of the mass of the analyzed molecule makes it possible to determine its elemental composition (see: elemental analysis). Mass spectrometry also provides important information about the isotopic composition of the analyzed molecules.
Methods for isolating and purifying enzymes Isolation of enzymes from biological material is the only real way obtaining enzymes . Enzyme Sources: fabrics; bacteria grown on a medium containing an appropriate substrate; cellular structures (mitochondria, etc.). It is necessary first to isolate the desired objects from the biological material.
Enzyme extraction methods: 1) Extraction(translation into solution): buffer solution (prevents acidification); drying with acetone ; treatment of the material with a mixture of butanol and water ; extraction with various organic solvents, aqueous solutions of detergents ; treatment of material with perchlorates, hydrolytic enzymes (lipases, nucleases, proteolytic enzymes)
Butanol destroys the lipoprotein complex, and the enzyme passes into the aqueous phase.
Detergent treatment results in true dissolution of the enzyme.
Fractionation. Factors affecting the results: pH, electrolyte concentration. It is necessary to constantly measure the activity of the enzyme.
Fractional precipitation with pH change
Fractional heat denaturation
fractional precipitation with organic solvents
salt fractionation - salting out
fractional adsorption (A. Ya. Danilevsky): the adsorbent is added to the enzyme solution, then each portion is separated by centrifugation
§ if the enzyme is adsorbed, then it is separated, then eluted from the adsorbent
§ if the enzyme is not adsorbed, then adsorbent treatment is used to separate the ballast substances
the enzyme solution is passed through a column with an adsorbent and fractions are collected
Enzymes are adsorbed selectively: column chromatography; electrophoresis; crystallization - obtaining highly purified enzymes.
The cell as the smallest unit of life.
Modern cell theory includes the following basic provisions: Cell - the basic unit of the structure and development of all living organisms, the smallest unit of life. Cl of all unicellular and multicellular organisms are similar (homologous) in structure, chemical composition, the main manifestations of vital activity. and metabolism. Reproduction of cells occurs by their division, i.e. every new cell. In complex multicellular organisms, cells are specialized in their function and form tissues; Organs are made up of tissues. Cl is an elementary living system capable of self-renewal, self-regulation and self-production.
Cell structure. the size of prokaryotic cells is on average 0.5-5 microns, the dimensions of eukaryotic cells are on average from 10 to 50 microns.
There are two types of cellular organization: prokaryotic and eukaryotic. Cells of the prokaryotic type are relatively simple. They do not have a morphologically distinct nucleus, the only chromosome is formed by circular DNA and is located in the cytoplasm. The cytoplasm contains numerous small ribosomes; microtubules are absent, so the cytoplasm is immobile, and the cilia and flagella have a special structure. Bacteria are classified as prokaryotes. Most modern living organisms belong to one of the three kingdoms - plants, fungi or animals, united in the supra-kingdom of eukaryotes. Organisms are divided into unicellular and multicellular. Unicellular organisms consist of a single cell that performs all functions. All prokaryotes are unicellular.
eukaryotes- organisms that, unlike prokaryotes, have a well-shaped cell nucleus, delimited from the cytoplasm by the nuclear membrane. The genetic material is enclosed in several linear double-stranded DNA molecules (depending on the type of organisms, their number per nucleus can vary from two to several hundred), attached from the inside to the membrane of the cell nucleus and forming in the vast majority of them a complex with histone proteins, called chromatin. Eukaryotic cells have a system of internal membranes that form, in addition to the nucleus, a number of other organelles (endoplasmic reticulum, Golgi apparatus, etc.). In addition, the vast majority have permanent intracellular symbionts of prokaryotes - mitochondria, and algae and plants also have plastids.
Biological membranes, their properties and functions One of the main features of all eukaryotic cells is the abundance and complexity of the structure of internal membranes. Membranes separate the cytoplasm from environment, and also form the shells of nuclei, mitochondria and plastids. They form a labyrinth of the endr-plasmic reticulum and flattened vesicles in the form of a stack that make up the Golgi complex. The membranes form lysosomes, large and small vacuoles of plant and fungal cells, pulsating vacuoles of protozoa. All these structures are compartments (compartments) designed for certain specialized processes and cycles. Therefore, without membranes, the existence of a cell is impossible. plasma membrane, or plasmalemma,- the most permanent, basic, universal membrane for all cells. It is the thinnest (about 10 nm) film covering the entire cell. The plasmalemma consists of molecules of proteins and phospholipids. Molecules of phospholipids are arranged in two rows - hydrophobic ends inward, hydrophilic heads to the internal and external aquatic environment. In some places, the bilayer (double layer) of phospholipids is permeated through with protein molecules (integral proteins). Inside such protein molecules there are channels - pores through which water-soluble substances pass. Other protein molecules permeate the lipid bilayer half from one side or the other (semi-integral proteins). On the surface of the membranes of eukaryotic cells there are peripheral proteins. Lipid and protein molecules are held together by hydrophilic-hydrophobic interactions. Properties and functions of membranes. All cell membranes are mobile fluid structures, since lipid and protein molecules are not interconnected covalent bonds and are able to move quickly enough in the plane of the membrane. Due to this, the membranes can change their configuration, i.e. they have fluidity. Membranes are very dynamic structures. They quickly recover from damage, and also stretch and contract with cellular movements. membranes different types cells differ significantly both in chemical composition and in the relative content of proteins, glycoproteins, lipids in them, and, consequently, in the nature of the receptors present in them. Each cell type is therefore characterized by an individuality that is determined mainly glycoproteins. Branched chain glycoproteins protruding from the cell membrane are involved in factor recognition external environment, as well as in the mutual recognition of related cells. For example, an egg and a sperm cell recognize each other by cell surface glycoproteins that fit together as separate elements of a whole structure. Such mutual recognition is a necessary stage preceding fertilization. Associated with recognition transport regulation molecules and ions through the membrane, as well as an immunological response in which glycoproteins play the role of antigens. Sugars can thus function as informational molecules (similar to proteins and nucleic acids). The membranes also contain specific receptors, electron carriers, energy converters, enzymatic proteins. Proteins are involved in ensuring the transport of certain molecules into or out of the cell, carry out the structural connection of the cytoskeleton with cell membranes, or serve as receptors for receiving and converting chemical signals from the environment. selective permeability. This means that molecules and ions pass through it at different speeds, and larger size molecules, the slower their passage through the membrane. This property defines the plasma membrane as osmotic barrier . Water and the gases dissolved in it have the maximum penetrating power; ions pass through the membrane much more slowly. The diffusion of water across a membrane is called osmosis.There are several mechanisms for the transport of substances across the membrane.
Diffusion- penetration of substances through the membrane along the concentration gradient (from the area where their concentration is higher to the area where their concentration is lower). With facilitated diffusion special membrane carrier proteins selectively bind to one or another ion or molecule and carry them across the membrane along a concentration gradient.
active transport is associated with energy costs and serves to transport substances against their concentration gradient. He carried out by special carrier proteins, which form the so-called ion pumps. The most studied is the Na - / K - pump in animal cells, actively pumping out Na + ions, while absorbing K - ions. Due to this, a large concentration of K - and a lower Na + in comparison with the environment are maintained in the cell. This process consumes the energy of ATP. As a result of active transport with the help of a membrane pump, the concentration of Mg 2- and Ca 2+ is also regulated in the cell.
At endocytosis (endo...- inside) a certain section of the plasmalemma captures and, as it were, envelops the extracellular material, enclosing it in a membrane vacuole that has arisen as a result of the invagination of the membrane. Subsequently, such a vacuole is connected to a lysosome, the enzymes of which break down macromolecules to monomers.
The reverse process of endocytosis is exocytosis (exo...- outside). Thanks to him, the cell removes intracellular products or undigested residues enclosed in vacuoles or vesicles. The vesicle approaches the cytoplasmic membrane, merges with it, and its contents are released into the environment. How digestive enzymes, hormones, hemicellulose, etc. are excreted.
Thus, biological membranes, as the main structural elements of the cell, serve not just as physical boundaries, but as dynamic functional surfaces. On the membranes of organelles, numerous biochemical processes are carried out, such as active absorption of substances, energy conversion, ATP synthesis, etc.
Functions of biological membranes the following: They delimit the contents of the cell from the external environment and the contents of the organelles from the cytoplasm. They provide transport of substances into and out of the cell, from the cytoplasm to organelles and vice versa. They play the role of receptors (receiving and converting signals from the environment, recognizing cell substances, etc.). They are catalysts (providing membrane chemical processes). Participate in the transformation of energy.
“Wherever we meet life, we find that it is associated with some protein body, and wherever we meet any protein body that is in the process of decomposition, we meet the phenomenon of life without exception”
Proteins are high-molecular nitrogen-containing organic compounds characterized by a strictly defined elemental composition and decomposing to amino acids upon hydrolysis.
Features that distinguish them from other organic compounds
1. The inexhaustible diversity of the structure and at the same time its high species uniqueness
2. Huge range of physical and chemical transformations
3. The ability to reversibly and quite naturally change the configuration of a molecule in response to external influences
4. Tendency to form supramolecular structures, complexes with other chemical compounds
Polypeptide theory of protein structure
only E. Fisher (1902) formulated the polypeptide theory buildings. According to this theory, proteins are complex polypeptides in which individual amino acids are linked to each other by peptide bonds arising from the interaction of α-carboxy COOH and α-NH 2 groups of amino acids. Using the example of the interaction of alanine and glycine, the formation of a peptide bond and a dipeptide (with the release of a water molecule) can be represented by the following equation:
The name of the peptides consists of the name of the first N-terminal amino acid with a free NH 2 group (ending in -yl, typical for acyl), the names of subsequent amino acids (also ending in -yl), and the full name of the C-terminal amino acid with a free COOH group. For example, a 5 amino acid pentapeptide can be designated by its full name: glycyl-alanyl-seryl-cysteinyl-alanine, or Gly-Ala-Ser-Cis-Ala for short.
experimental evidence for the polypeptide theory protein structures.
1. There are relatively few titratable free COOH and NH 2 groups in natural proteins, since the vast majority of them are in a bound state, participating in the formation of peptide bonds; titration available mainly free COOH - and NH 2 -groups at the N- and C-terminal amino acids of the peptide.
2. In the process of acid or alkaline hydrolysis squirrel stoichiometric amounts of titratable COOH and NH 2 groups are formed, which indicates the breakdown of a certain number of peptide bonds.
3. Under the action of proteolytic enzymes (proteinases), proteins are cleaved into strictly defined fragments, called peptides, with terminal amino acids corresponding to the selectivity of the action of proteinases. The structure of some of these fragments of incomplete hydrolysis was proved by their subsequent chemical synthesis.
4. Biuret reaction (blue-violet staining in the presence of a solution of copper sulfate in an alkaline medium) gives both biuret containing a peptide bond and proteins, which is also proof of the presence of similar bonds in proteins.
5. Analysis of X-ray patterns of protein crystals confirms the polypeptide structure of proteins. Thus, X-ray diffraction analysis at a resolution of 0.15–0.2 nm makes it possible not only to calculate interatomic distances and sizes of bond angles between C, H, O, and N atoms, but also to “see” the picture of the general arrangement of amino acid residues in the polypeptide chain and the spatial its orientation (conformation).
6. Significant confirmation of the polypeptide theory protein structures is the possibility of synthesizing by purely chemical methods polypeptides and proteins with an already known structure: insulin - 51 amino acid residues, lysozyme - 129 amino acid residues, ribonuclease - 124 amino acid residues. The synthesized proteins had physicochemical properties and biological activity similar to natural proteins.
MINISTRY OF EDUCATION AND SCIENCE OF THE RUSSIAN FEDERATION
TOMSK STATE UNIVERSITY
APPROVE Dean of the Faculty of Chemistry Yu.G. Slizhov "___" ___________
OK. bazyl
PHYSICAL METHODS OF RESEARCH IN CHEMISTRY
Tutorial
UDC 543.42 BBK 22.344a73 P 25
Bazyl O.K.
P 25 Physical research methods in chemistry: textbook. allowance.–Tomsk: Tomsk State University, 2013. - 88 p.
given short description theoretical foundations of a number of physical methods for studying matter. The purpose of this manual is to introduce the areas and possibilities of using optical (vibrational, rotational, electron spectroscopy and photophysics of molecules), resonance (EPR and NMR) methods and methods for measuring dipole moments.
For students of the Faculty of Chemistry studying the course "Structure of matter".
Reviewer -
cand. chem. sciences, prof. Department of Physics and colloid chemistry T.S. Minakova
UDC 543.42 BBK 22.344a73
Bazyl O.K., 2013 Tomsk State University, 2013
FOREWORD .............................................................. ................................................. ....................... |
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SECTION ONE. Electric dipole moment, its nature |
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and methods of determination ............................................................... ................................................. ........ |
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Chapter 1. Theoretical basis method ................................................. ................................. |
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1.1. The nature of the dipole moment ............................................................... ......................................... |
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1.2. Dipole in a static electric field. Molecule polarizability .............................. |
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1.3. Dielectric in a static electric field. Dielectric polarization .......... |
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1.4. Debye and Clausius–Mossotti equations.................................................................. ....................... |
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1.5. Polarization of a dielectric at high frequencies of an electromagnetic field. |
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Molar refraction .................................................................. ................................................. ... |
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Chapter 2. Methods for measuring the dipole moment and its use in chemistry ........ |
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2.1. Debye's first method ............................................................... ................................................. ..... |
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2.2. Determination of the dipole moment using the Stark effect .............................................. |
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2.3. Electrical resonance method .................................................................. ................................. |
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2.4. Use of data on dipole moments in chemistry.................................................... |
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SECTION TWO. Optical spectral methods .................................................................. ..... |
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Chapter 3. Theoretical Foundations of Spectral Methods .............................................. ........ |
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3.1. Bohr's postulates .................................................. ................................................. ............ |
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3.2. Separation of the energy of molecules into parts and the main types of spectra .............................................. |
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Chapter 4. Rotational spectra of diatomic molecules .............................................................. ....... |
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4.1. Energy of rotational stationary levels............................................................... ........... |
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4.1.1. Spherical top .............................................................. ............................................ |
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4.1.2. Symmetrical top .............................................................. ................................................ |
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4.2.3. Linear molecule .............................................................. ............................................... |
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4.2. Selection rules and rotational absorption spectrum .............................................................. ... |
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4.3. Determination of the geometric parameters of molecules from rotational spectra.... |
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Chapter 5 |
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Determination of the structure and properties of diatomic molecules .............................................. |
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5.1. Theoretical foundations of the method of IR spectroscopy .............................................. ........ |
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5.2. Vibrational spectrum of a harmonic oscillator............................................................... . |
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5.3. Vibrational spectrum of an anharmonic oscillator .............................................................. |
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Chapter 6. Vibrational spectra of polyatomic molecules .............................................................. ... |
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6.1. Classification of normal vibrations .................................................................. ......................... |
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6.2. Group and characteristic frequencies............................................................... ................... |
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6.3. Application of IR spectroscopy .............................................................. .................................... |
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Test questions................................................ ................................................. ............ |
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Tasks................................................. ................................................. ................................................ |
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Chapter 7 Electronic absorption and emission spectra of molecules. |
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Intramolecular photophysical processes ............................................................... ........ |
7.1. Electronic states and spectra of diatomic molecules ....................................................... |
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7.2. The Franck-Condon principle for intramolecular processes .............................................. |
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7.3. Electronic absorption spectra of polyatomic molecules. |
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Lambert-Beer law .............................................. ................................................. .. |
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7.4. Classification of electronic transitions ............................................................... ................... |
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7.5. Processes of deactivation of absorbed energy. |
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Energy level diagram .................................................................. ............................... |
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7.6. Fluorescence and its laws.................................................... ............................................ |
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7.7. Application of electronic spectra ............................................................... ............................... |
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Test questions................................................ ................................................. ........... |
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Tasks................................................. ................................................. ................................................ |
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SECTION THREE. Resonance research methods .............................................................. ..... |
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Chapter 8. Electron Paramagnetic Resonance Spectroscopy ............................................. |
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8.1. Theoretical foundations of the method. Zeeman effect .................................................................. ....... |
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8.2. Simple resonance condition. g - Factor ............................................... .................... |
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8.3. Electron - nuclear interaction .............................................................. ............................... |
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8.4. Hyperfine structure of EPR spectra ............................................................... ......................... |
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8.5. Application of EPR spectra in chemistry .............................................. ............................... |
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Test questions................................................ ................................................. ............ |
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Tasks................................................. ................................................. ................................................ |
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Chapter 9. Spectroscopy of nuclear magnetic resonance .................................................... ..... |
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9.1. The magnetic moment of the nucleus and its interaction with the magnetic field. |
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The condition of simple nuclear resonance .............................................................. ......................... |
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9.2. Chemical shift of the NMR signal............................................................... ................................... |
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9.3. Spin-spin interaction and multiplicity of NMR signals .............................. |
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9.4. Application of NMR spectra in chemistry ............................................... ............................... |
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Test questions................................................ ................................................. ........... |
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Tasks................................................. ................................................. ................................................ |
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PLANS OF SEMINAR LESSONS .............................................................. ................................. |
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LITERATURE................................................. ................................................. ......................... |
FOREWORD
At present, it is obvious that the development of chemistry is impossible without the widespread use of physical methods for studying the structure and properties of matter. The arsenal of modern physical methods in chemistry is so extensive, and their application is so diverse that it requires a systematic study of the theoretical principles underlying a particular method for a competent understanding of the capabilities of the method, practical application and interpretation of measurement results.
The measured characteristics of a substance in some cases are necessary to establish patterns that link the physical and chemical properties of a substance with the chemical structure of individual molecules, and in others - to optimize technological processes. In addition to determining the main characteristics and properties of molecules, some of the physical methods of research make it possible to study kinetic equilibria and the mechanisms of chemical reactions.
Along with the improvement of equipment and instruments used in research, important trend The modern use of physical methods is their complex use, especially in order to identify a substance and establish its chemical structure. The most widely used for these purposes are optical and resonant spectral methods (IR, UV, NMR (NMR) spectra) and mass spectroscopy. At present, data are required for a complete and reliable solution of the problem. more methods.
The curriculum of the section "Physical Methods of Research in Chemistry" of the course "Structure of Matter" includes lectures, seminars and laboratory classes. The present tutorial compiled to help students prepare for seminars. Due to the limited number of hours allocated by the plan for seminars, they consider only the methods of optical and resonance spectroscopy, as well as methods for measuring the dipole moment of molecules. It is these methods that are discussed in the manual. The manual outlines the theoretical foundations of each of the methods without cluttering with mathematical calculations and complex formulas, which is important for the first acquaintance of students with the subject, the areas of their application and possibilities are determined.
The manual consists of three sections containing 9 chapters, each of which is devoted to one method. Within the chapter, the theory on which the method is based, the scope of this method, its
advantages and disadvantages. The control questions following the theory are designed to test the student's understanding of the material being studied, the assignments are designed to try to apply the knowledge of each of the methods under consideration. For each method, the plan of the seminar is given.
In laboratory classes, students are engaged in deciphering the IR, PMR spectra of polyatomic molecules and mass spectrograms. The lecture course on the section "Physical Methods of Research in Chemistry" discusses all the most commonly used physical methods in chemistry at the present time, their modern technical base. Thus, this course covers an introduction to all currently used physical methods for the study of matter.
SECTION ONE. Electric dipole moment, its nature and measurement methods
CHAPTER 1. Theoretical foundations of the method
1.1. The nature of the dipole moment
IN In general, an electric dipole is understood as any system consisting of electric charges equal in magnitude and opposite in sign q i , located at a distance l i :
Radius - vector l i , directed from the center of gravity of the negative electronic charge to the center of gravity of the positive nuclear charge (Fig. 1.1). It follows from expression (1.1) that the dipole moment is a vector quantity. The different nature of the distribution of electron density in molecules divides them into two main classes - polar and non-polar. Polar molecules
ly have a dipole |
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moment, non-polar - |
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no. The concept of polarity |
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non-polarity) |
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Rice. 1.1. Centers of gravity of positive (OQ+) and negative |
be attributed |
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each of the chemical |
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(CQ - ) charges and the direction of the dipole moment in a diatomic |
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molecule. |
bonds forming mo- |
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T a b l e 1.1
The dependence of the polarity of the ABX molecule
on the geometric arrangement of atoms for the general case of a polar A-B connections
Molecule type |
Geometry |
The presence of a dipole |
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th moment |
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AB2 |
linear |
CO2 , CS2 |
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AB2 |
H2O, SO2 |
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AB3 |
BF3, SO3 |
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AB3 |
pyramidal |
NH3 , PF3 |
If there are several polar bonds in the molecule, when determining the dipole moment of the molecule, the dipole moments of these bonds are summed according to the law of summation of vectors, therefore, the dipole moment
the moment of the molecule is determined not only by the magnitude of the bond dipole moments, but also by their location in space relative to each other. That is, in similar molecules, the magnitude of the dipole moment characterizes the geometry of the molecules (Table 1.1).
The causes of the dipole moment of molecules are: 1) The shift of the center of gravity of the electron charges that form the chemical
chesky bond towards more electronegative bond atoms. In symmetrical diatomic molecules in the absence of an external electric
electronic |
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symmetrical about the nuclei. Next- |
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consequently, the center of gravity is positive |
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ny charges of nuclei and negative |
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Rice. 1.2. Emergence scheme |
charges of the binding electrons of each |
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homopolar dipole in the mol- |
of the bond atoms coincide and the dipole |
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moment is zero. |
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2) Appearance |
homopolar |
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Due to differences in the sizes of the atomic orbitals that form a chemical bond, the region of orbital overlap, i.e. the region of more probable location of binding electrons (negative charge) turns out to be shifted relative to the center of positive charges of the nuclei of atoms forming a chemical bond. This situation leads to the appearance of a homopolar chemical bond dipole (Fig. 1.2).
3) Asymmetry of a nonbonding electron pair. The appearance of a dipole due to the presence in the molecule of a non-
a dispersed pair of electrons conveniently |
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look at the example of NH3 molecules (a) and |
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NF3 (in) |
(fig.1.3). Comparison of electrical |
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denials of the atoms H (2.1), N (3.0), and |
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Rice. 1.3. Addition of vectors |
F (4.0) shows that despite |
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gape dipole moments with di- |
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dipole moments N-H bonds And |
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the full moment of the lone |
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N-F, dipole |
N-H bonds |
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total |
dipole |
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moment, the direction of which coincides with the direction of the dipole moment of the lone pair of nitrogen electrons. In the case of the NF3 molecule, the total bonding moment is directed against the dipole moment of the nitrogen lone pair. As a result, the dipole moment of ammonia is larger than the dipole moment of NF3.
All of the above concerns the dipole moment of a molecule outside an electric field.
1.2. Dipole in a static electric field. Molecule polarizability
In an external electric field, the charges that form a molecule (electrons are larger, nuclei are smaller) experience a displacement in different directions. As a result, in a constant electric field, the centers of gravity of positive and negative charges, even in nonpolar molecules, cease to coincide, and the molecule acquires a dipole moment under the action of the field, called the induced or induced dipole moment.
The property of a molecule to acquire a dipole moment under the action of an electric field is called polarizability. The value of the induced dipole moment of the molecule depends on the magnitude of the electric field strength and on the properties of the molecule itself
µ ≈ ε0 αE , (1.2) where ε0 is the permittivity of the vacuum, α is the polarizability of the
lecules, E is the strength of the external electric field.
Depending on the type of charge displacement, polarizability can be divided into the following components.
one). Electronic polarizability - αel. Occurs when the electron orbits are elastically displaced relative to the nuclei in the molecule. This type of polarizability is inertialess: αel disappears with the removal of the external electric field strength.
2). Nuclear polarizability - αnucleus. . Occurs when the nuclei in the molecule are displaced relative to each other. The nuclear polarizability is also practically inertial-free, but its magnitude is much less than the electronic one:
α poison.<< α эл.
Together, these two types of polarizability are referred to as bending polarizability:
α def.= α nuclear + α el.
Both types of polarizability are present in polar and nonpolar molecules; for nonpolar molecules, the total polarizability is equal to the deformation one.
In an external electric field in polar molecules, i.e. molecules having their own dipole moment, in addition to the deformation polarizability, an orientational dipole moment arises due to the tendency of the intrinsic dipole moment of the molecule to orient in the direction of the external electric field and, accordingly, the orientational polarizability αop. . Thus, the total polarizability of polar molecules is equal to:
Rice. 1.4. Electrostatic field induced by the field of a flat capacitor in a dielectric
α = αdef. + αop. = αnucleus. + αel. + αop. .
Since thermal motion destroys the orientation of the intrinsic dipole moments of molecules in a constant electric field, the orientational polarizability has inertia, i.e. aop. , as well as the total polarizability of polar molecules, when the external electric field strength is removed, it decreases with some delay.
1.3. Dielectric in a constant electric field. Dielectric polarization
Substances consisting of polar and non-polar molecules are mainly dielectrics. If a dielectric is placed in the electric field of a capacitor, polarization of the dielectric will occur, which will change the electric field strength of the capacitor. In a flat capacitor with the area of the plates A, the distance between them d and the charge density on the capacitor plate σ, the electric field strength is E.
On the surface of the dielectric located in the electric field of the capacitor, induced charges of density P arise, the dipole moment created by them is: µ = P × A × d, and the average dipole moment of a unit volume of the dielectric filling the entire space of the capacitor
torus is equal to:
µср = µ/V=(Р×А×d)/V=P, here V is the volume of the dielectric in the capacitor.
From the expression obtained, we can conclude that the dielectric polarization is the average dipole moment per unit volume of the dielectric.
Note that the strength of the electric field created by the induced charges on the surface of the capacitor is directed against the strength of the field of the condenser itself.
sator and reduces it (Fig. 1.4).
Since the polarization of a dielectric is the result of the addition of its own and induced dipole moments of its molecules, we can speak of the deformation and orientation components of the polarization of the entire dielectric if we relate the value of the induced dipole moment to a unit volume.
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Introduction
1. Experimental methods
1.1 X-ray electron spectroscopy
1.2 Infrared spectroscopy
1.3 Diffraction methods
2. Theoretical methods
2.1 Semi-empirical methods
2.2 Non-empirical methods
2.3 Quantum mechanical methods
2.4 Hückel method
Conclusion
List of sources used
INTRODUCTION
Various physical research methods are of great importance in modern organic chemistry. They can be divided into two groups. The first group includes methods that allow obtaining various information about the structure and physical properties of a substance without making any chemical changes in it. Of the methods of this group, perhaps the most widely used is spectroscopy in a wide range of spectral regions - from not too hard X-rays to radio waves of not very long wavelengths. The second group includes methods that use physical influences that cause chemical changes in molecules. In recent years, in addition to the previously used well-known physical means of influencing the reactivity of the molecule, new ones have been added. Among them, the effects of hard X-rays and high-energy particle flows produced in nuclear reactors are of particular importance.
The purpose of this course work is to learn about the methods of studying the structure of molecules.
The task of the course work:
Find out the types of methods and study them.
1. EXPERIMENTAL METHODS
1.1 Rx-ray electron spectroscopy
A method for studying the electronic structure of a chemical compound, the composition and structure of the surface of solids, based on the photoelectric effect using X-rays. When a substance is irradiated, an x-ray quantum hv is absorbed (h-Planck constant, v-radiation frequency), accompanied by the emission of an electron (called a photoelectron) from the inner or outer shells of the atom. The electron binding energy E St in the sample in accordance with the law of conservation of energy is determined by the equation: E St = hv-E kin, where E kin is the kinetic energy of the photoelectron. The values of E St of the electrons of the inner shells are specific for a given atom, so it is possible to unambiguously determine the composition of the chemical composition from them. connections. In addition, these quantities reflect the nature of the interaction of the atom under study with other atoms in the compound, i.e. depends on the nature of the chemical bond. The composition of the sample is determined by the intensity I of the photoelectron flux. The schematic diagram of the device for the RES-electronic spectrometer is shown in Figure 1. Samples are irradiated with X-rays from a Reitgen tube or synchrotron radiation. Photoelectrons enter the analyzer-device, in which electrons with a certain E kin are released from the general flow. To focus the monochromatic electron flow from the analyzer, it is directed to the detector, where its intensity I is determined. In the X-ray electron spectrum, different atoms have their own intensity maxima (Figure 2), although some maxima can merge, giving one band with increased intensity. Spectrum lines are designated as follows: next to the symbol of the element, the orbital under study is called (for example, the notation Cls means that photoelectrons are recorded from the 1s orbital of carbon).
Figure 1 - Scheme of the electronic spectrometer: 1-radiation source; 2-sample; 3- analyzer; 4-detector; 5-shield to protect against magnetic field
Figure 2 - X-ray spectrum of Cls ethyltrifluoroacetate
RES makes it possible to study all elements, except for H, when their content in the sample is ~ 10 -5 g (the limits of detection of an element using RES are 10 -7 -10 -9 g). The relative content of the element can be fractions of a percent. Samples may be solid, liquid or gaseous. The value E St of the electron of the inner shell of an atom A in chemical compounds depends on the effective charge q A on this atom and the electrostatic potential U created by all other atoms of the compound: E St = kq A + U, where k is the coefficient of proportionality.
For convenience, the RES introduces the concept of chemical shift E St, equal to the difference between E St in the compound under study and some standard. As a standard, the value of E St obtained for the crystalline modification of the element is usually used; for example, crystalline sulfur serves as the standard in the study of compound S. Since for a simple substance q A 0 and U = 0, then E St = kq A + U. Thus, the chemical shift indicates a positive effective charge on the studied atom A in a chemical compound, and a negative one indicates a negative charge, and the values of E St are proportional to effective charge on the atom. Since the change in the effective charge on the A atom depends on its oxidation state, the nature of the neighboring atoms, and the geometric structure of the compound, the nature of functional groups, the oxidation state of the atom, the method of coordination of ligands, etc. can be determined from Eb. The binding energies of electrons of functional atomic groups weakly depend on the type of chemical compound in which the given functional group is located.
1.2 ANDinfrared spectroscopy
A section of optical spectroscopy that studies the absorption and reflection spectra of electromagnetic radiation in the IR region, i.e. in the wavelength range from 10 -6 to 10 -3 m. In the coordinates of the intensity of the absorbed radiation - the wavelength (or wave number) IR spectrum is a complex curve with a large number of maxima and minima. Absorption bands appear as a result of transitions between the vibrational levels of the ground electronic state of the system under study. The spectral characteristics (positions of band maxima, their half-width, intensity) of an individual molecule depend on the masses of its constituent atoms, geometric structure, features of interatomic forces, charge distribution, etc. Therefore, IR spectra are highly individual, which determines their value in identifying and studying the structure connections. Spectra are recorded using classical spectrophotometers and Fourier spectrometers. The main parts of a classical spectrophotometer are a source of continuous thermal radiation, a monochromator, and a non-selective radiation detector. A cuvette with a substance (in any state of aggregation) is placed in front of the entrance (sometimes behind the exit) slit. Prisms made of various materials (LiF, NaCl, KCl, CsF, etc.) and a diffraction grating are used as the dispersing device of the monochromator. Sequential removal of radiation of different wavelengths to the exit slit and the radiation receiver (scanning) is carried out by turning the prism or grating. Radiation sources - rods heated by electric current from various materials. Receivers: sensitive thermocouples, metal and semiconductor thermal resistances (bolometers) and gas thermal converters, the heating of the vessel wall of which leads to heating of the gas and a change in its pressure, which is fixed. The output signal has the form of a conventional spectral curve. Advantages of devices of the classical scheme: simplicity of design, low cost. Disadvantages: the impossibility of registering weak signals due to the low signal-to-noise ratio, which greatly complicates work in the far IR region; relatively low resolution (up to 0.1 cm -1), long-term (within minutes) registration of spectra. Fourier spectrometers have no input and output slits, and the main element is an interferometer. The radiation flux from the source is divided into two beams that pass through the sample and interfere. The path difference of the beams is varied by a movable mirror reflecting one of the beams. The initial signal depends on the energy of the radiation source and on the absorption of the sample and has the form of the sum of a large number of harmonic components. To obtain the spectrum in the usual form, the corresponding Fourier transform is performed using a built-in computer. Advantages of the Fourier spectrometer: high signal-to-noise ratio, the ability to operate in a wide range of wavelengths without changing the dispersive element, fast (in seconds and fractions of seconds) registration of the spectrum, high resolution (up to 0.001 cm -1). Disadvantages: manufacturing complexity and high cost. All spectrophotometers are equipped with a computer that performs the primary processing of the spectra: accumulation of signals, their separation from noise, subtraction of the background and comparison spectrum (solvent spectrum), change of the recording scale, calculation of experimental spectral parameters, comparison of spectra with given ones, differentiation of spectra, etc. Cuvettes for IR spectrophotometers are made from materials that are transparent in the IR region. CCl 4 , CHCl 3 , tetrachlorethylene, vaseline oil are usually used as solvents. Solid samples are often crushed, mixed with KBr powder, and compressed into tablets. To work with aggressive liquids and gases, specially protective coatings (Ge, Si) are used on the cuvette windows. The interfering influence of air is eliminated by evacuating the device or purging it with nitrogen. In the case of weakly absorbing substances (rarefied gases, etc.), multipass cells are used, in which the length of the optical paths reaches hundreds of meters due to multiple reflections from a system of parallel mirrors. The matrix isolation method, in which the test gas is mixed with argon, and then the mixture is frozen, has become widely used. As a result, the half-width of the absorption bands sharply decreases and the spectrum becomes more contrasting. The use of a special microscopic technique makes it possible to work with objects of very small sizes (fractions of a mm). To register the spectra of the surface of solids, the method of frustrated total internal reflection is used. It is based on the absorption by the surface layer of a substance of the energy of electromagnetic radiation emerging from a total internal reflection prism, which is in optical contact with the surface under study. Infrared spectroscopy is widely used for the analysis of mixtures and the identification of pure substances. Quantitative analysis is based on the Bouguer-Lambert-Beer law, i.e., on the dependence of the intensity of absorption bands on the concentration of a substance in a sample. In this case, the number of substances is judged not by the separated absorption bands, but by the spectral curves as a whole in a wide range of wavelengths. If the number of components is small (4-5), then it is possible to mathematically extract their spectra even with a significant overlap of the latter. The error of quantitative analysis, as a rule, is a fraction of a percent. The identification of pure substances is usually carried out with the help of information retrieval systems by automatically comparing the analyzed spectrum with the spectra stored in the computer memory. Artificial intelligence systems are used to identify new substances (the molecules of which can contain up to 100 atoms). In these systems, based on spectral structural correlations, molar structures are generated, then their theoretical spectra are constructed, which are compared with experimental data. The study of the structure of molecules and other objects by means of infrared spectroscopy involves obtaining information about the parameters of models and mathematically reduces to solving the so-called. inverse spectral problems. The solution of such problems is carried out by successive approximation of the desired parameters, calculated using special. theory of spectral curves to experimental ones. Parameters say. models are the masses of the atoms that make up the system, bond lengths, bond and torsion angles, potential surface characteristics (force constants, etc.), dipole moments of bonds and their derivatives with respect to bond lengths, etc. Infrared spectroscopy makes it possible to identify spatial and conformational isomers, to study intra- and intermolecular interactions, the nature of chemical bonds, the distribution of charges in molecules, phase transformations, the kinetics of chemical reactions, register short-lived (lifetime up to 10 -6 s) particles, refine individual geomes. parameters, obtain data for calculating thermodynamic functions, etc. A necessary stage of such studies is the interpretation of spectra, i.e. determination of the form of normal vibrations, distribution of vibrational energy over degrees of freedom, selection of significant parameters that determine the position of the bands in the spectra and their intensity. Calculations of the spectra of molecules containing up to 100 atoms, incl. polymers are carried out with the help of a computer. In this case, it is necessary to know the characteristics of the mol. models (force constants, electro-optical parameters, etc.), which are found by solving the corresponding inverse spectral problems or by quantum chemical calculations. In both cases, it is usually possible to obtain data for molecules containing atoms of only the first four periods of the periodic system. Therefore, infrared spectroscopy as a method for studying the structure of molecules has become most widespread in organic and organoelement chemistry. In some cases, for gases in the IR region, it is possible to observe the rotational structure of vibrational bands. This makes it possible to calculate dipole moments and geom. parameters of molecules, specify force constants, etc.
1.3 Diffraction methods
Diffraction methods for studying the structure of a substance are based on the study of the angular distribution of the intensity of scattering by the substance under study of X-ray (including synchrotron) radiation, electron or neutron flux. Distinguish X-ray, electron diffraction, neutron diffraction. In all cases, the primary, most often monochromatic, beam is directed to the object under study and the scattering pattern is analyzed. Scattered radiation is registered photographically or with the help of counters. Since the radiation wavelength is usually no more than 0.2 nm, i.e., commensurate with the distances between atoms in a substance (0.1-0.4 nm), the scattering of the incident wave is diffraction by atoms. From the diffraction pattern, one can in principle reconstruct the atomic structure of a substance. The theory describing the connection between the pattern of elastic scattering and the spaces, the location of the scattering centers, is the same for all radiations. However, since the interaction of various kinds of radiation with matter has a different physical. nature, specific form and features of diffraction. the patterns are determined by the different characteristics of the atoms. Therefore, various diffraction methods provide information that complements each other.
Fundamentals of the theory of diffraction . Flat monochromatic. a wave with a wavelength and a wave vector, where it can be considered as a beam of particles with a momentum, where The amplitude of the wave scattered by a collection of atoms is determined by the equation:
The same formula is used to calculate the atomic factor, which describes the distribution of the scattering density inside the atom. The values of the atomic factor are specific for each type of radiation. X-rays are scattered by the electron shells of atoms. The corresponding atomic factor is numerically equal to the number of electrons in an atom, if expressed in the name of electronic units, that is, in relative units of the X-ray scattering amplitude by one free electron. The scattering of electrons is determined by the electrostatic potential of the atom. The atomic factor for an electron is related by:
research molecule spectroscopy diffraction quantum
Figure 2 - Dependence of the absolute values of the atomic factors of X-rays (1), electrons (2) and neutrons (3) on the scattering angle
Figure 3- Relative dependence of the angle-averaged atomic factors of X-rays (solid line), electrons (dashed line) and neutrons on the atomic number Z
Accurate calculations consider deviations of the distribution of the electron density or the potential of atoms from spherical symmetry and the name atomic temperature factor, which takes into account the effect of thermal vibrations of atoms on scattering. For radiation, in addition to scattering on the electron shells of atoms, there is a role that resonance scattering on nuclei can play. The scattering factor f m depends on the wave vectors and polarization vectors of the incident and scattered waves. The intensity I(s) of scattering by an object is proportional to the square of the amplitude modulus: I(s)~|F(s)| 2. Experimentally, only |F(s)| moduli can be determined, and to construct the scattering density function (r), it is also necessary to know the phases (s) for each s. Nevertheless, the theory of diffraction methods makes it possible to obtain the function (r) from the measured I(s), i.e., to determine the structure of substances. In this case, the best results are obtained in the study of crystals. Structural analysis . A single crystal is a strictly ordered system; therefore, during diffraction, only discrete scattered beams are formed, for which the scattering vector is equal to the reciprocal lattice vector.
To construct the function (x, y, z) from experimentally determined quantities, the trial and error method, the construction and analysis of the function of interatomic distances, the method of isomorphic substitutions, and direct methods for determining phases are used. The processing of experimental data on a computer makes it possible to reconstruct the structure in the form of scattering density distribution maps. Crystal structures are studied using X-ray structural analysis. More than 100 thousand crystal structures have been determined by this method.
For inorganic crystals, using various refinement methods (taking into account corrections for absorption, anisotropy of the atomic temperature factor, etc.), it is possible to restore the function with a resolution of up to 0.05
Figure 4 - Projection of the nuclear density of the crystal structure
This makes it possible to determine the anisotherapy of thermal vibrations of atoms, the features of the distribution of electrons due to chemical bonds, etc. With the help of X-ray diffraction analysis, it is possible to decipher the atomic structures of protein crystals, the molecules of which contain thousands of atoms. X-ray diffraction is also used to study defects in crystals (in X-ray topography), to study near-surface layers (in X-ray spectrometry), and to qualitatively and quantitatively determine the phase composition of polycrystalline materials. Electron diffraction as a method for studying the structure of crystals has a trace. features: 1) the interaction of matter with electrons is much stronger than with x-rays, so diffraction occurs in thin layers of matter with a thickness of 1-100 nm; 2) f e depends on the atomic nucleus weaker than f p, which makes it easier to determine the position of light atoms in the presence of heavy ones; Structural electron diffraction is widely used to study finely dispersed objects, as well as to study various kinds of textures (clay minerals, semiconductor films, etc.). Low-energy electron diffraction (10-300 eV, 0.1-0.4 nm) is an effective method for studying crystal surfaces: the arrangement of atoms, the nature of their thermal vibrations, etc. Electron microscopy restores the image of an object using a diffraction pattern and allows studying the structure of crystals with a resolution of 0.2 -0.5 nm. The sources of neutrons for structural analysis are fast neutron nuclear reactors, as well as pulsed reactors. The spectrum of the neutron beam leaving the reactor channel is continuous due to the Maxwellian velocity distribution of neutrons (its maximum at 100°C corresponds to a wavelength of 0.13 nm).
Beam monochromatization is carried out in different ways - with the help of monochromator crystals, etc. Neutron diffraction is used, as a rule, to refine and supplement X-ray data. The absence of a monotonic dependence of f and on the atomic number makes it possible to fairly accurately determine the position of light atoms. In addition, isotopes of the same element in the same element can have very different values of f and (for example, f and hydrocarbon 3.74.10 13 cm, deuterium 6.67.10 13 cm). This makes it possible to study the location of isotopes and get additional information. information about the structure by isotopic substitution. Research of magnetic interaction. neutrons with magnetic moments of atoms gives information about the spins of magnetic atoms. Mössbauer radiation is characterized by an extremely small line width - 10 8 eV (whereas the line width of the characteristic radiation of X-ray tubes is 1 eV). This causes a high temporal and space. consistency of resonant nuclear scattering, which makes it possible, in particular, to study the magnetic field and the electric field gradient on nuclei. The limitations of the method are the low power of Mössbauer sources and the obligatory presence in the crystal under study of nuclei for which the Mössbauer effect is observed. Structural analysis of non-crystalline substances. Individual molecules in gases, liquids, and amorphous solids are differently oriented in space; therefore, it is usually impossible to determine the phases of scattered waves. In these cases, the scattering intensity is usually represented using the so-called. interatomic vectors r jk , which connect pairs of different atoms (j and k) in molecules: r jk = r j - r k . The scattering pattern is averaged over all orientations:
2 THEORETICAL METHODS
2.1 Semi-empirical methods
Semi-empirical methods of quantum chemistry, methods for calculating mol. characteristics or properties of a substance with the involvement of experimental data. In essence, semi-empirical methods are similar to non-empirical methods for solving the Schrödinger equation for polyatomic systems, however, to facilitate calculations in semi-empirical methods, additional ones are introduced. simplification. As a rule, these simplifications are associated with the valence approximation, i.e., they are based on the description of only valence electrons, as well as with the neglect of certain classes of molecular integrals in the exact equations of the non-empirical method in which the semi-empirical calculation is carried out.
The choice of empirical parameters is based on a generalization of the experience of non-empirical calculations, taking into account chemical ideas about the structure of molecules and phenomenological regularities. In particular, these parameters are necessary for approximating the effect of internal electrons on valence electrons, for setting the effective potentials created by core electrons, and so on. The use of experimental data for the calibration of empirical parameters makes it possible to eliminate the errors caused by the simplifications mentioned above, but only for those classes of molecules whose representatives serve as reference molecules, and only for those properties from which the parameters were determined.
The most common semi-empirical methods based on ideas about the pier. orbitals (see Molecular orbital methods, Orbital). In combination with the LCAO approximation, this makes it possible to express the Hamiltonian of a molecule in terms of integrals on atomic orbitals. When constructing semi-empirical methods in the mol. integrals distinguish products of orbitals depending on the coordinates of the same electron (differential overlap), and neglect some classes of integrals. For example, if all integrals containing differential overlap cacb at a are considered zero. b, it turns out the so-called. method of complete neglect of the differential. overlap (PPDP, in English transcription CNDO-complete neglect of differential overlap). They also use partial or modified partial neglect of differential overlap (respectively, CHPD or MCHPD, in the English transcription INDO-intermediate neglect of differential overlap and MINDO-modified INDO), neglect of diatomic differential overlap - PDDP, or neglect of diatomic differential overlap (NDDO), - modified neglect of diatomic overlap (MTDO, or modified neglect of diatomic overlap, MNDO). As a rule, each of the semi-empirical methods has several variants, which are usually indicated in the name of the method by a number or a letter after the slash. For example, the PPDP/2, MCHPDP/3, MPDP/2 methods are parameterized for calculating the equilibrium configuration of molecular nuclei in the ground electronic state, charge distribution, ionization potentials, enthalpies of formation of chemical compounds, the PDDP method is used to calculate spin densities. To calculate the energies of electronic excitation, spectroscopic parametrization (the PPDP/S method) is used. It is also common to use the corresponding computer programs in the names of semi-empirical methods. For example, one of the extended variants of the TMAP method is called the Austin model, as is the corresponding program (Austin model, AM). There are several hundred different variants of semi-empirical methods, in particular, semi-empirical methods similar to the configuration interaction method have been developed. With external similarity of different variants of semi-empirical methods, each of them can be used to calculate only those properties for which the empirical parameters were calibrated. In naib. simple semi-empirical calculations each pier. an orbital for valence electrons is defined as a solution to the one-electron Schrödinger equation with a Hamilton operator containing a model potential (pseudopotential) for an electron located in the field of nuclei and the averaged field of all other electrons in the system. Such a potential is set directly with the help of elementary functions or integral operators based on them. In combination with the LCAO approximation, this approach allows for many conjugated and aromatic mole. systems are limited to the analysis of p-electrons (see the Hückel method), for coordination compounds, use the calculation methods of the ligand field theory and the crystal field theory, etc. When studying macromolecules, for example. proteins, or crystalline formations, semi-empirical methods are often used, in which the electronic structure is not analyzed, but the potential energy surface is determined directly. The energy of the system is approximately considered the sum of the pair potentials of the interaction of atoms, for example. Morse (Morse) or Lennard-Jones potentials (see Intermolecular interactions). Such semi-empirical methods make it possible to calculate the equilibrium geometry, conformational effects, isomerization energy, etc. Often, pair potentials are supplemented with multiparticle corrections determined for individual fragments of the molecule. Semi-empirical methods of this type are usually referred to as molecular mechanics. In a broader sense, semi-empirical methods include any methods in which the parameters of the pier determined by the solution of inverse problems. systems are used for predictions of new experimental data, construction of correlation relationships. In this sense, semi-empirical methods are methods for estimating reactivity, effective charges on atoms, etc. The combination of a semi-empirical calculation of the electronic structure with a correlation. ratios allows you to evaluate the biological activity of various substances, the speed of chemical reactions, the parameters of technological processes. Semi-empirical methods also include some additive schemes, for example. methods used in chemical thermodynamics for estimating the energy of formation as the sum of the contributions of individual fragments of a molecule. The intensive development of semi-empirical methods and non-empirical methods of quantum chemistry makes them important means of modern research into the mechanisms of chem. transformations, the dynamics of the elementary act of chem. reactions, modeling of biochemical and technological processes. When used correctly (taking into account the principles of construction and methods for calibrating parameters), semi-empirical methods provide reliable information about the structure and properties of molecules, their transformations.
2.2Non-empirical methods
A fundamentally different direction of computational quantum chemistry, which has played a huge role in the modern development of chemistry as a whole, consists in the complete or partial rejection of the calculation of one-electron (3.18) and two-electron (3.19)-(3.20) integrals that appear in the HF method. Instead of the exact Fock operator, an approximate one is used, the elements of which are obtained empirically. The parameters of the Fock operator are selected for each atom (sometimes taking into account a specific environment) or for pairs of atoms: they are either fixed or depend on the distance between atoms. In this case, it is often (but not necessarily - see below) that the many-electron wave function is assumed to be one-determinant, the basis is minimal, and the atomic orbitals X; - symmetric orthogonal combinations of OST Xr Such combinations can be easily obtained by approximating the original AO by the Slater functions "Xj(2.41) with the help of transformation Semi-empirical methods work much faster than non-empirical ones. They are applicable to large (often very large, for example, biological) systems and give more accurate results for some classes of compounds. However, it should be understood that this is achieved through specially selected parameters that are valid only within a narrow class of compounds. When transferred to other compounds, the same methods can give completely wrong results. In addition, the parameters are often chosen in such a way as to reproduce only certain molecular properties; therefore, one should not attach a physical meaning to the individual parameters used in the calculation scheme. Let us list the main approximations used in semi-empirical methods.
1. Only valence electrons are considered. It is believed that the electrons belonging to the atomic cores only screen the nuclei. Therefore, the influence of these electrons is taken into account by considering the interaction of valence electrons with atomic cores, and not with nuclei, and introducing the core repulsion energy instead of the internuclear repulsion energy. The core polarization is neglected.
2. MO takes into account only AO with the principal quantum number corresponding to the highest electron-populated orbitals of isolated atoms (minimum basis). It is assumed that the basis functions form a set of orthonormal atomic orbitals - OST, orthogonalized according to Löwdin.
3. For two-electron Coulomb and exchange integrals, the approximation of zero differential overlap (NDO) is introduced.
A molecular structure within a structural region can correspond to a set of modifications of a molecule that retain the same system of valence chemical bonds with different spatial organization of the nuclei. In this case, the deep minimum of the PES additionally has several shallow (equivalent or nonequivalent in energy) minima separated by small potential barriers. Various spatial forms of a molecule that transform into each other within a given structural region by continuously changing the coordinates of atoms and functional groups without breaking or forming chemical bonds make up the set of conformations of a molecule. A set of conformations whose energies are less than the lowest barrier adjacent to a given PES structural region is called a conformational isomer or conformer. Conformers corresponding to local PES minima are called stable or stable. Thus, the molecular structure can be defined as a set of conformations of a molecule in a certain structural region. A type of conformational transition that is often encountered in molecules is the rotation of individual groups of atoms about bonds: they say that there is an internal rotation, and various conformers are called rotational isomers, or rotamers. During rotation, the electronic energy also changes, and its value in the process of such movement can pass through a maximum; in this case one speaks of an internal rotation barrier. The latter are largely due to the ability of these molecules to easily adapt the structure when interacting with different systems. Each PES energy minimum corresponds to a pair of enantiomers with the same energy - right (R) and left (S). These pairs have energies differing by only 3.8 kcal/mol, but they are separated by a 25.9 kcal/mol high barrier and, therefore, are very stable in the absence of external influences. Results of quantum-chemical calculations of the energies of the internal rotation barriers for some molecules and the corresponding experimental values. The theoretical and experimental values of the rotational barriers for the C-C, C-P, C-S bonds differ by only 0.1 kcal/mol; for C-0, C-N, C-Si bonds, despite the use of the basis set with the inclusion of polarization functions (see below), the difference is noticeably higher. Nevertheless, one can state a satisfactory accuracy in the calculation of the energies of the barriers to internal rotation by the HF method.
Such calculations of the energies of the barriers of internal rotation for simple molecules, in addition to spectroscopic applications, are important as a criterion for the quality of one or another calculation method. Great attention deserves internal rotation in complex molecular systems, for example, in polypeptides and proteins, where this effect determines many of the biologically important functions of these compounds. The calculation of potential energy surfaces for such objects is a difficult task both in theoretical and practical terms. A common type of conformational transition is inversion, such as occurs in pyramidal molecules of the AX3 type (A = N, Si, P, As, Sb; X = H, Li, F, etc.). In these molecules, atom A can occupy positions both above and below the plane formed by three X atoms. For example, in the ammonia molecule NH3, the HF method gives an energy barrier value of 23.4 kcal/mol; this is in good agreement with the experimental value of the inversion barrier - 24.3 kcal/mol. If the barriers between the PES minima are comparable to the thermal energy of the molecule, this leads to the effect of structural non-rigidity of the molecule; conformational transitions in such molecules occur constantly. The self-consistent field method is used to solve the HF equations. In the process of solution, only the orbitals occupied by electrons are optimized, therefore, the energies of only these orbitals are found physically justified. However, the method. HF also gives the characteristics of free orbitals: such molecular spin orbitals are called virtual. Unfortunately, they describe the excited energy levels of a molecule with an error of about 100%, and they should be used to interpret spectroscopic data with caution - there are other methods for this. As for atoms, the HF method for molecules has different versions, depending on whether the one-determinant wave function is an eigenfunction of the squared total spin operator of the S2 system or not. If the wave function is built from space orbitals occupied by a pair of electrons with opposite spins (molecules with closed shells), this condition is met, and the method is called the restricted Hartree-Fock (OHF) method. If the requirement to be an eigenfunction of the operator is not imposed on the wave function, then each molecular spin orbital corresponds to a certain spin state (a or 13), that is, electrons with opposite spins occupy different spin orbitals. This method is usually applied to molecules with open shells and is called the unrestricted HF method (NHF), or the method of different orbitals for different spins. Sometimes low-lying energy states are described by orbitals doubly occupied by electrons, and valence states are described by singly occupied molecular spin orbitals; this method is called the restricted Hartree-Fock method for open shells (OHF-00). As in atoms, the wave function of molecules with open shells does not correspond to a pure spin state, and solutions can arise in which the symmetry of the wave function with respect to spin is lowered. They are called NHF-unstable solutions.
2.3 Quantum mechanical methods
The advances in theoretical chemistry and the development of quantum mechanics created the possibility of approximate quantitative calculations of molecules. Two important calculation methods are known: the electron pair method, also called the valence bond method, and the molecular orbit method. The first of these methods, developed by Heitler and London for the hydrogen molecule, became widespread in the 1930s. In recent years, the method of molecular orbits has become increasingly important (Hund, E. Hückel, Mulliken, Hertzberg, Lenard-Jones).
In this approximate calculation method, the state of a molecule is described by the so-called wave function w, which is composed according to a certain rule from a series of terms:
The sum of these terms should take into account all possible combinations resulting from the pairwise bonding of carbon atoms by p-electrons.
In order to facilitate the calculation of the wave function w, the individual terms (C1w1, C2w2, etc.) are conventionally depicted graphically in the form of the corresponding valence schemes, which are used as auxiliary means in the mathematical calculation. For example, when a benzene molecule is calculated in this way and only p-electrons are taken into account, then there are five such terms. These terms correspond to the following valence schemes:
Often the given valence schemes are depicted taking into account y-bonds, for example, for benzene
Such valence schemes are called "unperturbed structures" or "limit structures"
The functions w1, w2, w3, etc. of various limiting structures enter the wave function w with the greater the coefficients (with the greater the weight), the lower the energy calculated for the corresponding structure. The electronic state corresponding to the wave function w is the most stable in comparison with the electronic states represented by the functions w1, w2, w3, etc.; the energy of the state represented by the function w (of a real molecule) is naturally the smallest in comparison with the energies of the limiting structures.
When calculating the benzene molecule using the electron pair method, five limiting structures (I-V) are taken into account. Two of them are identical to the classical Kekule structural formula and three to the Dewar formula. Since the energy of the electronic states corresponding to the limiting structures III, IV, and V is higher than for structures I and II, the contribution of structures III, IV, and V to the mixed wave function of the benzene molecule is smaller than the contribution of structures I and II. Therefore, in the first approximation, two equivalent Kekule structures are sufficient to depict the electron density distribution in a benzene molecule.
About thirty years ago, L. Pauling developed qualitative empirical ideas that have some analogies with the electron pair method; these ideas were called by him the theory of resonance. According to the main postulate of this theory, any molecule for which several classical structural formulas can be written cannot be correctly represented by any of these individual formulas (limit structures), but only by a set of them. A qualitative picture of the electron density distribution in a real molecule is described by a superposition of limiting structures (each of which is represented with a certain weight).
Limiting structures do not correspond to any real electronic states in unexcited molecules, but it is possible that they can occur in an excited state or at the moment of a reaction.
The above qualitative side of the theory of resonance coincides with the concept of mesomerism, developed somewhat earlier by Ingold and independently by Arndt.
According to this concept, the true state of a molecule is intermediate ("mesomeric") between the states depicted by two or more "limit structures" that can be written for a given molecule using the valence rules.
In addition to this basic position of the theory of mesomerism, its apparatus includes well-developed ideas about electronic displacements, in the substantiation, interpretation and experimental verification of which Ingold plays an important role. According to Ingold, the mechanisms of electronic displacements (electronic effects) are different depending on whether the mutual influence of atoms is carried out through a chain of single or conjugated double bonds. In the first case, this is the induction effect I (or also the static induction effect Is), in the second case, the mesomeric effect M (static conjugation effect).
In a reacting molecule, the electron cloud can be polarized according to the inductive mechanism; such an electronic displacement is called the inductomeric effect Id. In molecules with conjugated double bonds (and in aromatic molecules), the polarizability of the electron cloud at the time of the reaction is due to the electromeric effect E (dynamic conjugation effect).
The theory of resonance raises no fundamental objections as long as we are talking about ways of depicting molecules, but it also has big claims. Just as in the electron vapor method, the wave function is described by a linear combination of other wave functions w1, w2, w3, etc., the resonance theory proposes to describe the true wave function of the wmolecule as a linear combination of the wave functions of the limiting structures.
However, mathematics does not provide criteria for choosing one or another "resonant structure": after all, in the method of electron pairs, the wave function can be represented not only as a linear combination of wave functions w1, w2, w3, etc., but also as a linear combination of any other functions selected with certain coefficients. The choice of limiting structures can only be made on the basis of chemical considerations and analogies, i.e. here the concept of resonance essentially does not give anything new in comparison with the concept of mesomerism.
When describing the distribution of electron density in molecules with the help of limiting structures, one must always keep in mind that individual limiting structures do not correspond to any real physical state and that there is no physical phenomenon of "electronic resonance".
Numerous cases are known from the literature when supporters of the concept of resonance ascribed to resonance the meaning of a physical phenomenon and believed that certain individual limiting structures are responsible for certain properties of substances. The possibility of such erroneous ideas is inherent in many points of the concept of resonance. Thus, when one speaks of "various contributions of the limiting structures" to the real state of the molecule, the idea of the real existence of these relations can easily arise. The real molecule in the concept of resonance is considered a "resonant hybrid"; this term may suggest a supposedly real interaction of limiting structures, similar to the hybridization of atomic orbits.
The term “stabilization due to resonance” is also unsuccessful, since the stabilization of a molecule cannot be due to a nonexistent resonance, but is a physical phenomenon of electron density delocalization, which is characteristic of conjugated systems. It is therefore appropriate to call this phenomenon stabilization due to conjugation. The conjugation energy (delocalization energy, or mesomerism energy) can be determined experimentally, independently of the "resonance energy" resulting from quantum mechanical calculations. This is the difference between the energy calculated for a hypothetical molecule with a formula corresponding to one of the limiting structures, and the energy found experimentally for a real molecule.
With the above reservations, the method of describing the distribution of electron density in molecules with the help of several limiting structures can undoubtedly be used along with two other methods that are also very common.
2.4 Hückel method
Hückel method, quantum-chemical method of approximate calculation of energy levels and mol. orbitals of unsaturated org. connections. It is based on the assumption that the motion of an electron near an atomic nucleus in a molecule does not depend on the states or number of other electrons. This allows you to simplify the task of determining the pier. orbitals (MO) in the representation of a linear combination of atomic orbitals. The method was proposed by E. Hückel in 1931 for calculating the electronic structure of hydrocarbons with conjugated bonds. It is believed that the carbon atoms of the conjugated system lie in the same plane, with respect to which the highest occupied and lowest virtual (free) MO (boundary mol. orbitals) are antisymmetric, i.e., they are orbitals formed by atomic 2pz-orbitals (AO) of the corresponding C atoms. The influence of other atoms, for example. N, or they say. fragments with saturated bonds are neglected. It is assumed that each of the M carbon atoms of the conjugated system contributes one electron to the system and is described by one atomic 2pz-orbital (k = 1, 2, ..., M). A simple model of the electronic structure of a molecule, given by the Hückel method, makes it possible to understand many chem. phenomena. For example, the non-polarity of alternative hydrocarbons is due to the fact that the effective charges on all carbon atoms are zero. On the contrary, the non-alternant condensed system of 5- and 7-membered cycles (azulene) has a dipole moment of approx. 1D (3.3 x 10 -30 C x m). In odd alternant hydrocarbons, the main energy. the state corresponds to an electronic system in which there is at least one singly occupied orbital. It can be shown that the energy of this orbital is the same as in a free atom, in connection with which it is called. nonbonding MO. The removal or addition of an electron changes the population of only a nonbonding orbital, which leads to the appearance of a charge on some atoms, which is proportional to the square of the corresponding coefficient in the expansion of a nonbonding MO in terms of AO. To determine such an MO, a simple rule is applied: the sum of the coefficient Ck for all atoms adjacent to any given data must be equal to zero. In addition, the values of the coefficient must correspond to the additional. normalization condition: This leads to a characteristic alternation (alternation) of charges on atoms in a mol. ions of alternative hydrocarbons. In particular, this rule explains the selection by chem. properties of the ortho and para positions in the benzene ring compared to the meta position. The patterns established within the framework of the simple Hückel method are distorted when all interactions in the molecule are taken into account more fully. However, usually the influence of many heterogeneous complementary factors (for example, core electrons, substituents, interelectron repulsion, etc.) does not qualitatively change the orbital pattern of the electron distribution. Therefore, the Hückel method is often used to model complex reaction mechanisms involving org. connections. When heteroatoms (N, O, S, ...) are introduced into the molecule, the parameters of the H matrix, taken for the heteroatom and for carbon atoms, become significant. In contrast to the case of polyenes, different types of atoms or bonds are described by different parameters or and their ratio significantly affects the type of MO; the quality of predictions obtained within the framework of the simple Hückel method, as a rule, deteriorates as a result. Simple in its idea, clear and not requiring complex Hückel calculations, the method is one of the most common means of creating a quantum chemical model of the electronic structure of complex mol. systems. Naib. its application is effective in those cases when the properties of the molecule are determined in the main topological structure of the chemical. bonds, in particular, the symmetry of the molecule. Attempts to build improved versions of the Hückel method within the framework of simple molecular orbital methods make little sense, since they lead to calculation methods comparable in complexity to the more accurate methods of quantum chemistry.
Conclusion
At present, “a whole branch of science has been created - quantum chemistry, which deals with the application of quantum mechanical methods to chemical problems. However, it would be fundamentally wrong to think that all questions of the structure and reactivity of organic compounds can be reduced to the problems of quantum mechanics. Quantum mechanics studies the laws of motion of electrons and nuclei, i.e., the laws of a lower form of motion compared to that studied by chemistry (the motion of atoms and molecules), and a higher form of motion can never be reduced to a lower one. Even for very simple molecules, questions such as the reactivity of substances, the mechanism and kinetics of their transformations cannot be studied only by the methods of quantum mechanics. The basis for the study of the chemical form of the motion of matter is chemical research methods, and the leading role in the development of chemistry belongs to the theory of chemical structure.
Listsources used
1. Minkin, V.I. Theory of the structure of molecules / V.I. Minkin. -M.: Higher school, 2006 - 640s.
2. Vilkov, L.V. Physical research methods in chemistry./ L.V. Vilkov, Yu.A. Pentin. - M.: Higher school, 2005-380s.
3. Gardymova, A.P. Scientific electronic library: elements and devices of computer technology and control systems / A.P. Gardymov. - 2005.
4. Elyashevich, M.A. Atomic and molecular spectroscopy / M.A. Elyashevich, V. Demtreder. -M.: Mir, 1989-260s.
5. Blatov, V.A. Semi-empirical calculation methods / V.A. Blatov, A.P. Shevchenko. - M .: "Univers-group" 2005-315s.
6. Tsirelson, V.G. Quantum chemistry, molecules, molecular systems and solids - M .: "BINOM" 2010-496s.
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