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Showing metabocard for Nonane (HMDB0029595)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 17:31:20 UTC
Update Date2022-03-07 02:52:13 UTC
HMDB IDHMDB0029595
Secondary Accession Numbers
  • HMDB29595
Metabolite Identification
Common NameNonane
DescriptionNonane, also known as N-nonane or CH3-[CH2]7-CH3, belongs to the class of organic compounds known as alkanes. These are acyclic branched or unbranched hydrocarbons having the general formula CnH2n+2 , and therefore consisting entirely of hydrogen atoms and saturated carbon atoms. Thus, nonane is considered to be a hydrocarbon. Nonane is an alkane and gasoline tasting compound. Nonane is found, on average, in the highest concentration within limes (Citrus aurantiifolia) and common oreganos (Origanum vulgare). Nonane has also been detected, but not quantified in, several different foods, such as garden tomato (var.), gingers (Zingiber officinale), pepper (spice), cauliflowers (Brassica oleracea var. botrytis), and celeriacs (Apium graveolens var. rapaceum). This could make nonane a potential biomarker for the consumption of these foods. Nonane is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Nonane.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0029595 (Nonane)

  Mrv1652303202018592D          

  9  8  0  0  0  0            999 V2000
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
Download

3D MOL for HMDB0029595 (Nonane)

HMDB0029595
     RDKit          3D
Nonane
 29 28  0  0  0  0  0  0  0  0999 V2000
    3.5879    1.1662    0.1973 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2891   -0.0610   -0.5833 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6896   -1.1904    0.1658 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3901   -0.9384    0.8255 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2882   -0.5376   -0.1334 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0109   -0.2954    0.6055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1157    0.1032   -0.3288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4065    0.3453    0.3935 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4556    0.7406   -0.6293 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4237    1.0204    0.9114 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9243    1.9516   -0.5128 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7341    1.5905    0.7482 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2414   -0.4129   -1.0344 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6270    0.1921   -1.4435 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5691   -2.0437   -0.5338 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4124   -1.5271    0.9359 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4165   -0.2142    1.6590 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0513   -1.9018    1.2824 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5384    0.4218   -0.6432 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0888   -1.2997   -0.8956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8422    0.5669    1.2950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3070   -1.1539    1.2411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7939    1.0430   -0.8411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2343   -0.6851   -1.0800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7091   -0.6257    0.8673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3271    1.1028    1.1907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4712    0.4149   -0.3364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4502    1.8636   -0.6556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1481    0.3641   -1.6158 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
  9 29  1  0
M  END
Download

3D SDF for HMDB0029595 (Nonane)

  Mrv1652303202018592D          

  9  8  0  0  0  0            999 V2000
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0029595

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C9H20/c1-3-5-7-9-8-6-4-2/h3-9H2,1-2H3

> <INCHI_KEY>
BKIMMITUMNQMOS-UHFFFAOYSA-N

> <FORMULA>
C9H20

> <MOLECULAR_WEIGHT>
128.2551

> <EXACT_MASS>
128.15650064

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
18.503349623160965

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
nonane

> <ALOGPS_LOGP>
5.24

> <JCHEM_LOGP>
4.4648438876666665

> <ALOGPS_LOGS>
-5.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
43.2112

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.17e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
nonane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0029595 (Nonane)

HMDB0029595
     RDKit          3D
Nonane
 29 28  0  0  0  0  0  0  0  0999 V2000
    3.5879    1.1662    0.1973 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2891   -0.0610   -0.5833 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6896   -1.1904    0.1658 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3901   -0.9384    0.8255 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2882   -0.5376   -0.1334 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0109   -0.2954    0.6055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1157    0.1032   -0.3288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4065    0.3453    0.3935 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4556    0.7406   -0.6293 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4237    1.0204    0.9114 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9243    1.9516   -0.5128 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7341    1.5905    0.7482 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2414   -0.4129   -1.0344 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6270    0.1921   -1.4435 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5691   -2.0437   -0.5338 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4124   -1.5271    0.9359 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4165   -0.2142    1.6590 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0513   -1.9018    1.2824 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5384    0.4218   -0.6432 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0888   -1.2997   -0.8956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8422    0.5669    1.2950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3070   -1.1539    1.2411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7939    1.0430   -0.8411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2343   -0.6851   -1.0800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7091   -0.6257    0.8673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3271    1.1028    1.1907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4712    0.4149   -0.3364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4502    1.8636   -0.6556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1481    0.3641   -1.6158 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
  9 29  1  0
M  END
Download

PDB for HMDB0029595 (Nonane)

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0       5.596   4.771   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      16.266   4.771   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0029595 (Nonane)

COMPND    HMDB0029595
HETATM    1  C1  UNL     1       3.588   1.166   0.197  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.289  -0.061  -0.583  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.690  -1.190   0.166  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.390  -0.938   0.826  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.288  -0.538  -0.133  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.011  -0.295   0.605  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.116   0.103  -0.329  1.00  0.00           C  
HETATM    8  C8  UNL     1      -3.407   0.345   0.394  1.00  0.00           C  
HETATM    9  C9  UNL     1      -4.456   0.741  -0.629  1.00  0.00           C  
HETATM   10  H1  UNL     1       4.424   1.020   0.911  1.00  0.00           H  
HETATM   11  H2  UNL     1       3.924   1.952  -0.513  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.734   1.590   0.748  1.00  0.00           H  
HETATM   13  H4  UNL     1       4.241  -0.413  -1.034  1.00  0.00           H  
HETATM   14  H5  UNL     1       2.627   0.192  -1.444  1.00  0.00           H  
HETATM   15  H6  UNL     1       2.569  -2.044  -0.534  1.00  0.00           H  
HETATM   16  H7  UNL     1       3.412  -1.527   0.936  1.00  0.00           H  
HETATM   17  H8  UNL     1       1.416  -0.214   1.659  1.00  0.00           H  
HETATM   18  H9  UNL     1       1.051  -1.902   1.282  1.00  0.00           H  
HETATM   19  H10 UNL     1       0.538   0.422  -0.643  1.00  0.00           H  
HETATM   20  H11 UNL     1       0.089  -1.300  -0.896  1.00  0.00           H  
HETATM   21  H12 UNL     1      -0.842   0.567   1.295  1.00  0.00           H  
HETATM   22  H13 UNL     1      -1.307  -1.154   1.241  1.00  0.00           H  
HETATM   23  H14 UNL     1      -1.794   1.043  -0.841  1.00  0.00           H  
HETATM   24  H15 UNL     1      -2.234  -0.685  -1.080  1.00  0.00           H  
HETATM   25  H16 UNL     1      -3.709  -0.626   0.867  1.00  0.00           H  
HETATM   26  H17 UNL     1      -3.327   1.103   1.191  1.00  0.00           H  
HETATM   27  H18 UNL     1      -5.471   0.415  -0.336  1.00  0.00           H  
HETATM   28  H19 UNL     1      -4.450   1.864  -0.656  1.00  0.00           H  
HETATM   29  H20 UNL     1      -4.148   0.364  -1.616  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3   13   14
CONECT    3    4   15   16
CONECT    4    5   17   18
CONECT    5    6   19   20
CONECT    6    7   21   22
CONECT    7    8   23   24
CONECT    8    9   25   26
CONECT    9   27   28   29
END
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SMILES for HMDB0029595 (Nonane)

CCCCCCCCC
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INCHI for HMDB0029595 (Nonane)

InChI=1S/C9H20/c1-3-5-7-9-8-6-4-2/h3-9H2,1-2H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
CH3-[CH2]7-CH3ChEBI
N-NonaneChEBI
NonanChEBI
NonaneMeSH
Chemical FormulaC9H20
Average Molecular Weight128.2551
Monoisotopic Molecular Weight128.15650064
IUPAC Namenonane
Traditional Namenonane
CAS Registry Number111-84-2
SMILES
CCCCCCCCC
InChI Identifier
InChI=1S/C9H20/c1-3-5-7-9-8-6-4-2/h3-9H2,1-2H3
InChI KeyBKIMMITUMNQMOS-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkanes. These are acyclic branched or unbranched hydrocarbons having the general formula CnH2n+2 , and therefore consisting entirely of hydrogen atoms and saturated carbon atoms.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassSaturated hydrocarbons
Sub ClassAlkanes
Direct ParentAlkanes
Alternative ParentsNot Available
Substituents
  • Acyclic alkane
  • Alkane
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-51 °CNot Available
Boiling Point149.00 to 152.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility0.00022 mg/mL at 25 °CNot Available
LogP5.65Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Membrane
Biospecimen Locations
  • Breath
  • Feces
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BreathDetected but not QuantifiedNot QuantifiedChildren (1-13 years old)Not SpecifiedAllergic asthma details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Nonalcoholic fatty liver disease (NAFLD)		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothCrohns disease details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothUlcerative colitis details
Associated Disorders and Diseases
Disease References
Asthma
  1. Caldeira M, Perestrelo R, Barros AS, Bilelo MJ, Morete A, Camara JS, Rocha SM: Allergic asthma exhaled breath metabolome: a challenge for comprehensive two-dimensional gas chromatography. J Chromatogr A. 2012 Sep 7;1254:87-97. doi: 10.1016/j.chroma.2012.07.023. Epub 2012 Jul 16. [PubMed:22835687 ]
Nonalcoholic fatty liver disease
  1. Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P, Bailey J, Myers RP, Rioux KP: Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin Gastroenterol Hepatol. 2013 Jul;11(7):868-75.e1-3. doi: 10.1016/j.cgh.2013.02.015. Epub 2013 Feb 27. [PubMed:23454028 ]
Crohn's disease
  1. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Ulcerative colitis
  1. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB000757
KNApSAcK IDC00034882
Chemspider ID7849
KEGG Compound IDC02445
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNonane
METLIN IDNot Available
PubChem Compound8141
PDB IDDD9
ChEBI ID32892
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .