The Dictionary of Marine Natural Products is a comprehensive database containing over 30,000 compounds. It is
a subset of the Dictionary of Natural Products (DNP) database. DNP is an ongoing project based on a 25-year
review of the natural product literature. For the present project, the subset of DNP entries referring to marine
natural products were carefully checked and reviewed and enhanced with a considerable amount of additional
information relating to their natural occurrence. Several careful reviews were also carried out to ensure that the
coverage of marine natural products in the finished publication was as complete as possible.
The compounds present in the Dictionary have been classified under the following major headings, which are
described in more in the Structural Types section below, available as a PDF file. (There are obvious overlaps between the categories.)
Aliphatic natural products
Carbohydrates
Oxygen heterocycles
Simple aromatic natural products
Terpenoids
Steroids
Aminoacids and peptides
that
Alkaloids
Polypyrroles
Biosynthetic information on these compound classes can also be found in the Structural Types section.
Taxonomic information on the organisms and their metabolites is covered in the Classification of Organisms
section available as a PDF file.
The definition of a marine natural product is imprecise. The coverage of this Dictionary in terms of
'mainstream' natural products is intended to be comprehensive and as far as can be determined by various crosschecks
carried out in the later stages of compilation, it comes extremely close to achieving aim. Natural
products which may be considered marginal are present to a great extent, but to include every compound that
might be found somewhere in the sea would be an unrealistic target. In particular, compounds of the following
type may not necessarily be present:
Biochemicals endogenous to the higher marine animals, e.g. bile acids of marine mammals, endocrine
hormones of crustaceans.
Microbial products isolated from organisms that are widespread on both sea and land and have in fact
been isolated from a marine-related source, e.g. an antibiotic from Streptomyces harvested from driftwood.
Natural products of a 'terrestrial' type isolated from plants and animals in marginal environments, e.g.
mangrove saltmarshes, may not be fully covered.
Widespread polysaccharides, e.g. Amylose, Amylopectin.
All of these are included in the parent database Dictionary of Natural Products, available on DVD or online from
CRC Press.
The coverage of lipids is extensive but not completely comprehensive. Numerous homologous series of fatty
acids with different unsaturation patterns occur in both terrestrial and marine organisms, and there may not be
an individual entry for every minor congener.
Natural Products in the Marine Environment; General Observations
The marine environment is an extremely complex one, showing immense biodiversity. Marine organisms produce
all of the main type of natural product found among their terrestrial counterparts, but with a very different range
of chemodiversity, so that, for example, the range of terpenoid skeletons includes some not found on land.
Conversely, there are large groups of natural product found in some higher plants (e.g. many terpenoid skeletons;
large categories of alkaloids) for which the enzymatic pathways have not evolved among marine organisms;
higher plants are essentially absent from the sea.
Elemental composition
Many marine natural products contain the elements nitrogen, sulfur and halogens available in seawater, but with
very uneven distribution across the phyla. A few compounds containing other elements such as arsenic and boron
are also known, and also metal complexes (Ni, V, Zn). Vanadium bromoperoxidases are involved in the
production of brominated marine natural products (but chlorinated metabolites arise by a different route).
The proportion of nitrogenous compounds is much higher in cyanobacteria, bryozoans and ascidians, and the
proportion of halogenated compounds is very high in the red algae (in marked contradistinction to the brown
algae). More details are given in the sections below describing these organisms.
Interspecific interactions
It is now clear that, whilst many marine natural products are located in the tissues of the larger marine animals
and plants, and are thus genuine natural products of those organisms, many others are produced by associated
endo- and epibiotic microorganisms. Most marine microorganisms have not yet been successfully cultured, and
definitive proof of origin is in most cases currently lacking. These products produced by symbiotic or epiphytic
microorganisms appear in many cases to play a role in chemical defence mechanisms.
In the past five years, however, much progress has been made in assigning a definite microbial origin to many
natural products. For example, in the case of Swinholide A, originally isolated from the sponge Theonella
swinhoei, centrifugation of macerated cell samples from the sponge showed that the alkaloid was located within
heterotrophic unicellular bacterial cells, was absent from the sponge cells themselves, but was also in the cells of
the co-occurring cyanobacterium Aphanocapsa feldmanni also present. More recently, however, Swinholide A has
been found in some cyanobacteria, and it has been speculated that it may be produced by one component of this
symbiont system, and stored by another. In the case of the isocyano- and related metabolites found in marine
invertebrate extracts, the isocyano group, possibly derived from cyanide ion, may be produced by an associated
microorganism, while the terpenoid component derives from the animal. Genomic techniques are now being used;
for example to show that Patellamides A and C are biosynthesised by a cyanobacterial symbiont of the originally
cited source. Other natural products isolated from the higher marine organisms, however, have a known dietary
origin, while a definite de novo biosynthesis of some mollusc products has been demonstrated.
It may be true in some cases that although a particular type of metabolite isolated from a higher animal has
not yet been found among the lower forms such as cyanophytes forming part of the same ecosystem, this is
merely an accident of the search process.
Haygood, M.G. et al, J. Mol. Microbiol. Biotechnol., 1999, 1, 33.43 (rev, microbial symbionts )
Paul, V.J. et al, Nat. Prod. Rep., 2004, 21, 189.209 (rev, chemical mediation of interorganism interactions)
Salomon, C.E. et al, Nat. Prod. Rep., 2004, 21, 105.121 (rev, microbial genetics and chemical diversity)
Hildebrand, M. et al, Nat. Prod. Rep., 2004, 21, 122.142 (rev, symbiont genetics)
Proksch, P. et al, BIOforum Eur., 2004, 8, 44
Moore, B.S., Nat. Prod. Rep., 2005, 22, 580.593; 2006, 23, 615.629 (rev, biosynth)
Organisation of Entries
The Dictionary is arranged alphabetically by entry name. Every entry is numbered to assist ready location. Many
compounds are included as derivatives of main entry compounds but important derivatives have their own
individual cross-referenced entries. Use of the on-line indexes enables the rapid location of all compounds in
the Dictionary by name or compound type, regardless of their location. Entries may sometimes contain data on
natural products which are not of marine origin, but this is obvious from the context and may provide valuable
links to relationships between marine and terrestrial sources. This is especially true of entries dealing with fungal
metabolites (see the section dealing with fungi, below).
A representative dictionary entry is shown in Figure 1.
Fig. 1. Sample entry from database
Chemical Names and Synonymns
2.1 CHEMICAL NAMES AND SYNONYMS
The Dictionary contains a wide range of synonyms which may be (a) those found in the primary literature, (b)
Chemical Abstracts names, or (c) names added editorially to achieve as much consistency as possible with other
closely related substances. Names corresponding to those used by CAS during the 9th and subsequent Collective
Index periods (1973) are labelled 9CI Names. All important derivatives embedded within entries are named (but
see comment on CAS nomenclature below). If a compound cannot be located immediately in the main body of
the entries, it is important to use the indexes. The on-line version of the Dictionary is much more highly
indexed than the printed version.
The most authoritative current statement of good practice on natural product nomenclature is the document
IUPAC Recommendations 1999 (Pure Appl. Chem., 1999, 71, 587.643) the full text of which can be read on the Dictionary of Marine Natural Products On-line.
Some marine natural products have been given trivial names which duplicate those already in the literature, or
which are simultaneously published for two or more non-identical substances. Where such a duplication is
noticed this is indicated by the dagger symbol (†) immediately following the name. Borderline cases, especially as
between presence or absence of terminal e or suffix A or 1, are considered to constitute duplicates for this
purpose.
Nomenclature
It is expected that this Dictionary will be used by a wide variety of scientists, not all of whom will be specialist organic chemists. Therefore compounds have been named so as to facilitate access to their factual data by keeping the nomenclature as simple as possible, whilst still adhering to good practice as determined by IUPAC
(the International Union of Pure and Applied Chemistry). A great deal of care has been taken to achieve this aim
as nearly as possible.
A much fuller description of the detailed nomenclature of individual classes of marine natural product is given
in the Structural Types section. The following notes are of general applicability throughout the Dictionary.
There are many examples in the primary literature of compounds being named in ways which are
violations of good IUPAC practice, e.g. where the substituents are ordered non-alphabetically. These are
not reported in their incorrect form but have been corrected.
The number of trivial names used for acylating substituents has been kept to a minimum but the following
are used throughout the Dictionary.
Many other trivial appellations have from time to time appeared in the literature for other acyl groups
(e.g. Senecioyl = 3-methyl-2-butenoyl, Feruloyl = 3-(4-hydroxy-3-methoxypheny1)-2-propenoyl or
4-hydroxy-3-methoxycinnamoyl).
The term prenyl for the common 3-methyl-2-butenyl substituent,(H3C)2C=CHCH2-, is used throughout the
Dictionary. Several other names for this substituent have from time to time been used and appear in the primary
literature including the following:
CAS Registry Number
CAS numbers are identifying numbers allocated to each distinctly definable chemical substance indexed by CAS
since 1965 (plus some retrospective allocation of numbers by CAS to compounds from earlier index periods). The
numbers have no chemical significance but they provide a label for each substance independent of any system of
nomenclature. They are extensively used for exchanging information between individuals and databases. The
numbers take the form NNNNNN-NN-R, where the total number of digits is five or more and R is a check digit.
For practical purposes, CAS numbers have certain shortcomings arising from their free allocation, resulting in
one substance having more than one potential number. Duplication may arise for one of several reasons to do
with the detailed chemistry of the substance, for example tautomerism, solvent formation, partially unspecified
stereochemistry. There are also replaced numbers. For this reason, Dictionary entries will often contain one or
more Additional CAS numbers which may help the user to obtain further information about the substance,
especially by online searching.
For practical purposes, CAS numbers have certain shortcomings arising from their free allocation, resulting in
one substance having more than one potential number. Duplication may arise for one of several reasons to do
with the detailed chemistry of the substance, for example tautomerism, solvent formation, partially unspecified
stereochemistry. There are also replaced numbers. For this reason, Dictionary entries will often contain one or
more Additional CAS numbers which may help the user to obtain further information about the substance,
especially by online searching.
Clearly, the additional CAS numbers given in this Dictionary have to be used with care. Their inclusion in the
entry is the result of an editorial decision by the Dictionary contributor that they refer to what is essentially the
same substance, but this decision may be a subjective one. Care has been taken to ensure that the main CAS
number given in this Dictionary for each substance is the correct one.
Further information on CAS number allocation policy can be obtained from CAS indexes or The Organic
Chemist's Desk Reference (Chapman & Hall, 1995).
Structural Formulae
Every attempt has been made to present the structures of chemical substances as accurately as possible according
to best current practice and recommendations of IUPAC. As much consistency as possible has aimed at between
closely-related structures. For example, all sugars are shown as Haworth formulae, and whenever possible in
complex structures the rings are oriented in the standard Haworth convention so that structural comparisons can
be quickly made.
Molecular Formula and Molecular Weight
The elements in the molecular formula are given according to the Hill convention (C, H, then other elements in
alphabetical order). The molecular weights given are formula weights (or more strictly, molar masses in daltons)
and are rounded to three places in decimals. In the case of some high molecular mass substances, such as proteins,
the value quoted may be that taken from an original literature source and may be an aggregate molar mass.
Physical Data
The Dictionary gives the following physical characteristics of substances, when available: appearance, melting
point, boiling point, optical rotation, density, refractive index, solubility, pKa. All of these fields are searchable
by numerical value (including range searching) in the on-line version of the Dictionary.
Appearance
Organic compounds are considered to be colourless unless otherwise stated. Where the compound contains a
chromophore which would be expected to lead to visible colour, but no colour is mentioned in the literature, the
Dictionary entry will mention this fact if it has been noticed by the contributor. An indication of crystal form and
recrystallisation solvent is often given but these are imprecise items of data; most compounds can be crystallised
from several solvent systems and the crystal form often varies. In the case of the small number of compounds
where crystal behaviour has been intensively studied (e.g. pharmaceuticals), it is found that polymorphism is a
very common phenomenon and there is no reason to believe that it is not widespread among organic compounds
generally.
Melting Points and Boiling Points
The policy followed in the case of conflicting data is as follows:
Where the literature melting points are closely similar, only one figure (the highest or most probable) is
quoted
Where two or more melting points are recorded and differ by several degrees (the most likely explanation
being that one sample was impure) the lower figure is given in parentheses, thus Mp 139° (134-135°)
Where quoted figures differ widely and some other explanation such as polymorphism or incorrect
identity seems the most likely explanation, both figures are quoted without parentheses, thus Mp 142°
Mp 205-206°
Known cases of polymorphism or double melting points are noted
Boiling point determination is less precise than that of melting points and conflicting boiling point data are not
usually reported except when there appears to be a serious discrepancy between the different authors.
Optical rotations
These are given wherever possible, and normally refer to what the Dictionary contributor believes to be the best
characterised sample of highest chemical and optical purity. Where available an indication of the optical purity
(op) or enantiomeric excess (ee) of the sample measured follows the specific rotation value. For a recent
discussion of the validity and applicability of these terms, see Gawley, R.E., J. Org. Chem., 2006, 71, 2411-2416.
Specific rotations are dimensionless numbers and the degree sign which was formerly universal in the
literature has been discontinued.
Spectroscopic Data
Many Dictionary entries include ultraviolet spectra which are presented in the format:
where ε is the absorption coefficient for a given UV maxima value (λmax). A description of the solvent conditions
used, if reported in the literature, is listed at the beginning and end of the UV data in parentheses. All peak
absorptions cited are maxima unless otherwise described, e.g. shoulder/inflection (sh) and end absorption (end).
In addition, UV data may be followed by the term 'Berdy' or 'DEREP' indicating from which database the data
originated. The absence of these terms implies that the data were abstracted from the primary literature.
On the on-line version, all the λmax values are indexed in the UV Maxima field and can be searched for
numerically including range searching. Similarly, the solvent data associated with the UV data are indexed in the UV Solvent field.
Hazard and Toxicity Information General
Toxicity and hazard information is highlighted by the symbol and has been selected to assist in risk assessments
for experimental, manufacturing and manipulative procedures with chemicals.
The Publishers cannot be held responsible for any inaccuracies in the reported information, neither does the
omission of hazard data in the Dictionary imply an absence of this data from the literature. Widely recognised
hazards are included, however, and where possible key toxicity reviews are identified in the references. Further
advice on the storage, handling and disposal of chemicals is given in The Organic Chemist's Desk Reference.
RTECS® Accession Numbers*
Many entries in this Dictionary contain one or more RTECS® Accession Numbers. Possession of these numbers
allows users to locate toxicity information on relevant substances from the NIOSH Registry of Toxic Effects of
Chemical Substances, which is a compendium of toxicity data extracted from the scientific literature.
Bibliographic References
The selection of references is made with the aim of facilitating entry into the literature for the user who wishes to
locate more detailed information about a particular compound. The contents of most references are indicated by
reference tags (suffixes) indicating their content and in particular the stereoisomers and derivatives of the parent
compound which they document. The number of references cited does not indicate the relative importance of a
compound; one key recent citation may supersede a number of older ones.
Journal abbreviations generally follow the practice of the Chemical Abstracts Service Source Index (CASSI),
except for a short list of very well known journals where the Dictionary gives shorter abbreviations to save space
(e.g. J.A.C.S. instead of J. Am. Chem. Soc.)
2.8.1 Further References
Further useful information on a variety of topics concerned with the structure, description, stereochemistry and
nomenclature of organic compounds can be found in the Organic Chemist's Desk Reference.
Abbreviations
The following is a selection of the most common Database abbreviations used:
Table 1. Abbreviations
Abbreviation
Meaning
[α]
specific
rotation
acac
acetylacetonato
Ac
acetyl
ACGIH
American
Conference of Governmental Industrial Hygienists
Ac2O
acetic
anhydride
AcOH
acetic
acid
ADI
Acceptable
Daily Intake
alk.
alkaline
amorph.
amorphous
ANSI
American
National Standards Institute
anhyd.
anhydrous
approx.
approximately
aq.
aqueous
asym.
asymmetrical,
unsymmetrical
B
base
BAN
British
Approved Name
biol.
biological
bipy
2,2¢-bipyridine
Bp
boiling
point
br
broad
BSI
British
Standards Institution
Bu
butyl
(But for tert-butyl etc.)
bwd
bird
(wild)
Bz
benzyl
c.
concentration
ca.
(circa)
about
CAS
Chemical
Abstracts Service
Ccp
cubic
close packed
cdt
1,5,9-cyclododecatriene
C6H6
benzene
C5Me5
pentamethylcyclopentadienyl
CNS
central
nervous system
cod
1,5-cyclooctadiene
col.
colour,
coloration
comly.
commercially
compd(s)
compounds(s)
conc.
concentrated
const.
constant
constit.
constituent
coord
coordinate(d),
coordination
cot
1,3,5,7-cyclooctatetraene
Cp
cyclopentadienyl
C5Ph5
pentaphenylcyclopentadienyl
cryst.
crystal(s)
cv
cultivar
CVD
chemical
vapour deposition
Cy
cyclohexyl
d
density
dba
dibenzylideneacetone
dck
duck
dec.
decomposes,
decomposition
degradn.
degradation
depe
1,2-bis(diethylphosphino)ethane
descr.
described
diars
diarsine
(generalised ligand)
dil.
dilute,
dilution
dimorph.
dimorphic
diphos
diphosphine
(generalised ligand)
diss.
dissolves,
dissolved
dissoc.
dissociates
dist.
distil,
distillation
DMA
dimethylacetamide
DMF
dimethylformamide
dmpe
1,2-bis(dimethylphosphino)ethane
dmpm
bis(dimethylphosphino)methane
DMSO
dimethyl
sulfoxide
dppe
1,2-bis(diphenylphosphino)ethane
dppm
bis(diphenylphosphino)methane
dppp
1,3-bis(diphenylphosphino)propane
EDTA
ethylenediaminetetracetate(4-)
ee
enantiomeric
excess
Eg
band
gap (electron volts)
en
ethylenediamine
equilib.
equilibrium
esp.
especially
Et
ethyl
EtOAc
ethyl
acetate
EtOH
ethanol
EtOH
aq.
aqueous ethanol
evapn.
evaporation
exp.
exposure
exp.
experimental
fac
facial
Fc
ferrocenyl
fl.
p.
flash
point
fluor.
fluoresces,
fluorescence
formn.
formation
Fp
freezing
point
g
gram(s)
ΔG0f
standard
free energy of formation
Glc
β-D-glucopyranosyl
gpg
guinea
pig
ham
hamster
ΔH0f
standard
enthalpy of formation
hcp
hexagonal
close packed
hydrol.
hydrolyses,
hydrolysed, hydrolysis
ihl
inhalation
im
imidazolato
ims
intramuscular
INN
International
Non-proprietary Name
inorg.
inorganic
insol.
insoluble
intermed.
intermediate
ipr
intraperitoneal
ISO
International
Standards Organisation
Ivg
intravaginal
ivn
intravenous
JAN
Japanese
Accepted Name
JMAF
Japanese
Ministry for Agriculture, Forestry and Fisheries
K
temperature
(Kelvin)
L
generalised
ligand
LC
lethal
concentration
LD
Lethal
dose; LD50: a dose which is lethal to 50% of the animals
tested
M
relative
molecular mass (formula weight)
M
metal
m
medium
mcd
magnetic
circular dichroism
Me
methyl
MEL
maximum
exposure limit
MeOH
methanol
mer
meridional
mes
mesityl
(1,3,5-trimethylphenyl)
Me2CO
acetone
misc.
miscible
misc.
miscellaneous
mixt.
mixture
mky
monkey
MOCVD
metal-organic
chemical vapour deposition
mod.
moderately
Mp
melting
point
mus
mouse
n
index
of refraction eg. (n20D for 20° and sodium
light).
Nbd
norbornadiene
nqr
nuclear
quadrupole resonance spectrum
obt.
obtained
oc
open
cup
oep
octaethylporphyrinato
OES
occupational
exposure standard
Oh
octahedral
op
optical
purity
org.
organic
orl
oral
ox
oxalato
Ph
phenyl
(C6H5)
pH
Measure
of soln. acidity where pH = log10 (1/[H+]) where
[H+] is the hydrogen ion
Phen
1,10-phenanthroline
phys.
physical
pK
Measure
of dissoc. const. (K) where pK = Log10(1/K)
Pm
picometres
(10?12 m)
PMDET
pentamethyldiethylenetriamine
polarog.
polarography
polym.
polymerised,
polymerisation
ppm
parts
per million
Pr
propyl
(Pri for isopropyl)
prob.
probably
purifn.
purification
Py
pyridine
pz
pyrazolato
R
generalised
alkyl group
rbt
rabbit
ref.
reference
rel.
relative(ly)
r.t.
room
temperature
s
strong
S0
standard
entropy
scu
subcutaneous
skn
skin
sl.
slightly
sol.
soluble
soln(s)
solution(s)
solv(s)
solvent(s)
soly.
solubility
sp.
species
(singular)
spar.
sparingly
spp.
species
(plural)
ssp.
subspecies
subl.
sublimation,
sublimes
tbp
triagonal
bipyramidal
Td
tetrahedral
Tf
triflate
THF
tetrahydrofuran
tht
tetrahydrothiophene
TLV
Threshold
Limit Value
TMED
tetramethylethylenediamine
tpp
tetraphenylporphyrinato
triphos
triphosphine
(generalised ligand)
Ts
tosyl
μeff
effective
magnetic moment (in Bohr magnetons μB)
unsatd.
unsaturated
USAN
United
States Adopted Name
Uv
ultraviolet
spectrum
v.
very
var.
variety
vis.
visible
vol.
volume
w
weak
WSSA
Weed
Science Society of America
X
generalised
anion, usually halide
Table 2. Reference tags
The following is a selection of the most common reference tags that
are used
Abbreviation
Meaning
abs
config absolute configuration
anal
analysis
bibl
bibliography
biodistribn
biodistribution
biosynth
biosynthesis
cd
circular dichroism
chromatog
chromatography
cmr
13C nuclear magnetic resonance spectrum
config
configuration
conformn
conformation
cryst struct
X-ray crystal structure determination
deriv(s)
derivative(s)
detn
etermination, detection
epr
electron paramagnetic (spin) resonance spectrum
glc
gas-liquid chromatography
haz
hazard
hplc
high performance liquid chromatogrpahy
ir
infrared spectrum
isol
isolation
isom
isomerism
manuf
manufacture
metab
metabolism
ms
mass spectrum
nmr
nuclear magnetic resonance spectrum
occur
occurrence
ord
optical rotatory dispersion
pharmacol
pharmacology
pmr
proton (1H) nuclear magnetic resonance spectrum
props
properties (chemical or physical)
resoln
resolution
rev
review
sepn
separation
spectra
struct
structure
synonyms
synth
synthesis
tautom
tautomerism
tlc
thin layer chromatography
tox
toxicity
use(s)
uv
ultra-violet visible spectrum
*RTECS® Accession Numbers are compiled and distributed by the
National Institute for Occupational Safety and Health Service of the
U.S. Department of Health and Human Services of the United States of
America. All rights reserved (1996
symbol and has been selected to assist in risk assessments
for experimental, manufacturing and manipulative procedures with chemicals.