Up the Garden Path: A Chemical Trail through the Cambridge

Sep 10, 2012 - Visitors to the gardens with quick response (QR) code readers on their mobile phones will also be able to access this enhanced chemical...
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Up the Garden Path: A Chemical Trail through the Cambridge University Botanic Garden Gary M. Battle,*,† Gwenda O. Kyd,† Colin R. Groom,† Frank H. Allen,† Juliet Day,§ and Timothy Upson§ †

Cambridge Crystallographic Data Centre (CCDC), 12 Union Road, Cambridge CB2 1EZ, United Kingdom Cambridge University Botanic Garden, 1 Brookside, Cambridge CB2 1JE, United Kingdom

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ABSTRACT: The living world is a rich source of chemicals with many medicines, dyes, flavorings, and foodstuffs having their origins in compounds produced by plants. We describe a chemical trail through the plant holdings of the Cambridge University Botanic Gardens. Visitors to the gardens are provided with a laminated trail guide with 22 stopping points marked on a map. For each of the 22 familiar plants, the principal chemical component(s) and their applications are identified. The virtual trail on the gardens Web site provides additional chemical information including links to the experimentally determined three-dimensional structures of the molecules from the Cambridge Structural Database. Visitors to the gardens with quick response (QR) code readers on their mobile phones will also be able to access this enhanced chemical information digitally. Our hope is that the trails (actual and virtual) will take advantage of students’ inherent interest in the chemistry of the natural world and encourage them to learn more about the myriad of vital chemicals that are available in the plant kingdom. KEYWORDS: General Public, High School/Introductory Chemistry, First-Year Undergraduate/General, Interdisciplinary/Multidisciplinary, Public Understanding/Outreach, Internet/Web-Based Learning, Plant Chemistry, X-ray Crystallography and of flavorings and colorings from herbs and spices. During childhood, we also learn about the toxicological properties of plants, for example, the unfortunate effects of deadly nightshade (belladonna), laurel, ivy, and so on, but we also begin to learn about the beneficial medicinal effects of plants as well: that dock leaves are the traditional treatment for nettle stings, tree bark extracts are used to treat malaria, and that medicinal benefits are ascribed to a whole host of plants including carrots, garlic, and many common herbs. All of these very direct connections between plants and the wellbeing and comfort of a wide variety of species, including humans, provide an ideal route through which to interest both high school students and undergraduates in the chemistry of the natural world, as documented by several authors in this Journal.4−6 This route promotes chemistry across the student population, taking advantage of some prior knowledge and natural inquisitiveness, and can do much to raise awareness of both chemistry and botany in the wider population.

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he relationship between humans and plants is extensive and complex. At a very basic level, plants provide a huge variety of foodstuffs, building materials, clothing items, and fuels. Many plants are admired for their beauty, providing inspiration for generations of artists and designers, whereas some have highly effective physical and toxicological defense mechanisms. Importantly, many plants have become wellknown over thousands of years, and in all major cultures, for their important medicinal properties.1 As many as 25% of modern active pharmaceutical compounds have their origins in the plant kingdom.2 Indeed, the study of natural products from plants was a driving force for the origin and continued development of organic and medicinal chemistry, and the topic is nowadays also expressed in the subfield of phytochemistry and its associated medicinal area of phytotherapy.3 However, plants are also important to a wide variety of other species and plants produce chemicals for a variety of their own reasons, with a key reason being for defense. We may be familiar with the physical defenses: tough leathery leaves or spines and thorns that deter animals from feeding, but perhaps the most effective deterrent is through chemistry. Plants are nature’s great chemists, producing a bewildering range of chemicals to deter feeding species, from small insects to large grazing mammals and such chemicals can be found in all parts of a plant, from roots to shoots and from seeds to leaves. Our human interest and knowledge of plants and plant products begins early in life. For example, we learn from an early age the dietary importance of vitamins from fruits and vegetables, fibers from cereal crops, oils from nuts and fruits, © 2012 American Chemical Society and Division of Chemical Education, Inc.

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THE CHEMICAL TRAIL To reinforce this inherent interest in plant chemistry, the Cambridge Crystallographic Data Centre (CCDC) and the Cambridge University Botanic Garden (CUBG) have joined forces to create a chemical trail through the 40 acre gardens. The basic idea is to create a permanent and developing route with various identified plant species as stopping points and to Published: September 10, 2012 1390

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Web site.16 When the virtual trail is accessed online, information and graphics additional to those provided on the printed visitor trail guide are immediately available on the CUBG Web pages. This is shown in Figure 2 for aspirin, a

link the route to electronic resources which provide more information on the key chemical components of the plants. The visitor to the Cambridge University Botanic Garden is provided with a laminated trail guide with the 22 stopping points marked on a map of the gardens. For each numbered point, the trail guide provides brief details of each plant, its major chemical constituent(s), and their applications. A notice beside each plant in the garden provides the plant number, its name, and a two-dimensional (2D) quick response (QR) code that provides access to additional online chemical and structural information via a smart phone. Use of the Web enables enhances the visitor experience, either at home or within the classroom, by making available an extended “virtual trail” which can also be followed and enjoyed by a much wider audience of virtual visitors (Figure 1). This

Figure 2. CUBG Web page for aspirin, a derivative of salicylic acid that occurs naturally in the willow tree (Salix).

derivative of salicylic acid that occurs naturally in the bark of the willow tree (Salix). The chemical information is further enhanced through clickable links to the relevant CSD structure(s) displayed via WebCSD (Figure 3). Within Figure 1. Interactive online version of the trail map showing locations of all 22 plant or chemical stopping points.

trail includes all 22 of the onsite stopping points together with an increasing number of additional plant and chemical combinations to extend the scientific range of the project. These methods enable additional information through Internet links to chemical and structural information. Links to the Wikipedia and ChemSpider7 entries for the compounds of interest provide a wealth of chemical information. A key feature of the trail is the link to the experimentally determined threedimensional (3D) structures of the compounds from the Cambridge Structural Database (CSD).8 As presented in this Journal and elsewhere,9−13 the CCDC maintains the CSD, a fully retrospective and comprehensive database of experimentally determined organic and metal− organic small-molecule crystal structures. The CSD records bibliographic and chemical text together with the 2D and 3D structures of over 600,000 chemical molecules. From the full database, a teaching subset of more than 500 structures has been compiled and was carefully selected for their educational relevance.9 This subset is freely available online and can be explored interactively using the online application WebCSD.14 By exploiting this resource, the basic plant and compound descriptions can be enhanced with chemical information extracted from the database and direct links are provided to the relevant CSD structures. The enhanced virtual trail is accessible via the CUBG Web site,15 which is also linked from the teaching area of the CCDC

Figure 3. CSD structure of aspirin displayed via WebCSD.

WebCSD, the 3D chemical structure can be rotated and manipulated, crystal packing diagrams can optionally be viewed to enhance the chemistry learning experience,10,16 and additional CSD information can also be displayed, for example, chemical formulas and literature references. The concept of smart phones being used advantageously to access chemistry teaching applications17 is also put into practice in the onsite chemical trail. Here the 2D quick response (QR) codes on the individual plant noticeboards within the garden 1391

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enables instant access by smart phone to the Web tools discussed above. Thus, the visitor to the garden is able to access enhanced information content while following the trail in person. A typical bar code is shown in Figure 4 and may be used by readers of this article to mimic the “in-garden” smart phone experience.

Table 1. The Plant and Chemical Combinations Chosen for the First Chemical Trail in the Cambridge University Botanic Garden Map No.a 1 2 3 4 5

6 7 8 9

Figure 4. Example of a quick response (QR) matrix barcode used to provide access to online content.

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SELECTION OF CHEMICALS AND PLANTS With more than 8000 species available in the gardens and more than 600,000 crystal structures in the CSD, there was a wide choice of the combination of plants and their chemical components to select from; hence, any selection must be regarded as subjective. Further, there is a natural tendency to emphasize the medicinal value of plant chemicals, but this was kept in balance to cover both well-known and less well-known phytochemical relationships and to cover as many areas of general public interest as can be accomplished within a limited number of examples and a reasonable walking distance: it is no coincidence that the trail, if followed in numerical order, leads inexorably to the excellent visitor café available within CUBG! CCDC staff began the selection from the chemical point of view and selected some 40 possible chemical and plant combinations. This initial list was then enhanced by CUBG staff who generated the final list of 22 combinations based on plant availability, current positioning in the garden, and so forth. The concept can be readily modified to allow for seasonal changes in plant availability and additions can be made in the future to keep the walk fresh. Such changes will extend the range of chemicals and plants that can be brought to public notice in the garden and on the Web. Indeed, the possibility of a longer virtual trail may be considered once the popularity and value of the current offering can be assessed. The full list of 22 selected plant and chemical combinations is available via the CUBG Web site,15 and virtual information boards can be accessed there by clicking on the numbered points on the CUBG map (Figure 1) or on a tabulated listing below the map. As all of this information cannot be reproduced here, a list of plant and chemical combinations are shown in Table 1, together with some indication of the compounds’ medicinal activity or other applications. An example of the full information available on the CUBG Web site is shown in Figure 2. Notes that are of general public interest are provided, together with sufficient chemical information to encourage the aspiring chemist to discover more about the selected compounds.

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15 16 17

18 19 20 21

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Chemical Name(s)b

Plant Salix species (willow) Pinus nigra (black pine) Daucus carota (wild carrot) Lupinus mutabilis (pearl lupin) Galium odoratum (sweet woodruff) Humula lupulus (common hop) Urtica dioica (stinging nettle) Euphorbia of f icinalis Mentha species (mints) Capsicum annuum (chilli pepper) Hyoscyamus niger (henbane) Nicotiana tabacum (tobacco) Digitalis species (foxglove) Asclepias syriaca (common milkweed) Allium sativum (garlic) Tanacetum parthenium (feverfew) Artemisia annua (sweet wormwood) Taxus baccata (European yew) Aloe vera Gossypium species (cotton) Cola nitida (cola)

Opuntia species (prickly pear)

salicylic acid [acetyl derivative is aspirin] α- and β-pinene [turpentine, perfumery] β-carotene [pigment, vitamin A precursor] sparteine [alkaloid, antiarrythmic] coumarin [‘new mown hay’ smell]

isoadhumulone [a bitter principle in beer] formic acid [one of the stinging agents] a derivative of cholestan-8-one [a purgative and a deterrent for herbivores] menthol [cooling action on skin, use in decongestants] capsaicin [hot component of chilli peppers] scopolamine [hallucinogenic alkaloid] nicotine [alkaloidal stimulant] digoxin [treating heart conditions] β-amyrin [analgesic triterpene]

diallyl disulfide [reported antibacterial, anticancer and cardio-protective effects] Melatonin [treats sleep disorders, jetlag] Artemisinin [malaria, skin disorders]

paclitaxel (taxol) [anticancer treatments] aloin B [laxative effect, cosmetics] gossypol [antimalarial and other effects] theobromine [bitter component of chocolate], caffeine [stimulant] and theophylline [tea, coffee, cocoa beans] quercetin [anticancer, anti-inflammatory, antiallergy, antioxidant]

a

The numbers in the table are the labeled points on the trail map in Figure 1. bOnly brief details of compound activities and uses are provided. For full notes on each compound, visit the CUBG Web site.15

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PLANT CHEMISTRY ILLUSTRATED IN THE TRAIL Most of the chemicals introduced in the trail (Table 1) are known as secondary plant compounds of which there are a number of major classes. One major class covers nitrogen compounds, which are well represented by the alkaloids, a group of toxic and bitter-tasting compounds, examples of which occur in Lupinus (lupin), Nicotiana (tobacco), and Hyoscyamus (henbane). Another major class, the terpenoids, are a highly variable group of naturally occurring organic chemicals based on the C5 isoprene subunit. Terpenoids are found extensively in flowering plants and are most familiar to us for their aromatic qualities such as those found in Pinus (pines) or Artemisia (wormwood). The phenolic class of compounds are 1392

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Figure 5. (A) CO···H−O hydrogen-bonded chains in formic acid (from Urtica dioica, stinging nettle). (B) Hydrogen-bonded dimers together with an intramolecular hydrogen bond in salicylic acid (from Salix species, willow). (C) Caffeine monohydrate crystallizes with one molecule of water per caffeine molecule to form infinite hydrogen-bonded chains. A second hydrogen bond to a caffeine N-atom results in a stacked arrangement of caffeine molecules.

represented by coumarin from Galium (sweet woodruff), which is known for its sweet odor, and the flavonoid class of compounds are frequently responsible for color in plants, as represented here by the red pigment quercetin from Opuntia (prickly pear). Many of the chemical compounds illustrated by the trail are familiar to us in our everyday lives. Compounds that are bitter or foul tasting to other animals are used to flavor human food, as illustrated by Mentha (the mints) and Capsicum annuum (chilli pepper), whereas Humulus lupulus (the common hop) provides the bitterness in beer. Other compounds are highly poisonous to humans, but when used in small quantities have medicinal benefits, such as digoxin from Digitalis (foxglove) used to treat heart problems or paclitaxel from Taxus baccata (yew), which is a highly effective anticancer drug. Other compounds are used as stimulants, an example being caffeine from Cola nitida (cola), which is usually imbibed through drinking coffee, tea, or cola. While most of the compounds illustrated in this trail have a primarily defensive function, some are involved in other aspects of a plant physiology. Thus, one of the functions of acetylsalicyclic acid produced by Salix (willow) is to prevent the growth of other plants within the vicinity that would compete for available resources. This is known as allelopathy. In the case of melatonin, found in Tanacetum parthenium (feverfew) and also found in animals, the compound helps regulate the plant’s response to photoperiods (the length of night and day) and also its ability to survive in harsh environments.

natural world will make them receptive to the chemical connections. The trail therefore provides an excellent starting point to introduce chemistry principles. The trail also exemplifies the value of modern online electronic chemistry resources that can be used to enhance the student experience throughout their chemistry courses. Although only a limited range of possible chemistry learning opportunities afforded by the trail are illustrated here, additional support and teaching materials will be provided in collaboration with the SAPs organization (Science and Plants for Schools).18 Much basic chemistry can be learned from the compounds included in the trail. At the simplest level, many of the compounds contain phenyl substituents and the 3D graphics reinforce the planarity of aromatic rings and ring systems. Other compounds provide illustrations of organic functional groups. Formic acid (from nettles) is the simplest of the carboxylic acids, and the −COOH function occurs elsewhere, for example, in salicylic acid from the willow. Further investigations of the crystal structure data, using the free Mercury visualizer downloaded from the CCDC Web site,16 show that the −COOH groups in these two compounds give rise to two different patterns of hydrogen bonding. In formic acid (Figure 5A) the molecules are linked in chains by C O···H−O hydrogen bonds, whereas in salicylic acid, −COOH group forms cyclic dimers using two such bonds (Figure 5B) together with an intramolecular hydrogen bond in each molecule. Very different hydrogen-bonding can be observed in caffeine monohydrate (Figure 5C) which crystallizes with one molecule of water per caffeine molecule. Each water molecule forms one hydrogen bond to another water molecule, forming infinite hydrogen-bonded water chains, and a second hydrogen bond to a caffeine N-atom to generate the stacked arrangement of caffeine molecules illustrated in Figure 5C. The compounds illustrated by the trail also provide opportunities for identifying and assigning chiral centers. Thus, menthol (Figure 6A), from the Mentha species (mints), consists of a cyclohexane ring (a good illustration of

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INTRODUCING CHEMISTRY PRINCIPLES USING PLANT THEMES The intention of this joint project has been to provide notes that are of general public interest, together with sufficient chemical information to encourage the aspiring chemist to discover more about the selected compounds. Capturing students’ attention with issues and themes that relate to the 1393

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ACKNOWLEDGMENTS We wish to thank John Parker, recently retired Director of the Cambridge University Botanic Garden, for his enthusiastic support during the early stages of this work.

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REFERENCES

(1) Bartram, T. The Encyclopedia of Herbal Medicine; Robinson Publishing: London, 1998. (2) Balandrin, M. F.; Klocke, J. A.; Wurtele, E. S.; Bollinger, W. H. Science 1985, 1154−1160. (3) Heinrich, M.; Barnes, J.; Gibbons, S.; Williamson, E. M. Fundamentals of Pharmacognosy and Phytotherapy; Churchill Livingstone: London, 2003. (4) Houghton, P. J. J. Chem. Educ. 2001, 78, 175−184. (5) Andreoli, K.; Calascibetta, F.; Campanella, L.; Favero, G.; Occhionera, F. J. Chem. Educ. 2002, 79, 976−979. (6) Séquin, M. J. Chem. Educ. 2005, 82, 1787−1790. (7) Pence, H. E.; Williams, A. J. Chem. Educ. 2010, 87, 1123−1124. (8) Allen, F. H. Acta Crystallogr. 2002, B58, 380−388. (9) Battle, G. M.; Allen, F. H.; Ferrence, G. M. J. Chem. Educ. 2010, 87, 809−812. (10) Battle, G. M.; Allen, F. H.; Ferrence, G. M. J. Chem. Educ. 2010, 87, 813−818. (11) Battle, G. M.; Allen, F. H.; Ferrence, G. M. J. Chem. Educ. 2011, 88, 886−890. (12) Battle, G. M.; Allen, F. H.; Ferrence, G. M. J. Chem. Educ. 2011, 88, 891−897. (13) Battle, G. M.; Ferrence, G. M.; Allen, F. H. J. Appl. Crystallogr. 2010, 43, 1208−1223. (14) Thomas, I. R.; Bruno, I. J.; Cole, J. C.; Macrae, C. F.; Pidcock, E.; Wood, P. A. J. Appl. Crystallogr. 2010, 43, 362−366. (15) Chemicals from Plants. http://www.botanic.cam.ac.uk/Botanic/ Trail.aspx?p=27&ix=11 (accessed Aug 2012). (16) CCDC Website (Teaching): http://www.ccdc.cam.ac.uk/free_ services/teaching/ (accessed Aug 2012). (17) Williams, A. J.; Pence, H. E. J. Chem. Educ. 2011, 88, 683−686. (18) Science and Plants for Schools (SAPs): http://www.saps.org. uk/ (accessed Aug 2012).

Figure 6. (A) The crystal structure of menthol (from Mentha species, Mints) is an example of a cyclohexane ring in the minimum-energy chair conformation. (B) The crystal structure of the orange pigment βcarotene (from Daucus carota, wild carrot) illustrating the planarity of the extended conjugated system of double bonds.

the minimum-energy chair conformation in 3D) with isopropyl, methyl, and hydroxy substituents. The natural form, (−)-menthol, has the (1R,2S,5R) configuration and students can then be asked how many other stereoisomers of menthol could exist, to sketch their stereochemistries and, perhaps, to determine the configurational assignments of the chiral carbons. The chemical structure of the orange pigment β-carotene provides the basis for a discussion of chromophores, and the 3D structure (Figure 6B) nicely illustrates the planarity of the extended conjugated system of double bonds.

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CONCLUSION A chemical trail through the plant holdings of the Cambridge University Botanic Gardens has been described. Visitors to the gardens are provided with a laminated trail guide with the 22 stopping points marked on a map of the gardens. For each of the 22 familiar plants, the principal chemical component(s) and their applications are identified. The virtual trail on the CUBG Web site allows further CSD information to be retrieved, including interactive 3D structures to encourage chemical exploration of these important natural product molecules. Such additional information is made available to visitors to the Cambridge University Botanic Gardens via 2D QR codes that enable chemical information to be viewed on site using a smart phone. Our hope is that the trails (actual and virtual) will take advantage of students’ inherent interest in the chemistry of the natural world and encourage them to learn more about the myriad of vital chemicals that are available in the plant kingdom. We would hope to change the trail on a regular basis and, perhaps, extend the virtual trail to include many more species and chemical component(s).

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Notes

The authors declare no competing financial interest. 1394

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