http://www.ch.ic.ac.uk/motm/ A Project started in December 1995 by Henry Rzepa (Imperial College) and Paul May (Bristol University) Imperial College London rzepa@imperial.ac.uk http://www.ch.ic.ac.uk/motm/motm.gif http://www.ch.ic.ac.uk/motm/ Molecules of the Month: A series of stories about interesting molecules or collections of molecules http://www.ch.ic.ac.uk/motm/cavities.html A pericyclic reaction is one in which bonds are made or broken in a concerted cyclic transition state. The accepted wisdom for such reactions is that they have several characteristic properties, once of which is that no catalyst is needed to promote the reactions. In the last twenty years however, many examples of catalysed pericyclic reactions have been discovered, included those mediated by transition metals, and by metals acting as Lewis acids. It has also been known for some time that it is also possible to accelerate some pericyclic reactions by the use of pressure, especially for those reactions involving a substantial decrease in volume such as Diels-Alder cycloadditions. This has prompted much recent interest in replacing simple pressure for inducing the reaction, by persuading the reactants to enter a cavity or binding site instead. Examples are now known for using the crystal lattice of a simple hydrogen bonded organic molecule to achieve this, as well as an "abzyme" or enzyme produced from artificial catalytic antibodies. Anthracene Resorcinol 2003-12-10T00:00:00-00:00 Henry S. Rzepa 1.12Beta/4C26H18O4.C6H8.2C5H8O2/c4*27-17-9-15(10-18(28)13-17)25-21-5-1-2-6-22(21)26(24-8-4-3-7-23(24)25)16-11-19(29)14-20(30)12-16;1-2-4-6-5-3-1;2*1-3-5(6)7-4-2/h4*1-14H,27-30H;1-4H,5-6H2;2*1H2,2H3,3H,4H2 http://www.ch.ic.ac.uk/motm/perkin.html Whilst the origin of the modern industrial revolution is often traced to the Ironbridge Gorge northwest of Birmingham in the UK, less credit is given to one of the birthplaces of the modern organic chemical industry. William Henry Perkin (1838-1907) who at the age of 18 had set out with idea of making quinine (C20H24N2O2) by oxidising allytoluidine (C10H12N), had accidentally produced instead the first ever synthetic dye (aniline purple, better known as mauveine (actual formula of principal component C26H23N4+X-, X= sulphate, acetate etc). It is worth noting that molecular structure of few compounds were known with certainty at this time, and even that of benzene had only recently been recognised by Kekule. Mauveine 1995-12-20T00:00:00-00:00 Henry S. Rzepa 1.12Beta/C26H22N4/c1-17-8-10-19(11-9-17)28-20-12-13-23-25(15-20)30(21-6-4-3-5-7-21)26-16-22(27)18(2)14-24(26)29-23/h1-2H3,3-16H,(H2,27,28)/p+1 http://www.ch.ic.ac.uk/motm/dna.html Hairpin loop DNA DNA 1995-12-20T00:00:00-00:00 Henry S. Rzepa 1.12Beta/C116H254N40O77P12/c1-45-25-149(113(170)141-97(45)158)81-17-53(66(215-81)34-204-236(179,180)223-50-14-78(146-10-6-74(118)130-110(146)167)213-64(50)32-202-244(195,196)232-59-23-87(155-43-127-91-95(155)135-107(123)139-103(91)164)221-71(59)39-209-238(183,184)224-51-15-79(147-11-7-75(119)131-111(147)168)212-63(51)31-201-243(193,194)230-57-21-85(219-62(57)30-199-234(174,175)176)153-41-125-89-93(153)133-105(121)137-101(89)162)226-239(185,186)205-35-67-54(18-82(216-67)150-26-46(2)98(159)142-114(150)171)227-240(187,188)206-36-68-55(19-83(217-68)151-27-47(3)99(160)143-115(151)172)228-241(189,190)207-37-69-56(20-84(218-69)152-28-48(4)100(161)144-116(152)173)229-242(191,192)210-40-72-60(24-88(222-72)156-44-128-92-96(156)136-108(124)140-104(92)165)233-245(197,198)203-33-65-52(16-80(214-65)148-12-8-76(120)132-112(148)169)225-237(181,182)208-38-70-58(22-86(220-70)154-42-126-90-94(154)134-106(122)138-102(90)163)231-235(177,178)200-29-61-49(157)13-77(211-61)145-9-5-73(117)129-109(145)166/h1-4H3,5-44H2,45-116H,117-124H2,125-144H,157-198H,234-245H/t45?,46?,47?,48?,49-,50-,51-,52-,53-,54-,55-,56-,57-,58-,59-,60-,61+,62+,63+,64+,65+,66+,67+,68+,69+,70+,71+,72+,73?,74?,75?,76?,77+,78+,79+,80+,81+,82+,83+,84+,85+,86+,87+,88+,89?,90?,91?,92?,93?,94?,95?,96?,97?,98?,99?,100?,101?,102?,103?,104?,105?,106?,107?,108?,109?,110?,111?,112?,113?,114?,115?,116?/m0/s1 http://www.ch.ic.ac.uk/motm/cyclooctene.html Nature is not symmetrical at least at the molecular level. Pasteur was one of the first to spot this in the asymmetry of tiny crystals of tartaric acid salts. The DNA double helix tends to spiral only one way even though it would be just as easy for it to twirl the other while nature almost invariably uses only the left-handed form of the amino acids to build its proteins. Numerous theories exist that attempt to explain the bias which lies at the very roots of life itself but now Japanese researchers think they have found evidence to support one of the more bizarre, that says the chemical solution lies in the stars. Chiral cyclo-octene 2003-12-10T00:00:00-00:00 David Bradley; Henry S. Rzepa 1.12Beta/C8H14/c1-2-4-6-8-7-5-3-1/h1-2H,3-8H2/b2-1+ http://www.ch.ic.ac.uk/motm/borkent/sharpless.html The Sharpless asymmetric epoxidation of allylic alcohols. This discussion is based on the paper by Y.D. Wu and D. Lai, J.Amer.Chem.Soc. 117 11327 (1995), a DFT study on the selectivity of this reaction. The structure below is not the outcome of their calculations; it is a hand-made reconstruction of the complex they suggest as a transition state that explains the experimental findings. asymmetric epoxidation 2003-12-10T00:00:00-00:00 Hens Borkent 1.12Beta/C8H14O5.C8H13O5.C4H9O.2C3H7O.C3H5O.H2O.2O.2Ti/c2*1-3-12-7(10)5-6(9)8(11)13-4-2;1-4(2,3)5;2*1-3(2)4;1-2-3-4;;;;;/h1-2H3,3-5H2,6H,8H;1-2H3,3-5H2,6H;1-3H3;2*1-2H3,3H;1H2,2H,3H2;1H2;;;;/q-2;5*-1;;;;2*+4/p-1/t6-,8?;6-;;;;;;;;;/m11........./s1 http://www.ch.ic.ac.uk/motm/spirala.html Helicoidal Graphite, otherwise known as helical bucky tubes Spiroidal Graphite 2003-12-10T00:00:00-00:00 Henry S. Rzepa http://www.ch.ic.ac.uk/motm/viagra.html Sildenafil, trade name VIAGRATM, chemical name 5-[2-ethoxy-5-(4-methylpiperazin-1-ylsulfonyl)phenyl]-1-methyl-3-propyl-1,6-dihydro-7H-pyrazolo[4,3- d]pyrimidin-7-one, formula C22H30N6O4S, was discovered through a rational drug design programme by the pharmaceutical company Pfizer. Viagra 2003-12-10T00:00:00-00:00 Henry S. Rzepa 1.12Beta/C22H30N6O4S/c1-5-7-17-19-20(27(4)25-17)22(29)24-21(23-19)16-14-15(8-9-18(16)32-6-2)33(30,31)28-12-10-26(3)11-13-28/h1-4H3,5-7H2,8-9H,10-13H2,14H,(H,23,24,29) http://www.ch.ic.ac.uk/motm/trefoil/ With the current interest in so called "nanoscale" devices with dimensions reaching down to molecular sizes, there exists a fascinating boundary between the shapes that materials (i.e. a large collection of molecules) and molecules themselves can adopt. Understanding how molecular building blocks can be used to construct nanoscale devices is the key to understanding nanotechnology. A second boundary exists, between idealised shapes, or topologies, defined by mathematical equations, and the actual shapes adopted by the collections of atoms (nuclei and electrons) we call molecules. The Trefoil Knot and the Mšbius Strip are two such topologies which span both boundaries. Trefoils 2003-12-10T00:00:00-00:00 Henry S. Rzepa 1.12Beta/C104H110N8O12.2Cu/c1-2-6-10-86-38-22-78-14-18-82-34-50-94(110-102(82)98(78)106-86)74-27-43-90(44-28-74)122-70-66-118-62-58-114-55-56-116-60-64-120-68-72-124-92-47-31-76(32-48-92)96-52-36-84-20-16-80-24-40-88(108-100(80)104(84)112-96)12-8-4-3-7-11-87-39-23-79-15-19-83-35-51-95(111-103(83)99(79)107-87)75-29-45-91(46-30-75)123-71-67-119-63-59-115-54-53-113-57-61-117-65-69-121-89-41-25-73(26-42-89)93-49-33-81-17-13-77-21-37-85(9-5-1)105-97(77)101(81)109-93;;/h1-12H2,13-27H,28H2,29H,30H2,31H,32H2,33-52H,53-72H2,98-100H;;/b94-74-,95-75-,96-76-;; http://www.ch.ic.ac.uk/motm/trefoil/ With the current interest in so called "nanoscale" devices with dimensions reaching down to molecular sizes, there exists a fascinating boundary between the shapes that materials (i.e. a large collection of molecules) and molecules themselves can adopt. Understanding how molecular building blocks can be used to construct nanoscale devices is the key to understanding nanotechnology. A second boundary exists, between idealised shapes, or topologies, defined by mathematical equations, and the actual shapes adopted by the collections of atoms (nuclei and electrons) we call molecules. The Trefoil Knot and the Mšbius Strip are two such topologies which span both boundaries. Mobius strips 2003-12-10T00:00:00-00:00 Henry S. Rzepa 1.12Beta/C16H32/c1-2-4-6-8-10-12-14-16-15-13-11-9-7-5-3-1/h1-16H2 http://www.ch.ic.ac.uk/motm/nanobiotic/ Conventional anti-biotics such as penicillins etc function metabolically, by interfering with bacterial synthesis of the cell wall. Many bacteria have evolved to develop resistance to common anti-biotics, and some bacterial are resistent to most. In 1993, a new approach to developing such agents was pioneered. Reza Ghadiri at the Scripps Research Institute in California developed a series of cyclic peptides using a combination of the natural (l) form with the un-natural (d) amino acid enantiomer. It has been known for some time that the stacking of crystals composed entirely of molecules of one chiral form (all in a so called R or an S configuration) can be quite different from the racemic form of the same molecule, which contains equal amounts of R and S isomers. Nanobiotics 2003-12-10T00:00:00-00:00 Henry S. Rzepa