Organic compounds are chemical compounds that contain carbon-hydrogen bonds Organic chemistry studies properties, reactions, and syntheses of organic
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CLASSIFICATION, NOMENCLATURE, ISOMERISM OF
ORGANIC COMPOUNDS. NATURE OF CHEMICAL BONDS.
ASSOC.PROF.BILETSM.V.
Ministry of Public Health of Ukraine
Ukrainian Medical StomatologicalAcademy
Department of biological and bioorganic chemistryLecture plan
Classification of bioorganic compounds.
Nomenclature of bioorganic compounds.
Isomerism of bioorganic compounds.
Electron structure and valency states of the carbon atom.Interaction of atoms in bioorganic compounds
Bioorganic compounds
Organic compoundsare chemical compoundsthat containcarbon-hydrogenbonds. Organic chemistry studies properties, reactions, and syntheses of organic compounds. -Examples of organiccompounds: -methane (CH4) -acetylene (C2H2) -ethanol (C2H5OH) -carbon tetrachloride (CCl4) -urea [CO(NH2)2] -Examples of inorganiccompounds: -water(H2O) -carbondioxide(CO2) -bimolecularoxygen(O2) -sodiumchloride(NaCl)Classification of bioorganic compounds.
The functional groupsThe functional groupsare specificsubstituentsormoietieswithinmoleculesthat may be responsible for the characteristicchemical reactionsof those molecules.Nomenclature of bioorganic compounds.
3typesofnomenclatureareusedfornaming
organiccompounds:trivial,rationalandNomenclature of bioorganic compounds.
smell(aromaticcompounds),etc. organiccompounds(saturatedhydrocarbons, ethylenes, acetylenes, alcohols, aldehydes, ketones, acids, etc.). Thesenamescontainthenameof themaintypeandthenamesof thesubstituents. Forexample: methylalcohol, trimethylaceticaldehyde, dimethylketone, chloroaceticacid.Nomenclature of bioorganic compounds.
Systematicnomenclature-IUPAC nomenclature(IUPAC)
InternationalUnionof PureandAppliedChemistry
A chemical name has three parts in the IUPAC system:Prefix-Parent-Suffix
Where are the substituents?Whatfamily?
Howmanycarbons?
IUPAC rules
Identify the longest carbon chain. This chain is called the parent chain. Identify all of the substituents (groups appending from the parent chain).Number the carbons of the parent chain from the end that gives the substituents the lowest numbers. When compairinga series of numbers, the series that is the "lowest" is the one which contains the lowest number at the occasion of the first difference.Iftwo or more side chains are in equivalent positions, assign the lowest number to the one which will come first in the name.
If the same substituent occurs more than once, the location of each point on which the substituent occurs is given. In addition,the number of times the substituent group occurs is indicated by a prefix (di, tri, tetra, etc.).
If there are two or more different substituents they are listed in alphabetical order using the base name (ignore the prefixes).The only prefix whichisused when putting the substituents in alphabetical order isisoas in isopropyl or isobutyl. The prefixes sec-and tert-are not used in determining alphabetical order except when compared with each other.
If chains of equal length are competing for selection as the parent chain, then the choice goes in series to:a) the chain which has the greatest number of side chains.b) the chain whose substituents have the lowest-numbers.c) the chain having the greatest number of carbon atoms in the smaller side chain.d)the chain having the least branched side chains.
A cyclic (ring) hydrocarbon is designated by the prefixcyclo-which appears directly in front of the base name.
In summary, the name of the compound is written out with the substituents in alphabetical order followed by the base name (derived from the number of carbons in the parent chain). Commas are used between numbers and dashes are used between letters and numbers. There arenospaces in the name.
Isomerism of bioorganic compounds.
Isomerismis the phenomenon in which more than one compounds have the same chemical formula but different chemical structures. Chemical compounds that have identical chemical formulae but differ in properties and the arrangement of atoms in the molecule are called isomers. https://en.wikipedia.org/wiki/IsomerStructural isomers
ChainIsomersinPentane
Pentane, C5H12, hasthreechainisomers.
Structural isomers
PositionalIsomersof bromopropane
Functional group isomers C3H6O
A molecularformulaC3H6OC3H6Ocouldbeeither
propanal(analdehyde) orpropanone(a ketone).Stereoisomers
Enantiomers. Diastereomers.
Enantiomersare two molecules that arenonsuperimposablemirror images: Diastereomersare stereoisomers that are not related as object and mirror image and are notenantiomers.Chyralcarbon. Chirality
Enantiomers contain chiral carbon atom.
Anasymmetric carbon atom(chiral carbon) is acarbonatomthat is attached to four different types of atoms or groups of atoms Inchemistry, a molecule or ion is calledchiral(/ޖܼ imageby any combination ofrotationsandtranslations. This geometric property is calledchirality. Electron structure and valency states of the carbon atom. Carbon is an element of second period of periodic table. Its atomic number is 6 and mass number is 12. It is represented as126C. The ground and excited states of carbon electronic configuration are:Types of electron orbitals
theatom'snucleus. particularmathematicalformoftheorbital.The covalent bonds. Ȉand ʌbonds.
Sigma and pi bondsare types of covalentbondsthat differ in the overlapping of atomic orbitals. Covalentbondsare formed by the overlapping of atomic orbitals.Sigma bondsare a result of the head-to-head overlapping of atomic orbitals whereaspi bondsare formed by the lateral overlap of two atomic orbitals.Hybridization
Hybridization is a theory that is used to explain certain molecular geometries that would have not been possible otherwise.
Thesp3hybridization -thesandporbitals of the excited state carbon are hybridized to formfour identicalin size, shape and energy orbitals.The foursp3-hybridized orbitals arrange in a tetrahedral geometry and make bonds by overlapping with the s orbitals of four hydrogens: This explains the symmetrical geometry of methane (CH4) where all the bonds have the same length and bond angle.All four C H bonds in methane are single bonds that are formed byhead-on (or end on)overlapping ofsp3orbitals of the carbon and s orbital of each hydrogen.
The bonds that form by the head-on overlap of orbitals are calledıbonds because the electron density is concentrated on the axis connecting the C and H atoms.
Hybridization
Thesp2hybridization occurs when the s orbital is mixed with only two p orbitals as opposed to the three p
orbitals in thesp3hybridization. So, three orbitals are mixed, and the outcome is three hybrid orbitals
which are calledsp2hybrid orbitals.Hybridization
Thesphybridization
In sphybridization, the s orbital of the excited state carbon is mixed with only one out of the three 2p orbitals. It is calledsphybridization because two orbitals (one s and one p) are mixed:
Interaction of atoms in bioorganic compounds
ofelectrons(orelectron density).An atom's electronegativity is affected by both itsatomic numberand the distance at which itsvalence electronsreside from the charged nucleus. The higher the associated electronegativity, the more an atom or a substituent group attracts electrons. On the most basic level, electronegativity is determined by factors like thenuclear charge(the moreprotonsan atom has, the more "pull" it will have on electrons) and the number and location of other electrons in theatomic shells(the more electrons an atom has, the farther from thenucleusthe valence electrons will be, and as a result, the less positive charge they will experienceboth because of their increased distance from the nucleus and because the other electrons in the lower energy coreorbitalswill act toshieldthe valence electrons from the positively charged nucleus).Themesomericeffect
Themesomericeffectinchemistryis a property ofsubstituentsorfunctional groupsin achemical compound. It is defined as the polarity produced in the molecule by the interaction of twopi bondsor between a pi bond and lone pair of electrons present on an adjacenTheeffect is used in a qualitative way and describes the electron withdrawing or releasing properties of substituents based on relevantresonance structuresand is symbolized by the letterM. The mesomericeffect is negative (M) when the substituent is an electron-withdrawing group and the effect is positive (+M) when the substituent is an electron releasing group.
+M EFFECT ORDER: O> NH2> OR> ARYAN > NHCOR > OCOR > Ph> CH3> F > Cl> Br > I -M EFFECT ORDER: NO2> CN > --S(=O)2OH > CHO > C=O > COOCOR > COOR > COOH > CONH2> COO t atom.The inductive effect
In chemistry, the inductive effect is an effect regarding the transmission of unequal sharing of the bonding electron through a chain ofatomsin amolecule, leading to a permanentdipolein a bond.It is present in aı(sigma) bondas opposed toelectromericeffectwhich is present on aʌhalogen atoms in alkyl halideare electron withdrawing andalkyl groupsare electron donating. If the electronegative atom (missing an electron, thus having a positive charge) is then joined to a chain of atoms, usually carbon, the positive charge is relayed to the other atoms in the chain. This is the electron-withdrawing inductive effect, also known as the-Ieffect. In short, alkyl groups tend to donate electrons, leading to the+Ieffect. Its experimental basis is theionization constant.
1) Negative inductive effect (-I):
The electron withdrawing nature of groups or atoms is called as negative inductive effect. It is indicated by -I. Following are the examples of groups in the decreasing order of their -I effect:
NH3+> NO2> CN > SO3H > CHO > CO > COOH > COCl> CONH2> F > Cl> Br > I > OH > OR > NH2> C6H5> H2) Positive inductive effect (+I):
It refers to the electron releasing nature of the groups or atoms and is denoted by +I. Following are the examples of groups in the decreasing order of their +I effect.