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Representation of Molecules

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Representation of Molecules Organic Chemistry Pharmacy REPRESENTATION OF MOLECULES Lewis’ formulas All valence electrons (either involved in bond or unshared pairs) are represented with dots .. H + H : : H .. .. .. .. .. C..l .. H.. .. H:O:H H:N:H : H:C::C:H H:C:::C:H .. H:N..:H .. H:C..:H :C..l:C..:C..l H H : : . H C..l Kekulé’s formulas Also called valence-bond formulas Each electron pair shared in covalent bonds is indicated with a dash (unshared pairs can be omitted or represented with dots) + .. .. H or H-O-H H-O-H .. H-N-H or H-N-H H N H H H H .. :Cl: H H Cl H .. .. H C H C C H C C H Cl-C-Cl or : C..l-C-C..l : H H H Cl : Cl.. : Organic Chemistry Pharmacy H H H H C H H H C H H H H :O: H H Long and painstaking H C C C C C C C C C H representation with H H C H H H H H HH C H H complex molecules H H Condensed Structural Formulas Molecule is written as a sequence of C atoms. Each C is followed by the atoms bound to it; the brackets are used in ambiguous cases. The first C on the left can be preceded by the atoms linked to it. H H or H CCH H C C H CH3CH3 3 3 H H H F H F is monovalent, therefore it does not H C C C H CH3CHFCH3 generate ambiguity H H H H H H O is bivalent and it is clear that the H H C C C O H CH CH CH OH 3 2 2 on its right is bound to it H H H Organic Chemistry Pharmacy H H H Bracket helps to avoid H C C C H CH3CH(OH)CH3 missunderstanding H OH H Equal groups linked to the same C are written only once, collected in brackets, with an index that tells how many equal groups are related to that C H H H H C H H H C H H H H : O: H H H C C C C C C C C C H (CH3)3CCH2CH2CH(CH3)CH2CH(OH)CH(CH3)2 H H C H H H H H HH C H H H H multiple bonds (double and triple) MUST always be written H H or H C=CH H C C H CH2=CH2 2 2 H C C H HC CH CAUTION!!!! Notice the difference between the following condensed formulas H H H H .. CH C(O)CH CH OCH = H C O C H = H C C C H 3 3 3 3 .. CH3COCH3 H H H :O: H Organic Chemistry Pharmacy Semi-condensed Formulas When condensed formulas are not sufficiently clear, "semicondensed" formulas can be used. Bonds among C atoms are evidenced with a dash. Examples (CH3)3CCH2CH2CH(CH3)CH2CH(OH)CH(CH3)2 condensed formula CH3 OH CH3 C CH2 CH2 CH CH2 CH CH CH3 semi-condensd formula CH CH CH3 3 3 Multiple bonds (double and triple) must ALWAYS be written Bond-line formulas This representation is very simple, but rules must be well understood, in order to write and read the molecules correctly ● C-C bonds are indicated with a line ● The H atoms linked to C atoms are omitted (this means that those bound to atoms other than C must be written). ● C bonds with atoms other than H are indicated (with lines). Organic Chemistry Pharmacy H F H F F H C C C H CH3CHFCH3 CH3 CH CH3 H H H H H H H C C C O H OH CH3CH2CH2OH CH3-CH2-CH2-OH H H H H H H H H H H H C C C C C C C H CH3CH2CH2CH2CH2CH2CH3 H H H H H H H CH3-CH2-CH2-CH2-CH2-CH2-CH3 Organic Chemistry Pharmacy H H H OH OH H C C C H CH3CH(OH)CH3 CH3 CH CH3 H OH H H H C H H H H H H H H C C C C C C C H CH3CH2CH2CH(CH3)CH2CH2CH3 H H H H H H H CH3 CH3 CH2 CH2 CH CH2 CH2 CH3 Organic Chemistry Pharmacy H H C H H H H H H H CH3CH2CH2C(CH3)2CH2CH2CH3 H C C C C C C C H CH3 H H H H H H CH3 CH2 CH2 C CH2 CH2 CH3 H C H CH3 H H H C H H H H CH3 (CH ) CCH CH H C C C C H 3 3 2 3 CH3 C CH2 CH3 CH3 HH C HH H H (CH3)3CCH2CH2CH(CH3)CH2CH(OH)CH(CH3)2 OH Organic Chemistry Pharmacy CH (CH ) CH 3 2 5 3 CH3-CH2-CH2-CH2-CH2-CH2-CH3 condensed formula semi-condensed formula bond-line formula CH3 CH CH3CH2C(CH3)2CH(CH3)CH2CH3 CH3 CH2 C CH CH2 3 CH3 CH3 condensed formula semi-condensed formula bond-line formula Bond-line formulas are particularly useful when rings must be represented. H H H H C CH C C 2 H H H2C CH2 CH H C C H H2C 2 CH H C H 2 Bond-line Formula H H Semi-condensed Formula Kekulé’s Formula CAUTION! Condensed formulas CANNOT BE USED to write rings. (CH2)6 Organic Chemistry Pharmacy Examples H H H H H C C C C H CH3CHClCH2CH3 H Cl H H H C CH CH CH 3 2 3 Cl Cl H H H H H C C C C H H H H CH CH(CH )CH CH H C H 3 3 2 3 H H3C CH CH2 CH3 CH3 Organic Chemistry Pharmacy H H CH CH OH H C C O H CH3CH2OH 3 2 H H OH H H H H H H H C C H OH H H O H H H H .. .. .. .. H H H H H H .. H : C : C : C : O : H .. .. .. .. H C C C O H or H C C C O.. H H H H H H H H H H Kekulé CH CH CH OH CH3CH2CH2OH 3 2 2 OH Organic Chemistry Pharmacy TRIDIMENSIONAL REPRESENTATION To represent a molecule showing the three-dimensional situation of atoms, the following rules apply: • The bonds that join atoms belonging to the same plane (writing plane) are indicated with a line • Bonds that come out of the writing plane, toward the viewer, are indicated with solid wedges. The atom at the wide end of the solid edge is in ftont of the writing plane. • Bonds that pointing back the writing plane are represented with a broken wedge For a given molecule, which atoms belong to the writing plane depends on how the molecule is oriented in space (remembering that a plan passes through three points). H H H C C H H C H H H H H H H Organic Chemistry Pharmacy CONVENTIONS FOR WRITING REACTIONS A B An arrow indicates an irreversible transformation. The tip of the arrow is directed towards the product of the reaction. A B An equilibrium reaction is indicated by a double arrow. If the balance is strongly displaced in one A B direction, the corresponding arrow is longer than the other Electron movements are represented by curved arrows, with the tip in the direction of electron movement. An arrow with a normal tip is used to move an electron pair + - - + A: + B A-B A + :B A-B To indicate the movement of a single electron, an half-tip arrow is used A. + . B A-B Organic Chemistry Pharmacy The molecular formula is not sufficient to completely characterize a compound it is a simple formula but with this molecular formula there C2H6O are two compounds, with different physical and chemical properties C H O H H 2 6 H H H C C O H H C O C H H H H H ethanol dimethyl ether Ethanol and dimethyl ether are structural isomers Organic Chemistry Pharmacy Structural isomers: compounds that have the same molecular formula, but different arrangement of atoms The problem grows rapidly as the number of C atoms increases with 9 atoms of C and only H as other 35 structural isomers element (C9H20) with 30 C atoms (C H ) 30 62 4 111 846 763 structural isomers It is necessary a system of identification of organic compounds that allows, given a name, to write the corresponding formula and vice versa, univocally IUPAC Nomenclature Organic Chemistry Pharmacy ORGANIC COMPOUNDS CLASSIFICATION ORGANIC COMPOUNDS ALIPHATICS CYCLICS HOMOCYCLICS HETEROCYCLICS ALICYCLICS AROMATICS Compounds made up with C and H only are called HYDROCARBONS Organic Chemistry Pharmacy 3 ALKANES Hydrocarbons in which all C atoms have sp hybridizatation general formula CnH2n+2 The foundations of the IUPAC system are the names of the continuous-chain alkanes RULE Alkane’s name is made by adding the ending -ane to a root, which indicates how many are the carbon atoms in the molecule. For alkanes with numbers of C atoms from 1 to 4, “traditional trivial" roots are used. For alkanes with higher numbers of C atoms, the names come from Latin or Greek numbers. H H H H C CH4 methane C C H H H 2 6 H C H H H ethane H H H H H C H H H C H C 3 8 H C C H C C 4 10 C C H propane H butane H H H H H H H Organic Chemistry Pharmacy H H H H C H C H C H C C C 5 12 pentane H H H H H H root "met-" 1 C root “prop-" 3 C root "eth-" 2 C root “but-" 4 C number Name Condensed Formula Bond-line Formula of C METHANE 1 CH4 2 ETHANE CH3CH3 3 PROPANE CH3CH2CH3 4 BUTANE CH3(CH2)2CH3 5 PENTANE CH3(CH2)3CH3 Organic Chemistry Pharmacy Names of the higher members of this series consist of a numerical term, followed by "-ane" with elision of terminal "a" from the numerical term.
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