PPAPs Database Structure

The database is structured as follows:

allData = [genericStructure1, genericStructure2, ...]

genericStructure = [description, compound1, compound2, ...]

description = ['filename', 'characteristic1', 'characteristic2', ...]

compound = [R_X_Groups, name, 'source', 'rotation', refs]

R_X_Groups = empty string (if only one compound for this generic structure)
or 'name of R' (if only one R group in this generic structure)
or ['name of R']
or ['name of R¹', 'name of R²', ...]
array perhaps appended with 'X = name of X' (if only one X group in this generic structure)
or 'X¹ = name of X¹', 'X² = name of X²', ...
array perhaps appended with '(diastereomer)' or '(enantiomer)' or '(prob. enantiomer)'

name = 'name'
or ['name', 'footnote letter(s)']
or ['name', 'footnote letter(s)', 'additional text']

refs = 'author'
or ['author year', 'URL']
or [['author year 1', 'URL1'], ['author year 2', 'URL2'], ...]

The data consist of an array of generic structures. Each individual generic structure is itself represented by an array of at least two members: the first member is a description of the generic structure, and subsequent members describe individual compounds that match that generic structure.

The description of the generic structure is itself an array. Its first member is the name of the .png file that contains an image representing that generic structure, and subsequent members describe structural characteristics of that generic structure. Every generic structure is described by at least one of the first five values in the list below. Structural characteristics recognized in the database:

Value	Description
bicyclononanes	bicyclo[3.3.1]nonanes and their further cyclized and seco derivatives
bicyclooctanes	bicyclo[3.2.1]octanes
fourPlusTwo	bicyclo[2.2.2]octanes produced by a formal [4 + 2] cycloaddition
otherBridgedBicycles	bridged bicyclic compounds not included above
spiroindanes
spiropentalanes
otherSpiro
exo	compounds with an exo substituent at C7
endo	compounds with an endo substituent at C7
noC7	compounds with no substituent at C7
noC3	compounds with no substituent at C3
OC3	compounds with an acyloxy substituent at C3
A	type A PPAPs (with an acyl group at C1)
B	type B PPAPs (with an acyl group at C3)
uncaged	PPAPs that have not undergone further cyclization to adamantanes or homoadamantanes
caged	PPAPs that have undergone further cyclization to adamantanes or homoadamantanes
seco	PPAPs with skeletal C–C bonds cleaved

As was already mentioned, subsequent members of each generic structure array describe individual compounds that match that generic structure. Each one of these descriptions is itself an array consisting of five members.

1. The first member of the array defines the R and X groups of the individual structure as depicted in the image of the generic structure. If the generic structure describes only one individual structure, then the image will contain no R or X groups, and this value of the array will be an empty string. If there is more than one R or X group, they will be written as an array. The name of an X group is preceded by 'X = ' or 'Xⁿ = ', but the name of an R group stands solo. If two structures have the same R group definitions, the second's may also include a parenthetical '(enantiomer)' or '(diastereomer)'. If an R group is lavandulyl, it is hyperlinked to the corresponding Wikipedia entry. Other groups with unconventional names, such as ω-isogeranyl, are given a reference to a footnote that defines the group.
2. The second member of the array is either just the name(s) of the compound, or it is an array containing the name of the compound, a reference to a footnote, and perhaps additional text to include (for example, 'one of two by that name'). If two compounds have the same name, the names are differentiated by inserting an extra space character into the name of one of the compounds, and a hyperlink is inserted to link each to the other. If a compound has more than one name, the names are separated by ', a.k.a. '. The program that converts the database to HTML format adds a hyperlink from the name(s) to its MOL structure. The MOL structures are stored in a different file, where they are identified by the name(s) of the compound exactly as it (they) appear here.
3. The third member of the array is the species source or sources of the compound.
4. The fourth member of the array is the specific rotation of the compound, including the concentration and the solvent if it is other than CHCl₃.
5. The fifth member of the array is a reference or references. A reference can be just a string, a two-member array, or an array of arrays.
   • The sole string contains the surname of the first author of the article and the year of the article. If different first authors have the same surname, we include their first initials as well. In this case, the program that converts the database to HTML format hyperlinks the article to the references page, refs.html.
   • In a two-member array, the first member is the author and year of the article, and the second member is the URL of the article. In this case, the program that converts the database to HTML format hyperlinks the article to its URL. If the second member is an enpty string, the program hyperlinks the article to the references page.
   • In an array of arrays, each member is either a sole string or a two-member array, as described above.

This is what the database looks like:

var data = [
		[ 	['hyperfirin', 'A', 'noC7', 'uncaged', 'bicyclononanes'],
			[	'',
				'hyperfirin',
				'<i>H. perforatum</i>',
				'NR',
				['Tatsis 2007', 'doi.org/10.1016/j.phytochem.2006.11.026']
			]
		],
		[	['sampsonioneO', 'endo', 'A', 'uncaged', 'bicyclononanes'],
			[	'prenyl',
				'sampsonione O',
				'<i>H. sampsonii</i>',
				'+87.9 (0.073)',
				['Xiao 2007', 'doi.org/10.1021/np0704147']
			],
			[	'geranyl',
				'otogirinin D',
				'<i>H. erectum</i> Thunb.',
				'+160.0 (0.03, m)',
				[	['Ishida 2010', 'doi.org/10.1248/cpb.58.336'], 
					['Li 2015a', 'doi.org/10.1039/C4RA11675E']
				]
			]
		],
		[ 	['hyperforin', 'exo', 'A', 'uncaged', 'bicyclononanes'],
			[	[	'Ph',
					'prenyl',
					'prenyl',
					'prenyl',
					'H'
				],
				['nemorosone', 'd'],
				'Cuban propolis, <i>C. rosea, C. grandiflora, C. insignis, C. nemorosa</i>',
				'+113 (0.1); OMe:,150 (m, 0.8) and,49 (1.4)',
				[	['de Oliveira 1996', 'doi.org/10.1016/0040-4039(96)00656-9'], 
					['de Oliveira 1999', 'doi.org/10.1016/S0031-9422(98)00476-2'], 
					['Lokvam 2000', 'doi.org/10.1016/S0031-9422(00)00193-X'], 
					['Cuesta-Rubio 2001a', 'doi.org/10.1016/S0031-9422(00)00510-0'],
					['Sparling 2015', '10.1021/acs.orglett.5b01121']
				]
			],
			[	[	'Ph',
					'prenyl',
					'<a href="https://en.wikipedia.org/wiki/Lavandulyl_acetate">lavandulyl</a>',
					'prenyl',
					'H'
				],
				['chamone I', 'e'],
				'<i>C. grandiflora</i>',
				'NR',
				['Lokvam 2000', 'doi.org/10.1016/S0031-9422(00)00193-X']
			],
			[	[	'3,4-dihydroxyphenyl',
					'prenyl',
					'prenyl',
					'(<i>S</i>)-isolavandulyl<sup>[<i><a href="#footnotes">g</a></i>]</sup>',
					'H'
				],
				'garcinialiptone D',
				'<i>G. subelliptica</i>',
				'&minus;79.1 (7.83, m)',
				['L.-J. Zhang 2010', 'doi.org/10.1021/np900620y']
			],
			...
		],
		[	['garsubellinC', 'exo', 'A', 'uncaged', 'bicyclononanes'],
			[	[	'Ph',
					'prenyl',
					'H',
					'X = H',
					'(enantiomer)'
				],
				'garcinielliptone I',
				'<i>G. subelliptica</i>',
				'&minus;37.7 (1.1)',
				[	['Weng 2003b', 'doi.org/10.1002/chem.200305209'], 
					['Ciochina 2006', 'doi.org/10.1021/cr0500582']
				]
			],
			...
		],
		...
];

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