Bioorganic chemistry (BOC), its importance in medicine. Subject of bioorganic chemistry. classification, structure, reactivity of organic compounds James Dewey Watson Gerard, Gerhardt Charles Frederic. Depending on the electronic nature of the reagents
Bioorganic chemistry is a fundamental science that studies the structure and biological functions of the most important components of living matter, primarily biopolymers and low-molecular bioregulators, focusing on elucidating the patterns of the relationship between the structure of compounds and their biological effects.
Bioorganic chemistry is a science at the intersection of chemistry and biology; it helps to reveal the principles of functioning of living systems. Bioorganic chemistry has a pronounced practical orientation, being the theoretical basis for obtaining new valuable compounds for medicine, agriculture, chemical, food and microbiological industries. The range of interests of bioorganic chemistry is unusually wide - this includes the world of substances isolated from living nature and playing an important role in life, and the world of artificially produced organic compounds that have biological activity. Bioorganic chemistry covers the chemistry of all substances of a living cell, tens and hundreds of thousands of compounds.
Objects of study, research methods and main tasks of bioorganic chemistry
Objects of study bioorganic chemistry are proteins and peptides, carbohydrates, lipids, mixed biopolymers - glycoproteins, nucleoproteins, lipoproteins, glycolipids, etc., alkaloids, terpenoids, vitamins, antibiotics, hormones, prostaglandins, pheromones, toxins, as well as synthetic regulators of biological processes : medicines, pesticides, etc.
The main arsenal of research methods bioorganic chemistry consists of methods; Physical, physico-chemical, mathematical and biological methods are used to solve structural problems.
Main tasks bioorganic chemistry are:
- Isolation in an individual state and purification of the studied compounds using crystallization, distillation, various types chromatography, electrophoresis, ultrafiltration, ultracentrifugation, etc. In this case, specific biological functions of the substance being studied are often used (for example, the purity of an antibiotic is monitored by its antimicrobial activity, of a hormone by its effect on a certain physiological process, etc.);
- Establishment of structure, including spatial structure, based on organic chemistry approaches (hydrolysis, oxidative cleavage, cleavage into specific fragments, for example, at methionine residues when establishing the structure of peptides and proteins, cleavage at 1,2-diol groups of carbohydrates, etc.) and physics -chemical chemistry using mass spectrometry, various types of optical spectroscopy (IR, UV, laser, etc.), X-ray diffraction analysis, nuclear magnetic resonance, electron paramagnetic resonance, optical rotation dispersion and circular dichroism, fast kinetics methods, etc. in combination with computer calculations. To quickly solve standard problems associated with establishing the structure of a number of biopolymers, automatic devices have been created and are widely used, the operating principle of which is based on standard reactions and properties of natural and biologically active compounds. These are analyzers for determining the quantitative amino acid composition of peptides, sequencers for confirming or establishing the sequence of amino acid residues in peptides and the nucleotide sequence in nucleic acids, etc. The use of enzymes that specifically cleave the studied compounds along strictly defined bonds is important when studying the structure of complex biopolymers. Such enzymes are used in studying the structure of proteins (trypsin, proteinases that cleave peptide bonds at glutamic acid, proline and other amino acid residues), nucleic acids and polynucleotides (nucleases, restriction enzymes), carbohydrate-containing polymers (glycosidases, including specific ones - galactosidases , glucuronidases, etc.). To increase the effectiveness of research, not only natural compounds are analyzed, but also their derivatives containing characteristic, specially introduced groups and labeled atoms. Such derivatives are obtained, for example, by growing the producer on a medium containing labeled amino acids or other radioactive precursors, which include tritium, radioactive carbon or phosphorus. The reliability of the data obtained from the study of complex proteins increases significantly if this study is carried out in conjunction with a study of the structure of the corresponding genes.
- Chemical synthesis and chemical modification of the studied compounds, including total synthesis, synthesis of analogues and derivatives. For low molecular weight compounds, counter synthesis is still an important criterion for the correctness of the established structure. The development of methods for the synthesis of natural and biologically active compounds is necessary to solve the next important problem of bioorganic chemistry - elucidating the relationship between their structure and biological function.
- Clarification of the relationship between the structure and biological functions of biopolymers and low-molecular bioregulators; study of the chemical mechanisms of their biological action. This aspect of bioorganic chemistry is becoming increasingly practical significance. Improving the arsenal of methods for chemical and chemical-enzymatic synthesis of complex biopolymers (biologically active peptides, proteins, polynucleotides, nucleic acids, including actively functioning genes) in combination with increasingly improved techniques for the synthesis of relatively simpler bioregulators, as well as methods for selective cleavage of biopolymers, allow deeper understand the dependence of biological effects on the structure of compounds. The use of highly efficient computing technology makes it possible to objectively compare numerous data from different researchers and find common patterns. The found particular and general patterns, in turn, stimulate and facilitate the synthesis of new compounds, which in some cases (for example, when studying peptides that affect brain activity) makes it possible to find practically important synthetic compounds that are superior in biological activity to their natural analogues. The study of chemical mechanisms of biological action opens up the possibility of creating biologically active compounds with predetermined properties.
- Obtaining practically valuable drugs.
- Biological testing of the obtained compounds.
The formation of bioorganic chemistry. Historical reference
The emergence of bioorganic chemistry in the world took place in the late 50s and early 60s, when the main objects of research in this area were four classes of organic compounds that play a key role in the life of cells and organisms - proteins, polysaccharides and lipids. Outstanding Achievements traditional chemistry of natural compounds, such as the discovery by L. Pauling of the α-helix as one of the main elements spatial structure polypeptide chain in proteins, A. Todd's establishment of the chemical structure of nucleotides and the first synthesis of a dinucleotide, F. Sanger's development of a method for determining the amino acid sequence in proteins and using it to decipher the structure of insulin, R. Woodward's synthesis of such complex natural compounds as reserpine, chlorophyll and vitamin In 12, the synthesis of the first peptide hormone oxytocin marked, in essence, the transformation of the chemistry of natural compounds into modern bioorganic chemistry.
However, in our country, interest in proteins and nucleic acids arose much earlier. The first studies on the chemistry of proteins and nucleic acids began in the mid-20s. within the walls of Moscow University, and it was here that the first scientific schools, successfully working in these important areas of natural science to this day. So, in the 20s. on the initiative of N.D. Zelinsky began systematic research on protein chemistry, main task which was the clarification of the general principles of the structure of protein molecules. N.D. Zelinsky created the first protein chemistry laboratory in our country, in which important work on the synthesis and structural analysis of amino acids and peptides was carried out. An outstanding role in the development of these works belongs to M.M. Botvinnik and her students, who achieved impressive results in studying the structure and mechanism of action of inorganic pyrophosphatases, key enzymes of phosphorus metabolism in the cell. By the end of the 40s, when the leading role of nucleic acids in genetic processes began to emerge, M.A. Prokofiev and Z.A. Shabarova began work on the synthesis of nucleic acid components and their derivatives, thereby marking the beginning of nucleic acid chemistry in our country. The first syntheses of nucleosides, nucleotides and oligonucleotides were carried out, and a great contribution was made to the creation of domestic automatic nucleic acid synthesizers.
In the 60s This direction in our country has developed consistently and rapidly, often ahead of similar steps and trends abroad. The fundamental discoveries of A.N. played a huge role in the development of bioorganic chemistry. Belozersky, who proved the existence of DNA in higher plants and systematically studied the chemical composition of nucleic acids, the classical studies of V.A. Engelhardt and V.A. Belitser on the oxidative mechanism of phosphorylation, world-famous studies by A.E. Arbuzov on the chemistry of physiologically active organophosphorus compounds, as well as fundamental works by I.N. Nazarov and N.A. Preobrazhensky on the synthesis of various natural substances and their analogues and other works. The greatest achievements in the creation and development of bioorganic chemistry in the USSR belong to Academician M.M. Shemyakin. In particular, he began work on the study of atypical peptides - depsipeptides, which subsequently received widespread development in connection with their function as ionophores. The talent, insight and vigorous activity of this and other scientists contributed to the rapid growth of the international authority of Soviet bioorganic chemistry, its consolidation in the most relevant areas and organizational strengthening in our country.
In the late 60s - early 70s. In the synthesis of biologically active compounds of complex structure, enzymes began to be used as catalysts (the so-called combined chemical-enzymatic synthesis). This approach was used by G. Korana for the first gene synthesis. The use of enzymes made it possible to carry out strictly selective transformation of a number of natural compounds and obtain new biologically active derivatives of peptides, oligosaccharides and nucleic acids in high yield. In the 70s The most intensively developed areas of bioorganic chemistry were the synthesis of oligonucleotides and genes, studies of cell membranes and polysaccharides, and analysis of the primary and spatial structures of proteins. The structures of important enzymes (transaminase, β-galactosidase, DNA-dependent RNA polymerase), protective proteins (γ-globulins, interferons), membrane proteins(adenosine triphosphatases, bacteriorhodopsin). Great importance acquired work on studying the structure and mechanism of action of peptide regulators nervous activity(so-called neuropeptides).
Modern domestic bioorganic chemistry
Currently, domestic bioorganic chemistry occupies leading positions in the world in a number of key areas. Major advances have been made in the study of the structure and function of biologically active peptides and complex proteins, including hormones, antibiotics, and neurotoxins. Important results have been obtained in the chemistry of membrane-active peptides. The reasons for the unique selectivity and effectiveness of the action of dispepside-ionophores were investigated and the mechanism of functioning in living systems was elucidated. Synthetic analogues of ionophores with specified properties have been obtained, which are many times more effective than natural samples (V.T. Ivanov, Yu.A. Ovchinnikov). The unique properties of ionophores are used to create ion-selective sensors based on them, which are widely used in technology. The successes achieved in the study of another group of regulators - neurotoxins, which are inhibitors of the transmission of nerve impulses, have led to their widespread use as tools for studying membrane receptors and other specific structures of cell membranes (E.V. Grishin). The development of work on the synthesis and study of peptide hormones has led to the creation of highly effective analogues of the hormones oxytocin, angiotensin II and bradykinin, which are responsible for the contraction of smooth muscles and the regulation of blood pressure. A major success was the complete chemical synthesis insulin preparations, including human insulin (N.A. Yudaev, Yu.P. Shvachkin, etc.). A number of protein antibiotics were discovered and studied, including gramicidin S, polymyxin M, actinoxanthin (G.F. Gause, A.S. Khokhlov, etc.). Work is actively developing to study the structure and function of membrane proteins that perform receptor and transport functions. The photoreceptor proteins rhodopsin and bacteriorhodopsin were obtained and the physicochemical basis of their functioning as light-dependent ion pumps was studied (V.P. Skulachev, Yu.A. Ovchinnikov, M.A. Ostrovsky). The structure and mechanism of functioning of ribosomes, the main systems for protein biosynthesis in the cell, are widely studied (A.S. Spirin, A.A. Bogdanov). Large cycles of research are associated with the study of enzymes, determination of their primary structure and spatial structure, study of catalytic functions (aspartate aminotransferases, pepsin, chymotrypsin, ribonucleases, phosphorus metabolism enzymes, glycosidases, cholinesterases, etc.). Methods for the synthesis and chemical modification of nucleic acids and their components have been developed (D.G. Knorre, M.N. Kolosov, Z.A. Shabarova), approaches are being developed to create new generation drugs based on them for the treatment of viral, oncological and autoimmune diseases. Using unique properties nucleic acids and on their basis, diagnostic drugs and biosensors, analyzers of a number of biologically active compounds are created (V.A. Vlasov, Yu.M. Evdokimov, etc.)
Significant progress has been made in the synthetic chemistry of carbohydrates (synthesis of bacterial antigens and the creation of artificial vaccines, synthesis of specific inhibitors of the sorption of viruses on the cell surface, synthesis of specific inhibitors of bacterial toxins (N.K. Kochetkov, A.Ya. Khorlin)). Significant progress has been made in the study of lipids, lipoamino acids, lipopeptides and lipoproteins (L.D. Bergelson, N.M. Sisakyan). Methods have been developed for the synthesis of many biologically active fatty acids, lipids and phospholipids. The transmembrane distribution of lipids in various types of liposomes, in bacterial membranes and in liver microsomes was studied.
An important area of bioorganic chemistry is the study of a variety of natural and synthetic substances that can regulate various processes occurring in living cells. These are repellents, antibiotics, pheromones, signaling substances, enzymes, hormones, vitamins and others (so-called low-molecular regulators). Methods have been developed for the synthesis and production of almost all known vitamins, a significant part of steroid hormones and antibiotics. Industrial methods have been developed for the production of a number of coenzymes used as medicinal preparations (coenzyme Q, pyridoxal phosphate, thiamine pyrophosphate, etc.). New strong anabolic agents have been proposed that are superior in action to well-known foreign drugs (I.V. Torgov, S.N. Ananchenko). The biogenesis and mechanisms of action of natural and transformed steroids have been studied. Significant progress has been made in the study of alkaloids, steroid and triterpene glycosides, and coumarins. Original research was carried out in the field of pesticide chemistry, which led to the release of a number of valuable drugs (I.N. Kabachnik, N.N. Melnikov, etc.). An active search is underway for new drugs needed to treat various diseases. Drugs have been obtained that have proven their effectiveness in the treatment of a number of oncological diseases (dopane, sarcolysin, ftorafur, etc.).
Priority directions and prospects for the development of bioorganic chemistry
Priority directions scientific research in the field of bioorganic chemistry are:
- study of the structural-functional dependence of biologically active compounds;
- design and synthesis of new biologically active drugs, including the creation of medicines and plant protection products;
- research into highly efficient biotechnological processes;
- study of the molecular mechanisms of processes occurring in a living organism.
Oriented basic research in the field of bioorganic chemistry are aimed at studying the structure and function of the most important biopolymers and low-molecular bioregulators, including proteins, nucleic acids, carbohydrates, lipids, alkaloids, prostaglandins and other compounds. Bioorganic chemistry is closely related to practical problems medicine and agriculture (production of vitamins, hormones, antibiotics and other medicines, plant growth stimulants and regulators of animal and insect behavior), chemical, food and microbiological industries. The results of scientific research are the basis for creating a scientific and technical base for production technologies of modern medical immunodiagnostics, reagents for medical genetic research and reagents for biochemical analysis, technologies for the synthesis of drug substances for use in oncology, virology, endocrinology, gastroenterology, as well as chemicals plant protection and technologies for their application in agriculture.
Solving the main problems of bioorganic chemistry is important for the further progress of biology, chemistry and a number of technical sciences. Without elucidating the structure and properties of the most important biopolymers and bioregulators, it is impossible to understand the essence of life processes, much less find ways to control such complex phenomena as reproduction and transmission of hereditary characteristics, normal and malignant cell growth, immunity, memory, transmission of nerve impulses and much more. At the same time, the study of highly specialized biologically active substances and the processes occurring with their participation can open up fundamentally new opportunities for the development of chemistry, chemical technology and engineering. Problems whose solution is associated with research in the field of bioorganic chemistry include the creation of strictly specific highly active catalysts (based on the study of the structure and mechanism of action of enzymes), the direct conversion of chemical energy into mechanical energy (based on the study of muscle contraction), and the use of chemical storage principles in technology and information transfer carried out in biological systems, the principles of self-regulation of multicomponent cell systems, primarily the selective permeability of biological membranes, and much more. The listed problems lie far beyond the boundaries of bioorganic chemistry itself, however, it creates the basic prerequisites for the development of these problems, providing the main supporting points for the development of biochemical research already related to the field molecular biology. The breadth and importance of the problems being solved, the variety of methods and the close connection with other scientific disciplines ensure the rapid development of bioorganic chemistry. Bulletin of Moscow University, series 2, Chemistry. 1999. T. 40. No. 5. P. 327-329.
Bender M., Bergeron R., Komiyama M. Bioorganic chemistry of enzymatic catalysis. Per. from English M.: Mir, 1987. 352 S.
Yakovishin L.A. Selected Chapters of Bioorganic Chemistry. Sevastopol: Strizhak-press, 2006. 196 pp.
Nikolaev A.Ya. Biological Chemistry. M.: Medical Information Agency, 2001. 496 pp.
Subject of bioorganic chemistry.Structure and isomerism of organic
connections.
Chemical bond and interaction
atoms in organic compounds.
Types chemical reactions.
Poly- and heterofunctional
connections.
Basic textbook – Tyukavkina N.A., Baukov Yu.I.
Bioorganic chemistry.
Text of lectures and manual “Bioorganic chemistry in
questions and answers" see on the TSU website http://tgumed.ru
tab “Student Help”, section “Lectures on
disciplines curriculum" And, of course, VK
Bioorganic chemistry studies the structure and properties of substances involved in life processes in connection with the knowledge of their biological
Bioorganic chemistry studies the structure and properties of substancesparticipating in life processes, in connection with
knowledge of their biological functions.
The main objects of study are biological
polymers (biopolymers) and bioregulators.
Biopolymers
–
high molecular weight
natural
compounds that are the structural basis of all living things
organisms and playing a certain role in the processes
life activity. Biopolymers include peptides and
proteins, polysaccharides (carbohydrates), nucleic acids. IN
This group also includes lipids, which themselves are not
are high molecular weight compounds, but in
the body are usually associated with other biopolymers.
Bioregulators are compounds that chemically
regulate metabolism. These include vitamins,
hormones, many synthetic biologically active
compounds, including drugs.
The set of chemical reactions occurring in the body is called metabolism, or metabolism. Substances produced in cells
The set of chemical reactions occurring in the bodycalled metabolism, or metabolism. Substances
formed in cells, tissues and organs of plants and animals
during metabolism are called metabolites.
Metabolism includes two directions - catabolism and
anabolism.
Catabolism refers to the breakdown reactions of substances that enter
into the body with food. As a rule, they are accompanied by the oxidation of organic compounds and proceed with the release
energy.
Anabolism is the synthesis of complex molecules from
simpler ones, as a result of which the formation and renewal of structural elements living organism.
Metabolic processes occur with the participation of enzymes,
those. specific proteins that are found in cells
organism and play the role of catalysts for biochemical
processes (biocatalysts).
Metabolism
catabolismanabolism
Decomposition of biopolymers
with highlighting
energy
Synthesis of biopolymers
with absorption
energy
Glycerin and
fatty acid
Basic principles of the theory of the structure of organic compounds A.M. Butlerov
1. Atoms in a molecule are located in a certainsequences according to their valency.
Valency of carbon atom in organic
connections is equal to four.
2. The properties of substances depend not only on what
atoms and in what quantities they are included in the composition
molecules, but also on the order in which they
connected to each other.
3. Atoms or groups of atoms that make up
molecules mutually influence each other, causing
depend on chemical activity and reaction
ability of molecules.
4. Studying the properties of substances allows us to determine them
chemical structure.
H o m o l o g h i c y r a y d
Homologousrow
A number of structurally similar compounds that have
similar chemical properties, in which individual
members of a series differ from each other only in quantity
groups -CH2- is called a homological series, and the group
CH2 – homological difference.
Members of any homologous series have an overwhelming
most reactions proceed the same way (exception
constitute only the first members of the series). Therefore, knowing
chemical reactions of only one member of the series, it is possible with
with a high degree of probability to assert that the same
type of transformations also occur with the remaining members
homologous series.
For any homologous series one can derive
general formula reflecting the relationship between atoms
carbon and hydrogen in members of this series; this is the formula
called general formula homologous series.
Classification of organic compounds according to the structure of the carbon skeleton
Classification of organic compounds according to the presence of functional groups
Functional groupClass
Example
halogen atoms (F, Cl, Br, I) halogen derivatives CH3CH2Cl (chloroethane)
hydroxyl (–OH)
alcohols (phenols)
CH3CH2OH (ethanol)
thiol or mercapto- (– thiols (mercaptans) CH3CH2SH (ethanethiol)
SН)
ethereal (–O–)
ethers
CH3CH2–O–CH2CH3
(diethyl
ether)
ester
carboxyl –C UN
esters
CH3CH2COOCH3 (methyl acetate)
carboxylic acids CH3COOH (acetic acid)
amide –С ОНН2
amides
carbonyl (–C=O)
sulfo- (–SO3H)
amino- (–NH2)
aldehydes and
ketones
sulfonic acids
amines
nitro- (–NO2)
nitro compounds
acids
CH3CONH2 (acetamide)
CH3CHO (ethanal)
CH3COCH3 (propanone)
СН3SO3Н (methanesulfonic acid)
CH3CH2NH2
(ethylamine,
primary amine)
CH3NHCH3
(dimethylamine,
secondary amine)
CH3CH2NO2 (nitroethane)
Nomenclature of organic compounds
Isomerism of organic compounds
If two or more individual substances havethe same quantitative composition (molecular formula),
but differ from each other in the binding sequence
atoms and (or) their location in space, then in general
In this case they are called isomers.
Since the structure of these compounds is different, then
chemical or physical properties of isomers
are different.
Types of isomerism: structural (structure isomers) and
stereoisomerism (spatial).
Structural isomerism can be of three types:
- isomerism of the carbon skeleton (chain isomers),
- position isomers (multiple bonds or functional
groups),
- isomers of the functional group (interclass).
Stereoisomerism is subdivided
configuration
on
conformational
And
This is geometric isomerism
Plane polarized light
Signs of optical activity:- presence of an asymmetric carbon atom;
- absence of molecular symmetry elements
Enantiomers of adrenaline
protein
Anionic
Flat
center
surface
not occupied
Flat
Anionic
surface
center
busy
(+) - adrenaline
(-)- adrenaline
incomplete
correspondence
low
activity
complete
correspondence
high
activity
Biological activity of enantiomers
asparagineDARVON
analgesic
NOVRAD
antitussive drug
mirror
L-asparagine
D-asparagine
(from asparagus)
(from peas)
bitter taste
sweet taste
enantiomers
Thalidomide victims
Acidity and basicity of organic compounds
Bronsted acids (protic acids) -neutral molecules or ions that can
donate a proton (proton donors).
Typical Brønsted acids are carboxylic acids
acids. They have weaker acidic properties
hydroxyl groups of phenols and alcohols, as well as thio-,
amino and imino groups.
Bronsted bases are neutral molecules or
ions capable of accepting a proton (acceptors
protons).
Typical Bronsted bases are amines.
Ampholytes - compounds, in molecules
which contain both acidic and
main groups.
Types of acids and bases according to Brønsted
The main centers in the novocaine molecule
Use of basic properties to obtain water-soluble forms of drugs
Basicproperties
medicinal
drugs
are used to obtain their water-soluble forms.
When interacting with acids, compounds with
ionic bonds - salts that are highly soluble in water.
Yes, novocaine for injection
used in the form of hydrochloride.
the strongest main center,
which the proton joined
Acid-base properties of substances and their entry into the body
lipidmembrane
Stomach pH 1
UNS
lipid
membrane
blood plasma
pH 7.4
UNS
OSOSN3
Stomach pH 1
+
OSOSN3
NH3
SOOOOSCH3
SOO-
NH2
NH2
OSOSN3
Intestine pH 7-8
blood plasma
pH 7.4
Intestine pH 7-8
Acidic drugs are better absorbed from the stomach (pH 1-3),
and the absorption of drugs or xenobiotic bases occurs only
after they pass from the stomach to the intestines (pH 7-8). During
In one hour, almost 60% of acetylsalicylic acid is absorbed from the stomach of rats.
acid and only 6% aniline of the administered dose. In the intestines of rats
56% of the administered dose of aniline is already absorbed. Such a weak foundation
like caffeine (рKВH + 0.8), absorbed in the same time in a much greater
degree (36%), since even in the highly acidic environment of the stomach, caffeine
is predominantly in a non-ionized state.
Types of reactions in organic chemistry
Organic reactions are classified according tofollowing signs:
1. According to the electronic nature of the reagents.
2. By the change in the number of particles during the reaction.
3. Based on specific characteristics.
4. According to elementary mechanisms
stages of reactions.
Depending on the electronic nature of the reagents, reactions are distinguished: nucleophilic, electrophilic and free radical
Free radicals are electrically neutral particleshaving an unpaired electron, for example: Cl, NO2.
Free radical reactions are characteristic of alkanes.
Electrophilic reagents are cations or molecules
which by themselves or in the presence of a catalyst
have an increased affinity for an electron pair or
negatively charged centers of molecules. These include
cations H+, Cl+, +NO2, +SO3H, R+ and molecules with free
orbitals AlCl3, ZnCl2, etc.
Electrophilic reactions are characteristic of alkenes, alkynes,
aromatic compounds (addition at a double bond,
proton substitution).
Nucleophilic reagents are anions or molecules that
having centers with increased electron density. To them
include anions and molecules such as
HO-, RO-, Cl-, Br-, RCOO-, CN-, R-, NH3, C2H5OH, etc. By change
number of particles during
reactions are distinguished
substitution reactions,
accessions,
splitting off
(elimination),
decomposition
Classification of reactions according to particular characteristics
Reactivity is always considered
only in relation to the reactionary partner.
During a chemical transformation, it is usually
not the whole molecule is affected, but only part of it -
reaction center.
An organic compound may contain
several unequal reaction centers.
Reactions can lead to isomeric products.
Reaction selectivity – qualitative
characteristic meaning predominant
reaction proceeds in one direction from
several possible ones.
There are regioselectivity,
chemoselectivity, stereoselectivity of the reaction.
Selectivity of reactions in organic chemistry
Regioselectivity - preferential reaction according toone of several reaction centers of a molecule.
CH3-CH2-CH3 + Br2
СН3-СНВr-СН3 + НВr
The second isomer, 1-bromopropane, is practically not formed.
Chemoselectivity - preferential reaction according to
one of the related functional groups.
Stereoselectivity - preferential formation in a reaction
one of several possible stereoisomers. Multifunctional compounds contain
several identical functional groups.
Heterofunctional compounds contain
several different functional groups.
Heteropolyfunctional
compounds contain both
different and the same
functional groups.
Properties of poly- and heterofunctional compounds
Each group in poly- and heterofunctionalcompounds can undergo the same reactions as
corresponding group in monofunctional
connections Specific properties of poly- and
heterofunctional compounds
Cyclization reactions
Formation of chelate complexes Polyfunctional compounds as antidotes
The toxic effect of heavy metals is
binding of thiol groups of proteins. As a result, they are inhibited
vital enzymes of the body.
The principle of action of antidotes is the formation of strong
complexes with heavy metal ions.
LECTURE 1
Bioorganic chemistry (BOC), its importance in medicine
HOC is a science that studies the biological function of organic substances in the body.
BOH arose in the 2nd half of the twentieth century. The objects of its study are biopolymers, bioregulators and individual metabolites.
Biopolymers are high-molecular natural compounds that are the basis of all organisms. These are peptides, proteins, polysaccharides, nucleic acids (NA), lipids, etc.
Bioregulators are compounds that chemically regulate metabolism. These are vitamins, hormones, antibiotics, alkaloids, medications, etc.
Knowledge of the structure and properties of biopolymers and bioregulators allows us to understand the essence of biological processes. Thus, the establishment of the structure of proteins and NAs made it possible to develop ideas about matrix protein biosynthesis and the role of NAs in the preservation and transmission of genetic information.
BOX plays an important role in establishing the mechanism of action of enzymes, drugs, processes of vision, respiration, memory, nerve conduction, muscle contraction, etc.
The main problem of HOC is to elucidate the relationship between the structure and mechanism of action of compounds.
BOX is based on organic chemistry material.
ORGANIC CHEMISTRY
This is the science that studies carbon compounds. Currently, there are ~16 million organic substances.
Reasons for the diversity of organic substances.
1. Compounds of C atoms with each other and other elements periodic table D. Mendeleev. In this case, chains and cycles are formed:
Straight chain Branched chain
Tetrahedral Planar Configuration
C atom configuration of C atom
2. Homology is the existence of substances with similar properties, where each member of the homologous series differs from the previous one by a group
–CH 2 –. For example, the homologous series of saturated hydrocarbons:
3. Isomerism is the existence of substances that have the same qualitative and quantitative composition, but a different structure.
A.M. Butlerov (1861) created a theory of the structure of organic compounds, which to this day serves scientific basis organic chemistry.
Basic principles of the theory of the structure of organic compounds:
1) atoms in molecules are connected to each other by chemical bonds in accordance with their valency;
2) atoms in molecules of organic compounds are connected to each other in a certain sequence, which determines the chemical structure of the molecule;
3) the properties of organic compounds depend not only on the number and nature of their constituent atoms, but also on the chemical structure of the molecules;
4) in molecules there is a mutual influence of atoms, both connected and not directly connected to each other;
5) the chemical structure of a substance can be determined by studying its chemical transformations and, conversely, its properties can be characterized by the structure of a substance.
Let us consider some provisions of the theory of the structure of organic compounds.
Structural isomerism
She shares:
1) Chain isomerism
2) Isomerism of the position of multiple bonds and functional groups
3) Isomerism of functional groups (interclass isomerism)
Newman's formulas
Cyclohexane
The “chair” shape is more energetically beneficial than the “bathtub”.
Configuration isomers
These are stereoisomers, the molecules of which have different arrangements of atoms in space without taking into account conformations.
Based on the type of symmetry, all stereoisomers are divided into enantiomers and diastereomers.
Enantiomers (optical isomers, mirror isomers, antipodes) are stereoisomers whose molecules are related to each other as an object and an incompatible mirror image. This phenomenon is called enantiomerism. All chemical and physical properties of enantiomers are the same, except for two: rotation of the plane of polarized light (in a polarimeter device) and biological activity. Conditions for enantiomerism: 1) the C atom is in a state of sp 3 hybridization; 2) absence of any symmetry; 3) the presence of an asymmetric (chiral) C atom, i.e. atom having four different substituents.
Many hydroxy and amino acids have the ability to rotate the plane of polarization of a light beam to the left or to the right. This phenomenon is called optical activity, and the molecules themselves are optically active. The deviation of the light beam to the right is marked with a “+” sign, to the left – “-” and the angle of rotation is indicated in degrees.
The absolute configuration of molecules is determined by complex physicochemical methods.
The relative configuration of optically active compounds is determined by comparison with a glyceraldehyde standard. Optically active substances having the configuration of dextrorotatory or levorotatory glyceraldehyde (M. Rozanov, 1906) are called substances of the D- and L-series. An equal mixture of right- and left-handed isomers of one compound is called a racemate and is optically inactive.
Research has shown that the sign of the rotation of light cannot be associated with the belonging of a substance to the D- and L-series; it is determined only experimentally in instruments - polarimeters. For example, L-lactic acid has a rotation angle of +3.8 o, D-lactic acid - -3.8 o.
Enantiomers are depicted using Fischer's formulas.
L-row D-row
Among the enantiomers there may be symmetrical molecules that do not have optical activity, and are called mesoisomers.
 |
| For example: Wine house |
| D – (+) – row L – (–) – row | Mezovinnaya k-ta |
Racemate – grape juice
Optical isomers that are not mirror isomers, differing in the configuration of several, but not all asymmetric C atoms, having different physical and chemical properties, are called s- di-A-stereoisomers.
p-Diastereomers (geometric isomers) are stereomers that have a p-bond in the molecule. They are found in alkenes, unsaturated higher carbonic acids, unsaturated dicarbonic acids
The biological activity of organic substances is related to their structure.
For example:
Cis-butenediic acid, Trans-butenediic acid,
maleic acid - fumaric acid - non-toxic,
very toxic found in the body
All natural unsaturated higher carbon compounds are cis-isomers.
LECTURE 2
Conjugate systems
In the simplest case, conjugated systems are systems with alternating double and single bonds. They can be open or closed. An open system is found in diene hydrocarbons (HCs).
Examples:CH 2 = CH – CH = CH 2
Butadiene-1, 3
ChloretheneCH 2 = CH – Cl
Here the conjugation of p-electrons with p-electrons occurs. This type of conjugation is called p, p-conjugation.
A closed system is found in aromatic hydrocarbons.
C 6 H 6
Aromaticity
This is a concept that includes various properties of aromatic compounds. Conditions for aromaticity: 1) flat closed ring, 2) all C atoms are in sp 2 hybridization, 3) a single conjugated system of all ring atoms is formed, 4) Hückel’s rule is satisfied: “4n+2 p-electrons participate in conjugation, where n = 1, 2, 3...”
The simplest representative of aromatic hydrocarbons is benzene. It satisfies all four conditions of aromaticity.
Hückel's rule: 4n+2 = 6, n = 1.
Mutual influence of atoms in a molecule
In 1861, the Russian scientist A.M. Butlerov expressed the position: “Atoms in molecules mutually influence each other.” Currently, this influence is transmitted in two ways: inductive and mesomeric effects.
Inductive effect
This is the transfer of electronic influence through the s-bond chain. It is known that the bond between atoms with different electronegativity (EO) is polarized, i.e. shifted to a more EO atom. This leads to the appearance of effective (real) charges (d) on the atoms. This electronic displacement is called inductive and is designated by the letter I and the arrow ®.
, X = Hal -, HO -, HS -, NH 2 - etc.
The inductive effect can be positive or negative. If substituent X attracts electrons chemical bond stronger than the H atom, then it exhibits – I. I(H) = O. In our example, X exhibits – I.
If the X substituent attracts bond electrons weaker than the H atom, then it exhibits +I. All alkyls (R = CH 3 -, C 2 H 5 -, etc.), Me n + exhibit +I.
Mesomeric effect
The mesomeric effect (conjugation effect) is the influence of a substituent transmitted through a conjugated system of p-bonds. Denoted by the letter M and a curved arrow. The mesomeric effect can be “+” or “–”.
It was said above that there are two types of conjugation p, p and p, p.
A substituent that attracts electrons from a conjugated system exhibits –M and is called an electron acceptor (EA). These are substituents having double
 |
communication, etc.
A substituent that donates electrons to a conjugated system exhibits +M and is called an electron donor (ED). These are substituents with single bonds that have a lone electron pair (etc.).
Table 1 Electronic effects of substituents
| Deputies | Orientants in C 6 H 5 -R | I | M |
| Alk (R-): CH 3 -, C 2 H 5 -... | Orientants of the first kind: direct ED substituents to ortho- and para-positions | + | |
| – H 2 , –NНR, –NR 2 | – | + | |
| – N, – N, – R | – | + | |
| –H L | – | + | |
|
LECTURE 3 Acidity and basicity To characterize the acidity and basicity of organic compounds, the Brønsted theory is used. The main provisions of this theory: 1) An acid is a particle that donates a proton (H + donor); The base is the particle that accepts the proton (H+ acceptor). 2) Acidity is always characterized in the presence of bases and vice versa. A – H + : B Û A – + B – H + basis CH 3 COOH + NOH Û CH 3 COO – + H 3 O + Assets Basic Conjugate Conjugate basis HNO 3 + CH 3 COOH Û CH 3 COOH 2 + + NO 3 - Assets Main Conjugate Conjugate basis Bronsted acids 3) Bronsted acids are divided into 4 types depending on the acid center: SН compounds (thiols), OH compounds (alcohols, phenols, carbon compounds), NH compounds (amines, amides), SN to-you (UV). In this row, from top to bottom, acidity decreases. 4) The strength of the compound is determined by the stability of the anion formed. The more stable the anion, the stronger the effect. The stability of the anion depends on the delocalization (distribution) of the “-” charge throughout the particle (anion). The more delocalized the “-” charge is, the more stable the anion and the stronger the charge. Charge delocalization depends on: a) on the electronegativity (EO) of the heteroatom. The more EO of a heteroatom, the stronger the corresponding effect. For example: R – OH and R – NH 2 Alcohols are stronger than amines, because EO (O) > EO (N). b) on the polarizability of the heteroatom. The greater the polarizability of the heteroatom, the stronger the corresponding voltage. For example: R – SH and R – OH Thiols are stronger than alcohols, because The S atom is more polarized than the O atom. c) on the nature of the substituent R (its length, the presence of a conjugated system, delocalization of the electron density). For example: CH 3 – OH, CH 3 – CH 2 – OH, CH 3 – CH 2 – CH 2 – OH Acidity<, т.к. увеличивается длина радикала
CH 3 – OH, C 6 H 5 – OH, Your strength increases Phenols are stronger compounds than alcohols due to the p, p-conjugation (+M) of the –OH group.
In addition, the carboxylate anion is more stable than the alcohol anion due to p, p-conjugation in the carboxyl group.
For example: r-Nitrophenol is stronger than r-aminophenol, because the –NO2 group is EA. CH 3 –COOH CCl 3 –COOH pK 4.7 pK 0.65 Trichloroacetic acid is many times stronger than CH 3 COOH due to the – I Cl atoms as EA. The formic acid H–COOH is stronger than CH 3 COOH due to the +I group of CH 3 – acetic acid. e) on the nature of the solvent. If the solvent is a good acceptor of H + protons, then the force Bronsted foundations 5) They are divided into: a) p-bases (compounds with multiple bonds); b) n-bases (ammonium bases containing an atom, oxonium containing atom, sulfonium containing atom) The strength of the base is determined by the stability of the resulting cation. The more stable the cation, the stronger the base. In other words, the strength of the base is greater, the weaker the bond with the heteroatom (O, S, N) having a free electron pair attacked by H +. The stability of the cation depends on the same factors as the stability of the anion, but with the opposite effect. All factors that increase acidity decrease basicity. The strongest bases are amines, because the nitrogen atom has a lower EO compared to O. At the same time, secondary amines are stronger bases than primary ones, tertiary amines are weaker than secondary ones due to the steric factor, which impedes the access of a proton to N.
Aromatic amines are weaker bases than aliphatic ones, which is explained by the +M group –NH2. The electron pair of nitrogen, participating in conjugation, becomes inactive. The stability of the conjugated system makes the addition of H+ difficult. In urea NН 2 –СО– NН 2 there is an EA group > C = O, which significantly reduces the basic properties and urea forms salts with only one equivalent of the substance. Thus, the stronger the substance, the weaker the foundation it forms and vice versa. Alcohols These are hydrocarbon derivatives in which one or more H atoms are replaced by an –OH group. Classification: I. Based on the number of OH groups, monohydric, dihydric and polyhydric alcohols are distinguished: CH 3 -CH 2 -OH Ethanol Ethylene glycol Glycerin
II. According to the nature of R, they are distinguished: 1) limiting, 2) non-limiting, 2) CH 2 = CH-CH 2 -OH Allyl alcohol
retinol (vitamin A) and cholesterol
vitamin-like substance |
With the same acid center, the strength of alcohols, phenols and carbonates is not the same. For example,
The O–H bond is more polarized in phenols. Phenols can even interact with salts (FeC1 3) - a qualitative reaction to phenols. Carbon 
d) from the introduction of substituents into the radical. EA substituents increase acidity, ED substituents reduce acidity.
3) Unsaturated cyclic alcohols include:
InositolIII. According to the position of the gr. –OH distinguishes between primary, secondary and tertiary alcohols.
IV. Based on the number of C atoms, low molecular weight and high molecular weight are distinguished.
CH 3 –(CH 2) 14 –CH 2 –OH (C 16 H 33 OH) CH 3 –(CH 2) 29 –CH 2 OH (C 31 H 63 OH)
Cetyl alcohol Myricyl alcohol
Cetyl palmitate is the basis of spermaceti, myricyl palmitate is found in beeswax.
Nomenclature:
Trivial, rational, MN (root + ending “ol” + Arabic numeral).
Isomerism:
chains, gr. positions –OH, optical.
The structure of the alcohol molecule
CH acid Nu center
Electrophilic Center Acidic
center of basicity center
Oxidation solutions
1) Alcohols are weak acids.
2) Alcohols are weak bases. They add H+ only from strong acids, but they are stronger than Nu.
3) –I effect gr. –OH increases the mobility of H at the neighboring carbon atom. Carbon acquires d+ (electrophilic center, S E) and becomes the center of nucleophilic attack (Nu). The C–O bond breaks more easily than the H–O bond, which is why S N reactions are characteristic of alcohols. They, as a rule, go in an acidic environment, because... protonation of the oxygen atom increases the d+ of the carbon atom and makes it easier to break the bond. This type includes solutions for the formation of ethers and halogen derivatives.
4) The shift in electron density from H in the radical leads to the appearance of a CH-acid center. In this case, there are processes of oxidation and elimination (E).
Physical properties
Lower alcohols (C 1 – C 12) are liquids, higher alcohols are solids. Many properties of alcohols are explained by the formation of H-bonds:
Chemical properties
I. Acid-base
Alcohols are weak amphoteric compounds.
2R–OH + 2Na ® 2R–ONa + H 2
Alcoholate
Alcoholates are easily hydrolyzed, which shows that alcohols are weaker acids than water:
R–ОНа + НОН ® R–ОН + NaОН
The main center in alcohols is the O heteroatom:
CH 3 -CH 2 -OH + H + ® CH 3 -CH 2 - -H ® CH 3 -CH 2 + + H 2 OIf the solution comes with hydrogen halides, then the halide ion will join: CH 3 -CH 2 + + Cl - ® CH 3 -CH 2 Cl
HC1 ROH R-COOH NH 3 C 6 H 5 ONa
C1 - R-O - R-COO - NH 2 - C 6 H 5 O -
Anions in such solutions act as nucleophiles (Nu) due to the “-” charge or lone electron pair. Anions are stronger bases and nucleophilic reagents than alcohols themselves. Therefore, in practice, alcoholates, and not alcohols themselves, are used to obtain ethers and esters. If the nucleophile is another alcohol molecule, then it adds to the carbocation:
|
This is an alkylation solution (introduction of alkyl R into a molecule).
Substitute –OH gr. on halogen is possible under the action of PCl 3, PCl 5 and SOCl 2.
Tertiary alcohols react more easily by this mechanism.
The ratio of S E in relation to the alcohol molecule is the ratio of the formation of esters with organic and mineral compounds:
R – O N + H O – R – O – + H 2 O
Ester
This is the acylation procedure - the introduction of an acyl into the molecule.
CH 3 -CH 2 -OH + H + CH 3 -CH 2 - -H CH 3 -CH 2 +With an excess of H 2 SO 4 and a higher temperature than in the case of the formation of ethers, the catalyst is regenerated and an alkene is formed:
CH 3 -CH 2 + + HSO 4 - ® CH 2 = CH 2 + H 2 SO 4
The E solution is easier for tertiary alcohols, more difficult for secondary and primary alcohols, because in the latter cases, less stable cations are formed. In these districts, A. Zaitsev’s rule is followed: “During the dehydration of alcohols, the H atom is split off from the neighboring C atom with a lower content of H atoms.”
CH 3 -CH = CH -CH 3
Butanol-2
In the body gr. –OH is converted into easy-to-leave by forming esters with H 3 PO 4:
CH 3 -CH 2 -OH + HO–PO 3 H 2 CH 3 -CH 2 -ORO 3 H 2IV. Oxidation solutions
1) Primary and secondary alcohols are oxidized by CuO, solutions of KMnO 4, K 2 Cr 2 O 7 when heated to form the corresponding carbonyl-containing compounds:
Nitroglycerin is a colorless oily liquid. In the form of diluted alcohol solutions (1%) it is used for angina pectoris, because has a vasodilating effect. Nitroglycerin is a powerful explosive that can explode on impact or when heated. In this case, in the small volume occupied by the liquid substance, a very large volume of gases is instantly formed, which causes a strong blast wave. Nitroglycerin is part of dynamite and gunpowder.
Representatives of pentitol and hexitol are xylitol and sorbitol, which are open-chain penta- and hexahydric alcohols, respectively. The accumulation of –OH groups leads to the appearance of a sweet taste. Xylitol and sorbitol are sugar substitutes for diabetics.
Glycerophosphates are structural fragments of phospholipids, used as a general tonic.
Benzyl alcohol
Position isomers
Plan 1. Subject and significance of bioorganic chemistry 2. Classification and nomenclature of organic compounds 3. Methods of depicting organic molecules 4. Chemical bonding in bioorganic molecules 5. Electronic effects. Mutual influence of atoms in a molecule 6. Classification of chemical reactions and reagents 7. Concept of the mechanisms of chemical reactions 2
Subject of bioorganic chemistry 3 Bioorganic chemistry is an independent branch of chemical science that studies the structure, properties and biological functions of chemical compounds of organic origin that take part in the metabolism of living organisms.
The objects of study of bioorganic chemistry are low-molecular biomolecules and biopolymers (proteins, nucleic acids and polysaccharides), bioregulators (enzymes, hormones, vitamins and others), natural and synthetic physiologically active compounds, including drugs and substances with toxic effects. Biomolecules are bioorganic compounds that are part of living organisms and specialized for the formation of cellular structures and participation in biochemical reactions, form the basis of metabolism (metabolism) and the physiological functions of living cells and multicellular organisms in general. 4 Classification of bioorganic compounds
Metabolism is a set of chemical reactions that occur in the body (in vivo). Metabolism is also called metabolism. Metabolism can occur in two directions - anabolism and catabolism. Anabolism is the synthesis in the body of complex substances from relatively simple ones. It occurs with the expenditure of energy (endothermic process). Catabolism, on the contrary, is the breakdown of complex organic compounds into simpler ones. It occurs with the release of energy (exothermic process). Metabolic processes take place with the participation of enzymes. Enzymes play the role of biocatalysts in the body. Without enzymes, biochemical processes would either not occur at all, or would proceed very slowly, and the body would not be able to maintain life. 5
Bioelements. The composition of bioorganic compounds, in addition to carbon atoms (C), which form the basis of any organic molecule, also includes hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P) and sulfur (S). These bioelements (organogens) are concentrated in living organisms in quantities that are over 200 times higher than their content in inanimate objects. The noted elements make up over 99% of the elemental composition of biomolecules. 6
Bioorganic chemistry arose from the depths of organic chemistry and is based on its ideas and methods. In the history of development, organic chemistry has the following stages: empirical, analytical, structural and modern. The period from man's first acquaintance with organic substances to the end of the 18th century is considered empirical. The main result of this period was that people realized the importance of elemental analysis and the establishment of atomic and molecular masses. The theory of vitalism - life force (Berzelius). The analytical period continued until the 60s of the 19th century. It was marked by the fact that from the end of the first quarter of the 19th century a number of promising discoveries were made that dealt a crushing blow to the vitalistic theory. The first in this series was Berzelius's student, the German chemist Wöhler. He made a number of discoveries in 1824 - the synthesis of oxalic acid from cyanogen: (CN) 2 HOOC - COOH r. – synthesis of urea from ammonium cyanate: NH 4 CNO NH 2 – C – NH 2 O 8
In 1853, C. Gerard developed the “theory of types” and used it to classify organic compounds. According to Gerard, more complex organic compounds can be produced from the following four main types of substances: HHHH type HHHH O type WATER H Cl type HYDROGEN CHLORIDE HHHHN N type AMMONIA Since 1857, at the suggestion of F. A. Kekule, hydrocarbons began to be classified as methane type HHHNNHH C 9
Basic provisions of the theory of the structure of organic compounds (1861) 1) atoms in molecules are connected to each other by chemical bonds in accordance with their valency; 2) atoms in molecules of organic substances are connected to each other in a certain sequence, which determines the chemical structure (structure) of the molecule; 3) the properties of organic compounds depend not only on the number and nature of their constituent atoms, but also on the chemical structure of the molecules; 4) in organic molecules there is interaction between atoms, both bound to each other and unbound; 5) the chemical structure of a substance can be determined by studying its chemical transformations and, conversely, its properties can be characterized by the structure of a substance. 10
Basic provisions of the theory of the structure of organic compounds (1861) A structural formula is an image of the sequence of bonds of atoms in a molecule. Gross formula - CH 4 O or CH 3 OH Structural formula Simplified structural formulas are sometimes called rational Molecular formula - the formula of an organic compound, which indicates the number of atoms of each element in the molecule. For example: C 5 H 12 - pentane, C 6 H 6 - gasoline, etc. eleven
Stages of development of bioorganic chemistry How separate area knowledge, which combines the conceptual principles and methodology of organic chemistry on the one hand and molecular biochemistry and molecular pharmacology on the other hand, bioorganic chemistry was formed in the twentieth century based on the development of the chemistry of natural substances and biopolymers. Modern bioorganic chemistry has acquired fundamental significance thanks to the work of W. Stein, S. Moore, F. Sanger (analysis of amino acid composition and determination of the primary structure of peptides and proteins), L. Pauling and H. Astbury (clarification of the structure of the -helix and -structure and their significance in the implementation of the biological functions of protein molecules), E. Chargaff (deciphering the features of the nucleotide composition of nucleic acids), J. Watson, Fr. Crick, M. Wilkins, R. Franklin (establishing the patterns of the spatial structure of the DNA molecule), G. Corani (chemical gene synthesis), etc. 14
Classification of organic compounds according to the structure of the carbon skeleton and the nature of the functional group The huge number of organic compounds prompted chemists to classify them. The classification of organic compounds is based on two classification characteristics: 1. Structure of the carbon skeleton 2. Nature of functional groups Classification according to the method of structure of the carbon skeleton: 1. Acyclic (alkanes, alkenes, alkynes, alkadienes); 2. Cyclic 2.1. Carbocyclic (alicyclic and aromatic) 2.2. Heterocyclic 15 Acyclic compounds are also called aliphatic. These include substances with an open carbon chain. Acyclic compounds are divided into saturated (or saturated) C n H 2n+2 (alkanes, paraffins) and unsaturated (unsaturated). The latter include alkenes C n H 2n, alkynes C n H 2n -2, alkadienes C n H 2n -2.
16 Cyclic compounds contain rings (cycles) within their molecules. If the cycles contain only carbon atoms, then such compounds are called carbocyclic. In turn, carbocyclic compounds are divided into alicyclic and aromatic. Alicyclic hydrocarbons (cycloalkanes) include cyclopropane and its homologues - cyclobutane, cyclopentane, cyclohexane, and so on. If the cyclic system, in addition to the hydrocarbon, also includes other elements, then such compounds are classified as heterocyclic.
Classification by the nature of a functional group A functional group is an atom or a group of atoms connected in a certain way, the presence of which in a molecule of an organic substance determines the characteristic properties and its belonging to one or another class of compounds. Based on the number and homogeneity of functional groups, organic compounds are divided into mono-, poly- and heterofunctional. Substances with one functional group are called monofunctional; substances with several identical functional groups are called polyfunctional. Compounds containing several different functional groups are heterofunctional. It is important that compounds of the same class are combined into homologous series. A homologous series is a series of organic compounds with the same functional groups and the same structure; each representative of the homologous series differs from the previous one by a constant unit (CH 2), which is called the homologous difference. Members of a homologous series are called homologues. 17
Nomenclature systems in organic chemistry - trivial, rational and international (IUPAC) Chemical nomenclature a set of names of individual chemical substances, their groups and classes, as well as rules for compiling their names. Chemical nomenclature is a set of names of individual chemical substances, their groups and classes, as well as rules for compiling their names. The trivial (historical) nomenclature is associated with the process of obtaining substances (pyrogallol - a product of pyrolysis of gallic acid), the source of origin from which it was obtained (formic acid), etc. Trivial names of compounds are widely used in the chemistry of natural and heterocyclic compounds (citral, geraniol, thiophene, pyrrole, quinoline, etc.). Trivial (historical) nomenclature is associated with the process of obtaining substances (pyrogallol is a product of pyrolysis of gallic acid), the source of origin, from which was obtained (formic acid), etc. Trivial names of compounds are widely used in the chemistry of natural and heterocyclic compounds (citral, geraniol, thiophene, pyrrole, quinoline, etc.). Rational nomenclature is based on the principle of dividing organic compounds into homologous series. All substances in a certain homologous series are considered as derivatives of the simplest representative this series- the first or sometimes the second. In particular, for alkanes - methane, for alkenes - ethylene, etc. The rational nomenclature is based on the principle of dividing organic compounds into homologous series. All substances in a certain homologous series are considered as derivatives of the simplest representative of this series - the first or sometimes the second. In particular, for alkanes - methane, for alkenes - ethylene, etc. 18
International nomenclature (IUPAC). The rules of modern nomenclature were developed in 1957 at the 19th Congress of the International Union of Pure and Applied Chemistry (IUPAC). Radical functional nomenclature. These names are based on the name of the functional class (alcohol, ether, ketone, etc.), which is preceded by the names of hydrocarbon radicals, for example: alyl chloride, diethyl ether, dimethyl ketone, propyl alcohol, etc. Substitute nomenclature. Nomenclature rules. The parent structure is the structural fragment of the molecule (molecular skeleton) underlying the name of the compound, the main carbon chain of atoms for alicyclic compounds, and the cycle for carbocyclic compounds. 19
Chemical bond in organic molecules Chemical bond is the phenomenon of interaction between the outer electron shells (valence electrons of atoms) and atomic nuclei, which determines the existence of a molecule or crystal as a whole. As a rule, an atom, accepting or donating an electron or forming a common electron pair, tends to acquire the configuration of an external electron shell similar to inert gases. The following types of chemical bonds are characteristic of organic compounds: - ionic bond - covalent bond - donor - acceptor bond - hydrogen bond. There are also some other types of chemical bonds (metallic, one-electron, two-electron three-center), but they are practically not found in organic compounds. 20
Types of bonds in organic compounds The most characteristic of organic compounds is a covalent bond. A covalent bond is the interaction of atoms, which is realized through the formation of a common electron pair. This type of bond is formed between atoms that have comparable electronegativity values. Electronegativity is a property of an atom that shows the ability to attract electrons to itself from other atoms. A covalent bond can be polar or non-polar. A non-polar covalent bond occurs between atoms with the same electronegativity value
Types of bonds in organic compounds A polar covalent bond is formed between atoms that have different electronegativity values. IN in this case bonded atoms acquire partial charges δ+δ+ δ-δ- A special subtype of covalent bond is the donor-acceptor bond. As in previous examples, this type of interaction is due to the presence of a common electron pair, but the latter is provided by one of the atoms forming the bond (donor) and accepted by another atom (acceptor) 24
Types of bonds in organic compounds An ionic bond is formed between atoms that differ greatly in electronegativity values. In this case, the electron from the less electronegative element (often a metal) is completely transferred to the more electronegative element. This electron transition causes the appearance of a positive charge on the less electronegative atom and a negative charge on the more electronegative one. Thus, two ions with opposite charges are formed, between which there is an electrovalent interaction. 25
Types of Bonds in Organic Compounds A hydrogen bond is an electrostatic interaction between a hydrogen atom, which is bonded in a highly polar manner, and electron pairs of oxygen, fluorine, nitrogen, sulfur and chlorine. This type of interaction is quite weak interaction. Hydrogen bonding can be intermolecular or intramolecular. Intermolecular hydrogen bond (interaction between two molecules of ethyl alcohol) Intramolecular hydrogen bond in salicylic aldehyde 26
Chemical bonding in organic molecules Modern theory chemical bonding is based on the quantum mechanical model of the molecule as a system consisting of electrons and atomic nuclei. The cornerstone concept of quantum mechanical theory is the atomic orbital. An atomic orbital is a part of space in which the probability of finding electrons is maximum. Bonding can thus be viewed as the interaction (“overlap”) of orbitals that each carry one electron with opposite spins. 27
Hybridization of atomic orbitals According to quantum mechanical theory, the number of covalent bonds formed by an atom is determined by the number of one-electron atomic orbitals (the number of unpaired electrons). The carbon atom in its ground state has only two unpaired electrons, but the possible transition of an electron from 2s to 2 pz makes it possible to form four covalent bonds. The state of a carbon atom in which it has four unpaired electrons is called “excited.” Despite the fact that carbon orbitals are unequal, it is known that the formation of four equivalent bonds is possible due to the hybridization of atomic orbitals. Hybridization is a phenomenon in which the same number of orbitals of the same shape and number are formed from several orbitals of different shapes and similar in energy. 28
Hybrid states of the carbon atom in organic molecules FIRST HYBRID STATE The C atom is in a state of sp 3 hybridization, forms four σ bonds, forms four hybrid orbitals, which are arranged in the shape of a tetrahedron (bond angle) σ bond 31
Hybrid states of the carbon atom in organic molecules SECOND HYBRID STATE The C atom is in a state of sp 2 hybridization, forms three σ-bonds, forms three hybrid orbitals, which are arranged in the shape of a flat triangle (bond angle 120) σ-bonds π-bond 32
Hybrid states of the carbon atom in organic molecules THIRD HYBRID STATE The C atom is in a state of sp-hybridization, forms two σ-bonds, forms two hybrid orbitals, which are arranged in a line (bond angle 180) σ-bonds π-bonds 33
Characteristics of chemical bonds POLING scale: F-4.0; O – 3.5; Cl – 3.0; N – 3.0; Br – 2.8; S – 2.5; C-2.5; H-2.1. difference 1.7
Characteristics of chemical bonds Bond polarizability is a shift in electron density under the influence of external factors. Bond polarizability is the degree of electron mobility. As the atomic radius increases, the polarizability of electrons increases. Therefore, the polarizability of the Carbon - halogen bond increases as follows: C-F 
Electronic effects. Mutual influence of atoms in a molecule 39 According to modern theoretical concepts, the reactivity of organic molecules is predetermined by the displacement and mobility of electron clouds that form covalent bond. In organic chemistry, two types of electron displacements are distinguished: a) electronic displacements occurring in the -bond system, b) electronic displacements transmitted by the -bond system. In the first case, the so-called inductive effect takes place, in the second - a mesomeric effect. The inductive effect is a redistribution of electron density (polarization) resulting from the difference in electronegativity between the atoms of a molecule in a system of bonds. Due to the insignificant polarizability of the -bonds, the inductive effect quickly fades away and after 3-4 bonds it almost does not appear.
Electronic effects. Mutual influence of atoms in a molecule 40 The concept of the inductive effect was introduced by K. Ingold, and he also introduced the following designations: –I-effect in the case of a decrease in electron density by a substituent +I-effect in the case of an increase in electron density by a substituent A positive inductive effect is exhibited by alkyl radicals (CH 3, C 2 H 5 - etc.). All other substituents bonded to the carbon atom exhibit a negative inductive effect.
Electronic effects. Mutual influence of atoms in a molecule 41 The mesomeric effect is the redistribution of electron density along a conjugated system. Conjugated systems include molecules of organic compounds in which double and single bonds alternate or when an atom with a lone pair of electrons in the p-orbital is located next to the double bond. In the first case, - conjugation takes place, and in the second case, p, -conjugation takes place. Coupled systems come in open and closed circuit configurations. Examples of such compounds are 1,3-butadiene and gasoline. In the molecules of these compounds, carbon atoms are in a state of sp 2 hybridization and, due to non-hybrid p-orbitals, form -bonds that mutually overlap and form a single electron cloud, that is, conjugation takes place.
Electronic effects. Mutual influence of atoms in a molecule 42 There are two types of mesomeric effect - positive mesomeric effect (+M) and negative mesomeric effect (-M). A positive mesomeric effect is exhibited by substituents that provide p-electrons to the conjugated system. These include: -O, -S -NH 2, -OH, -OR, Hal (halogens) and other substituents that have a negative charge or a lone pair of electrons. The negative mesomeric effect is characteristic of substituents that absorb electron density from the conjugated system. These include substituents that have multiple bonds between atoms with different electronegativity: - N0 2 ; -SO 3 H; >C=O; -COON and others. The mesomeric effect is graphically reflected by a bent arrow, which shows the direction of electron displacement. Unlike the induction effect, the mesomeric effect does not go out. It is transmitted completely throughout the system, regardless of the length of the interfacing chain. C=O; -COON and others. The mesomeric effect is graphically reflected by a bent arrow, which shows the direction of electron displacement. Unlike the induction effect, the mesomeric effect does not go out. It is transmitted completely throughout the system, regardless of the length of the interfacing chain."> 
Types of chemical reactions 43 A chemical reaction can be considered as the interaction of a reagent and substrate. Depending on the method of breaking and forming a chemical bond in molecules, organic reactions divided into: a) homolytic b) heterolytic c) molecular Homolytic or free radical reactions are caused by homolytic cleavage of the bond, when each atom has one electron left, that is, radicals are formed. Homolytic cleavage occurs at high temperatures, the action of a light quantum, or catalysis.
Heterolytic or ionic reactions proceed in such a way that a pair of bonding electrons remains near one of the atoms and ions are formed. A particle with an electron pair is called nucleophilic and has a negative charge (-). A particle without an electron pair is called electrophilic and has a positive charge (+). 44 Types of chemical reactions
Mechanism of a chemical reaction 45 The mechanism of a reaction is the set of elementary (simple) stages that make up a given reaction. The reaction mechanism most often includes the following stages: activation of the reagent with the formation of an electrophile, nucleophile or free radical. To activate a reagent, a catalyst is usually needed. In the second stage, the activated reagent interacts with the substrate. In this case, intermediate particles (intermediates) are formed. The latter include -complexes, -complexes (carbocations), carbanions, and new free radicals. At the final stage, the addition or elimination of a particle to (from) the intermediate formed in the second stage takes place with the formation of the final reaction product. If a reagent generates a nucleophile upon activation, then these are nucleophilic reactions. They are marked with the letter N - (in the index). In the case where the reagent generates an electrophile, the reactions are classified as electrophilic (E). The same can be said about free radical reactions (R).
Nucleophiles are reagents that have a negative charge or an atom enriched in electron density: 1) anions: OH -, CN -, RO -, RS -, Hal - and other anions; 2) neutral molecules with lone pairs of electrons: NH 3, NH 2 R, H 2 O, ROH and others; 3) molecules with excess electron density (having - bonds). Electrophiles are reagents that have a positive charge or an atom depleted in electron density: 1) cations: H + (proton), HSO 3 + (hydrogen sulfonium ion), NO 2 + (nitronium ion), NO (nitrosonium ion) and other cations; 2) neutral molecules with a vacant orbital: AlCl 3, FeBr 3, SnCl 4, BF 4 (Lewis acids), SO 3; 3) molecules with depleted electron density on the atom. 46
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Chemistry- the science of the structure, properties of substances, their transformations and accompanying phenomena.
Tasks:
1. Study of the structure of matter, development of the theory of the structure and properties of molecules and materials. It is important to establish a connection between the structure and various properties of substances and, on this basis, to construct theories of the reactivity of a substance, the kinetics and mechanism of chemical reactions and catalytic phenomena.
2. Implementation of targeted synthesis of new substances with specified properties. Here it is also important to find new reactions and catalysts for more efficient synthesis of already known and industrially important compounds.
3. The traditional task of chemistry has acquired special significance. It is associated both with an increase in the number of chemical objects and properties being studied, and with the need to determine and reduce the consequences of human impact on nature.
Chemistry is a general theoretical discipline. It is designed to give students a modern scientific understanding of matter as one of the types of moving matter, about the ways, mechanisms and methods of converting some substances into others. Knowledge of basic chemical laws, mastery of chemical calculation techniques, understanding of the opportunities provided by chemistry with the help of other specialists working in its individual and narrow fields significantly speeds up obtaining the desired result in various fields of engineering and scientific activity.
The chemical industry is one of the most important industries in our country. Produced by her chemical compounds, various compositions and materials are used everywhere: in mechanical engineering, metallurgy, agriculture, construction, electrical and electronic industries, communications, transport, space technology, medicine, everyday life, etc. The main directions of development of the modern chemical industry are: the production of new compounds and materials and increasing the efficiency of existing production.
IN medical school students study general, bioorganic, biological chemistry, as well as clinical biochemistry. Students' knowledge of the complex of chemical sciences in their continuity and interconnection provides greater opportunity, greater scope for research and practical use of various phenomena, properties and patterns, and contributes to personal development.
Specific features studying chemical disciplines at a medical university are:
· interdependence between the goals of chemical and medical education;
· universality and fundamentality of these courses;
· the peculiarity of constructing their content depending on the nature and general goals of the doctor’s training and his specialization;
· the unity of the study of chemical objects at the micro and macro levels with the disclosure of different forms of their chemical organization as a single system and the different functions it exhibits (chemical, biological, biochemical, physiological, etc.) depending on their nature, environment and conditions;
· dependence on the connection of chemical knowledge and skills with reality and practice, including medical practice, in the system “society - nature - production - man”, due to the unlimited possibilities of chemistry in the creation of synthetic materials and their importance in medicine, the development of nanochemistry, as well as in solving environmental and many other global problems humanity.
1. The relationship between metabolic processes and energy in the body
Life processes on Earth are determined to a large extent by the accumulation of solar energy in nutrients - proteins, fats, carbohydrates and the subsequent transformations of these substances in living organisms with the release of energy. The understanding of the relationship between chemical transformations and energy processes in the body was realized especially clearly after works by A. Lavoisier (1743-1794) and P. Laplace (1749-1827). They showed by direct calorimetric measurements that the energy released in the process of life is determined by the oxidation of food by air oxygen inhaled by animals.
Metabolism and energy - a set of processes of transformation of substances and energy occurring in living organisms, and the exchange of substances and energy between the body and environment. Metabolism and energy is the basis of the life of organisms and is one of the most important specific signs living matter, distinguishing living from nonliving. In metabolism, or metabolism, ensured by the most complex regulation on different levels, many enzyme systems are involved. During the metabolic process, substances entering the body are converted into tissues’ own substances and into final products excreted from the body. During these transformations, energy is released and absorbed.
With the development in the XIX-XX centuries. thermodynamics - the science of the interconversion of heat and energy - it became possible to quantitatively calculate the transformation of energy in biochemical reactions and predict their direction.
Energy exchange can be carried out by transferring heat or doing work. However, living organisms are not in equilibrium with their environment and therefore can be called non-equilibrium open systems. However, when observed over a certain period of time, there are no visible changes in the chemical composition of the body. But this does not mean that the chemical substances that make up the body do not undergo any transformations. On the contrary, they are constantly and quite intensively renewed, as can be judged by the rate at which stable isotopes and radionuclides introduced into the cell as part of simpler precursor substances are incorporated into complex substances of the body.
There is one thing between metabolism and energy metabolism fundamental difference. The earth does not lose or gain any appreciable amount of matter. Matter in the biosphere is exchanged in a closed cycle, etc. used repeatedly. Energy exchange is carried out differently. It does not circulate in a closed cycle, but is partially dispersed into external space. Therefore, to maintain life on Earth, a constant flow of energy from the Sun is necessary. For 1 year in the process of photosynthesis on globe absorbed around 10 21 feces solar energy. Although it represents only 0.02% of the total energy of the Sun, it is immeasurably more than the energy used by all man-made machines. The amount of substance participating in the circulation is equally large.
2. Chemical thermodynamics as theoretical basis bioenergy. Subject and methods of chemical thermodynamics
Chemical thermodynamics studies the transitions of chemical energy into other forms - thermal, electrical, etc., establishes the quantitative laws of these transitions, as well as the direction and limits of the spontaneous occurrence of chemical reactions under given conditions.
The thermodynamic method is based on a number of strict concepts: “system”, “state of the system”, “internal energy of the system”, “state function of the system”.
Object studying in thermodynamics is a system
The same system can be in different states. Each state of the system is characterized by a certain set of values of thermodynamic parameters. Thermodynamic parameters include temperature, pressure, density, concentration, etc. A change in at least one thermodynamic parameter leads to a change in the state of the system as a whole. The thermodynamic state of a system is called equilibrium if it is characterized by constancy of thermodynamic parameters at all points of the system and does not change spontaneously (without the expenditure of work).
Chemical thermodynamics studies a system in two equilibrium states (final and initial) and on this basis determines the possibility (or impossibility) of a spontaneous process under given conditions in a specified direction.
Thermodynamics studies mutual transformations of various types of energy associated with the transfer of energy between bodies in the form of heat and work. Thermodynamics is based on two basic laws, called the first and second laws of thermodynamics. Subject of study in thermodynamics is energy and the laws of mutual transformations of energy forms during chemical reactions, processes of dissolution, evaporation, crystallization.
Chemical thermodynamics - section physical chemistry, studying the processes of interaction of substances using thermodynamic methods.
The main directions of chemical thermodynamics are:
Classical chemical thermodynamics, which studies thermodynamic equilibrium in general.
Thermochemistry, which studies the thermal effects accompanying chemical reactions.
The theory of solutions, which models the thermodynamic properties of a substance based on ideas about the molecular structure and data on intermolecular interactions.
Chemical thermodynamics is closely related to such branches of chemistry as analytical chemistry; electrochemistry; colloid chemistry; adsorption and chromatography.
The development of chemical thermodynamics proceeded simultaneously in two ways: thermochemical and thermodynamic.
The emergence of thermochemistry as an independent science should be considered the discovery by Herman Ivanovich Hess, a professor at St. Petersburg University, of the relationship between the thermal effects of chemical reactions -- Hess's laws.
3. Thermodynamic systems: isolated, closed, open, homogeneous, heterogeneous. The concept of phase.
System- this is a collection of interacting substances, mentally or actually isolated from the environment (test tube, autoclave).
Chemical thermodynamics considers transitions from one state to another, while some may change or remain constant. options:
· isobaric– at constant pressure;
· isochoric– at constant volume;
· isothermal– at constant temperature;
· isobaric - isothermal– at constant pressure and temperature, etc.
The thermodynamic properties of a system can be expressed using several system state functions, called characteristic functions: internal energyU , enthalpy H , entropy S , Gibbs energy G , Helmholtz energy F . Characteristic functions have one feature: they do not depend on the method (path) of achieving a given state of the system. Their value is determined by the parameters of the system (pressure, temperature, etc.) and depends on the amount or mass of the substance, so it is customary to refer them to one mole of the substance.
According to the method of transferring energy, matter and information between the system under consideration and the environment, thermodynamic systems are classified:
1. Closed (isolated) system- this is a system in which there is no exchange of energy, matter (including radiation), or information with external bodies.
2. Closed system- a system in which there is an exchange only with energy.
3. Adiabatically isolated system - This is a system in which there is an exchange of energy only in the form of heat.
4. Open system is a system that exchanges energy, matter, and information.
System classification:
1) if heat and mass transfer are possible: insulated, closed, open. An isolated system does not exchange either matter or energy with the environment. A closed system exchanges energy with the environment, but does not exchange matter. An open system exchanges both matter and energy with its environment. Concept isolated system used in physical chemistry as theoretical.
2) by internal structure and properties: homogeneous and heterogeneous. A system is called homogeneous, inside which there are no surfaces dividing the system into parts that differ in properties or chemical composition. Examples of homogeneous systems are aqueous solutions of acids, bases, and salts; gas mixtures; individual pure substances. Heterogeneous systems contain natural surfaces within them. Examples of heterogeneous systems are systems consisting of substances with different states of aggregation: metal and acid, gas and solid, two liquids insoluble in each other.
Phase- this is a homogeneous part of a heterogeneous system, having the same composition, physical and chemical properties, separated from other parts of the system by a surface, upon passing through which the properties of the system change abruptly. The phases are solid, liquid and gaseous. A homogeneous system always consists of one phase, a heterogeneous one - of several. Based on the number of phases, systems are classified into single-phase, two-phase, three-phase, etc.
5.The first law of thermodynamics. Internal energy. Isobaric and isochoric thermal effects .
First law of thermodynamics- one of the three basic laws of thermodynamics, represents the law of conservation of energy for thermodynamic systems.
The first law of thermodynamics was formulated in the middle of the 19th century as a result of the work of the German scientist J. R. Mayer, the English physicist J. P. Joule and the German physicist G. Helmholtz.
According to the first law of thermodynamics, thermodynamic system can commit work only due to its internal energy or any external energy sources .
The first law of thermodynamics is often formulated as the impossibility of the existence of a perpetual motion machine of the first kind, which would do work without drawing energy from any source. A process occurring at a constant temperature is called isothermal, at constant pressure - isobaric, at constant volume – isochoric. If during a process the system is isolated from the external environment in such a way that heat exchange with the environment is excluded, the process is called adiabatic.
Internal energy of the system. When a system transitions from one state to another, some of its properties change, in particular internal energy U.
The internal energy of a system is its total energy, which consists of the kinetic and potential energies of molecules, atoms, atomic nuclei and electrons. Internal energy includes the energy of translational, rotational and vibrational motions, as well as potential energy due to the forces of attraction and repulsion acting between molecules, atoms and intra-atomic particles. It does not include the potential energy of the system’s position in space and the kinetic energy of the system’s motion as a whole.
Internal energy is a thermodynamic function of the state of the system. This means that whenever the system finds itself in a given state, its internal energy takes on a certain value inherent in this state.
∆U = U 2 - U 1
where U 1 and U 2 are the internal energy of the system V final and initial states, respectively.
First law of thermodynamics. If the system exchanges thermal energy Q and mechanical energy(work) A, and at the same time transitions from state 1 to state 2, the amount of energy that is released or absorbed by the system of forms of heat Q or work A is equal to the total energy of the system during the transition from one state to another and is recorded.
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