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General aspects of chemical structure and reactivity of organic compounds, слайд №1

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Information Discipline: Bioorganic chemistry Final assessment: test Lecturer: PhD, docent Irina Vyacheslavovna Tarasova (department of organic chemistry) e-mail: tarasova_iv_mrsu@mail.ru web:

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General aspects of chemical structure and reactivity of organic compounds Lecture №1

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Chemical bonding and mutual atoms’ influence in organic molecules

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Electronic configuration of carbon atom in organic molecules

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Atomic orbitals

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Hybridization of orbitals Hybridization is the process of atomic orbitals alignment in form and energy.

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sp3-Hybridization

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sp2-Hybridization

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sp-Hybridization

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Chemical bonds in organic compounds Covalent bonds  - bond π - bond

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Conjugation Conjugation is the formation of delocalized electronic cloud in molecule as a result of p-orbitals overlap. π,π-Conjugation is the type of orbital interaction when the p-orbitals are delocalized over the entire π system. p,π-Conjugation is the overlap of a p-orbital on an atom adjacent to a double bond.

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π,π-Conjugation

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р,π-Conjugation

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Aromaticity

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Inductive effect Inductive effect (I) is the shifting of electrons in a -bond in response to electronegativity of nearby atoms. present in any polar molecule; decrease and fade after 2-3 bonds. СН3СН2Сl CH3CH2MgCl

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Mesomeric effect Mesomeric effect (М) is the shifting of electron density caused by a substituent in conjugation system through p-orbital overlap. present only in conjugation systems; distribute throughout the conjugated system.

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Electron donors (D) and electron withdrawers (W)

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Spatial structure of organic compounds

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Isomerism of organic compounds Isomers are the compounds which have the same composition but different sequence of atoms or their location in space, therefore have different properties.

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Stereoisomerism Stereoisomers are the compounds that have the same order of atoms attachment but differ only in the arrangement of their atoms or groups in space.

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Configuration is the arrangement of atoms and groups in space without regard to arrangements that differ only due to rotation about one or more single bonds. Configuration is the arrangement of atoms and groups in space without regard to arrangements that differ only due to rotation about one or more single bonds. Carbon atom configurations

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Chirality Chirality is the property of the object to be nonsuperposable with its mirror image. The simple example of chirality is presence the chiral center in molecule. It may be carbon atom with four different atoms or groups - asymmetric carbon atom (*С). Such molecules have optical activity – they rotate the plane of polarized light. Types of isomers: enantiomers diastereomers

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Enantiomers Enantiomers are the stereoisomers, the molecules of which relate to each other as an object and its nonsuperposable mirror image. enantiomers have the same physical and chemical properties; enantiomers have optical activity.

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Fischer projections

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D,L-Nomenclature Glyceraldehyde is the configurational standard. Fischer projection writes in “standard view”. We can do the interchanges or rotate the projection through 180o to achieve the “standard view”. If the group lies on the left side we name it as levorotatory enantiomer (L). If the group lies on the right side we name it as dextrorotatory enantiomer (D).

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R,S-Nomenclature The least substituent near the chiral center must lie at the bottom of the Fischer projection. Atoms attached directly to the chiral center are first arranged according to decreased atomic number. If the remaining three groups are arranged clockwise, the configuration is symbolized by R. If they form a counterclockwise array, the configuration is symbolized by S.

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Diastereomers Diastereomers are the stereoisomers that are not mirror images of one another. they have different physical and chemical properties.

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meso Compounds

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Acidity and basicity of organic compounds

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Acidity and basicity are the key notions, determining many fundamental physico-chemical and biochemical properties of organic compounds. Acidity and basicity are the key notions, determining many fundamental physico-chemical and biochemical properties of organic compounds.

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Brønstedt-Lowry concept

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Brønstedt acids Acidic site is a part of molecule that involves hydrogen together with an atom attached to it.

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Brønstedt bases Basic site is a heteroatom with a lone-pair of electrons or a -bond which are capable to accept a proton.

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Comparison the acidity The more stable is an anion, the stronger is an acid! The factors which influence the stability of conjugate bases: electronegativity and polarizability of the atom in the acidic site; delocalization of a negative charge due to the effect of substituens in a molecule; solvation effects.

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The influence of atom nature in acidic site СН NH ОН SH СН NH ОН SH

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The influence of substituents effects inductive effect mesomeric effect

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Comparison the basicity The more stable is an cation and the more available a lone-pair of electrons, the stronger is an base! The factors which influence the stability of conjugate acids is the same but they act in the opposite direction: .