Analysis Spectra AbioFunctionalGrpsVollIRspect

7/27/2019 Analysis Spectra AbioFunctionalGrpsVollIRspect

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Functional groups.In organic chemistry, functional groups are specific groups of atoms withinmolecules that are responsible for the characteristic chemical reactions of

those molecules. The same functional group will undergo the same orsimilar chemical reaction(s) regardless of the size of the molecule it is apart of. If we replaced the H-atoms in ethene with CH3 groups, that wouldbe a methyl group.

Functional groups are attached to the carbon backbone of organicmolecules. They determine the characteristics and chemical reactivity ofmolecules. Functional groups are far less stable than the carbon backboneand are likely to participate in chemical reactions. Six common biologicalfunctional groups are

hydrogen, hydroxyl, carboxyl, carbonyl, amino, phosphate, and methyl.

The following is

1. A list of common functional groups. In the formulas, the symbols R and R'usually denotes an attached hydrogen, or a hydrocarbon side chain of anylength, but may sometimes refer to any group of atoms.

The first carbon after the carbon that attaches to the functional group iscalled the alpha carbon.

Combining the names of functional groups with the names of the parentalkanes generates a powerful systematic nomenclature for naming organic

compounds. Unfortunately not all listings of functional groups agree, and the

British system avoids functional groups altogether, maintaining that it is acategorization that obscures what is really going on in organic chemistry.

The non-hydrogen atoms of functional groups are always associated with eachother and with the rest of the molecule by covalent bonds. When the group ofatoms is associated with the rest of the molecule primarily by ionic forces, thegroup is referred to more properly as a polyatomic ion or complex ion. And allof these are called radicals, by a meaning of the term radical that predates thefree radical.

Notice that some important classes of molecules, like cyclic aromatics(conjugated hydrocarbon rings) and heterocycles (related) are not listed.

2. A (more useful) table of the main functional groups that are important inelementary biochemistry (but several are omitted).

3. Finally some infrared spectra to show how these types of groups can actuallybe identified in the spectra of planets and other astronomical objects.


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Chemical

classGroup Formula

Structural

FormulaPrefix Suffix

Acyl halide Haloformyl RCOX haloformyl-

-oyl

Alcohol Hydroxyl ROH hydroxy-

-ol

Aldehyde Aldehyde RCHO oxo-

-al

Alkane* Alkyl RH alkyl-

-ane

Alkene* Alkenyl R2C=CR2 alkenyl-

-ene

Alkyne* Alkynyl RCCR' alkynyl--yne

AmideCarboxami

deRCONR2

carboxamido

--amide

Primary

amineRNH2 amino-

-amine

Secondaryamine

R2NH amino- -amine

Tertiary

amineR3N amino-

-amineAmines

4

ammonium

ion

R4N+ ammonio-

-ammonium


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Azo

compound

Azo

(Diimide)RN2R' azo-

-diazene

Toluenederivative

BenzylRCH2C6H5RBn

benzyl- 1-(substituent)toluene

CarbonateCarbonateester

ROCOOR alkyl carbonate

CarboxylateCarboxylate

RCOO carboxy- -oate

Carboxylic

acidCarboxyl RCOOH carboxy-

-oic acid

Cyanate ROCN cyanato- alkyl cyanate

CyanatesThiocyanate

RSCN thiocyanato- alkyl thiocyanate

Ether Ether ROR' alkoxy-alkyl alkyl ether

Ester Ester RCOOR'

alkyl alkanoate

Haloalkane Halo RX halo-

alkyl halide

Hydroperoxide

Hydroperoxy ROOH hydroperoxy-

alkylhydroperoxide

IminePrimaryketimine

RC(=NH)R'

imino- -imine


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Secondaryketimine

RC(=NR)R

'imino- -imine

Primaryaldimine

RC(=NH)H imino- -imine

Secondary

aldimine

RC(=NR')

Himino- -imine

Isocyanide Isocyanide RNC isocyano- alkyl isocyanide

Isocyanate RNCO isocyanato-

alkyl isocyanate

Isocyanates

Isothiocyanate

RNCSisothiocyanato-

alkyl isothiocyanate

Ketone Ketone RCOR' keto-, oxo-

-one

Nitrate Nitrate RONO2nitrooxy-,nitroxy-

alkyl nitrate

Nitrile Nitrile RCN cyano-

alkanenitrile

alkyl cyanide

Nitrite Nitrite RONO nitrosooxy- alkyl nitrite

Nitrocompound

Nitro RNO2 nitro-


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Nitrosocompound

Nitroso RNO nitroso-

Peroxide Peroxy ROOR peroxy- alkyl peroxide

Benzenederivative

Phenyl RC6H5 phenyl- -benzene

Phosphine Phosphino R3P phosphino- -phosphane

Phosphodies

terPhosphate

HOPO

(OR)2

phosphoricacid

di(substituen

t) ester

di(substituent)

hydrogenphosphateDNA

Phosphonic

acidPhosphono

RP(=O)

(OH)2phosphono-

substituent

phosphonic acid

Phosphate PhosphateROP(=O)

(OH)2phospho-

Pyridinederivative

Pyridyl RC5H4N

4-pyridyl (pyrid

in-4-yl)

3-pyridyl (pyrid

in-3-yl)

2-pyridyl (pyrid

in-2-yl)

-pyridine

Sulfide RSR'di(substituent)sulfide

Sulfone Sulfonyl RSO2R' sulfonyl-

di(substituent)

sulfone

Sulfonic acid Sulfo RSO3H sulfo-substituent

sulfonic acid


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Sulfoxide Sulfinyl RSOR' sulfinyl-

di(substituent)sulfoxide

Thiol Sulfhydryl RSHmercapto-,sulfanyl-

-thiol


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PAH features


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Pre-Planetary Nebula

Titan


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Titan


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Tholins


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Vanilla


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Analysis Spectra AbioFunctionalGrpsVollIRspect