AloysHüttermann TheHydrogenBond Also of interest ChemicalSynergies. FromtheLabtoInSilicoModelling Bandeira,Tylkowski(Eds.), ISBN----,e-ISBN---- PhysicsofWetting. PhenomenaandApplicationsofFluidsonSurfaces Bormashenko, ISBN----,e-ISBN---- Hydrochemistry. BasicConceptsandExercises Worch, ISBN----,e-ISBN---- AquaticChemistry. forWaterandWastewaterTreatmentApplications Lahav,Birnhack, ISBN----,e-ISBN---- Aloys Hüttermann The Hydrogen Bond A Bond for Life Author Dr.AloysHüttermann [email protected] ISBN978-3-11-062794-7 e-ISBN(PDF)978-3-11-062801-2 e-ISBN(EPUB)978-3-11-062804-3 LibraryofCongressControlNumber:2019932010 BibliographicinformationpublishedbytheDeutscheNationalbibliothek TheDeutscheNationalbibliothekliststhispublicationintheDeutscheNationalbibliografie; detailedbibliographicdataareavailableontheInternetathttp://dnb.dnb.de. ©2019WalterdeGruyterGmbH,Berlin/Boston Typesetting:IntegraSoftwareServicesPvt.Ltd. Printingandbinding:CPIbooksGmbH,Leck Coverimage:Dr.MalteReimold www.degruyter.com Preface Areyouoneofthosepeoplewhousuallyskiptheprefaceofabook?Iamdefinitely one of them, which is why drafting this preface was actually the hardest part of writingthisbook. Inmybook,Iwouldliketoelaborateonhydrogenbonding.Ihavechosenthis subjectbecauseIwantedtopresenttoyouabookaboutafieldofchemistrythat – firstofall,iseasyenoughtounderstandwithoutneedingauniversitydegree – second,alsoplaysanimportantroleinoureverydaylivesand – third,isalsohighlyrelevantinmodernscience,soasnottoonlypresentdeca- des-oldfindings. Although these three attributes actually conflict with each other, Ibelieve that my subject, hydrogen bonding, is an exception and indeed meets all these require- ments.Youwillseethatthistypeofbondiswellworthstudying. This book is roughly divided into three sections. After giving you an explana- tion of what a hydrogen bond is (first section), I will guide you through everyday phenomena (second section) all the way to modern science in which hydrogen bonds play an important role (third section). By “modern”, I mean individual re- searchprojectsandevensomeentireareasofresearchthatonlycameintobeinga fewyearsago. Of course, I also wrote this book because I enjoy writing. So I hope you will enjoyreadingit! Düsseldorf,November2018 AloysHüttermann https://doi.org/10.1515/9783110628012-201 Contents Preface V 1 Beforegettingstarted 1 2 The“bond”inhydrogenbonding 11 3 The“water”inhydrogenbonding 15 4 Theorderintheice 21 5 Dissolvinglikesugarinwater 27 6 Soapsandcells 35 7 Recogniseyourvis-à-vis 45 8 JerryDonohueandtheDNA 51 9 Howtomakehydrogenbondsvisible 61 10 “Nowlet’sstepontheaccelerator” 71 11 Substancesthatbuildthemselves 89 12 LikeAvalokiteśvaraandDurga 97 13 Conclusionandacknowledgements 115 Bibliography 117 Index 121 1 Before getting started Thisbookdealswithwhatiscalledhydrogenbonding. The word “bond” implies or means that something “comes together”. In a broadersense,chemistryisbasicallyallaboutbonding.Ahydrogenbondisabond betweenmolecules.Tounderstandthisingreaterdetail,wefirstneedtotakealook athowbondsworktobeginwith. Iam goingto startwith theverybasics– but don’t worry,it’snotthat hardto understand! So, if what I am about to tell you is something you already learnt in school,feelfreetogostraighttothenextchapter. BeforeIgetintobonds,Iwouldliketotalkaboutthe“buildingblocks”thatare capableofformingbondsinthefirstplace.Theessentialbuildingblocksinchemis- tryareelements. Youhave probablyheardofthat.Theseelementsbasicallyrepre- sent letters of a chemical alphabet, meaning all existing compounds are made up exclusivelyoftheseelements,justlikeallwordsofour(written)languagearemade upoflettersofthealphabet. Justlikealllettershaveaname–namely“A”,“B”,“C”andsoon–everyele- menthasanameandasymbolthatareusedworldwide.Mostofthemarederived fromLatinorGreek.Forexample,silveriscalled“Ag”(shortfor“argentum”=Latin for “silver”)andhydrogen“H”(shortfor“hydrogen”=Greekfor “water-former”– which is a good name, because water actually contains hydrogen). While many metals have been known and named since ancient times – mostly metals such as iron,silverandgold–mostoftheotherelementswerenamedbythosewhodiscov- eredthem.Foralongtime,nameswerechosenbasedonapropertyoftheelement, suchasinthecaseofhydrogen.Oxygen,forexample,hasthesymbol“O”for“oxy- genium” = “acid-former”, because it is found in many acids that were known in thosedays.Itwasthoughtthatthefactthatacidsareacidicwasduetothepresence ofoxygen.Althoughthisturnedouttobeincorrect,thenamewasleftunchanged. Naming conventions changed slightly over the years and, mainly in the nine- teenth century, many elements were named after cities or countries, usually the country of the person who discovered the element. This includes “Ga” (short for “gallium” = France) – right next to “Ge” (short for “germanium” = Germany). Franceisrepresentedtwice,bytheway,becausethereisalso“Fr”=francium.The element“Po”=poloniumgainedunfortunatefameduetothepoisoningofRussian Putin critic Alexander Litvinenko in 2006. By contrast, no elements were named after Great Britain and the United States during that period (which I find surpris- ing), while the small Swedish village of Ytterby inspired the names of as many as four elements because of the minerals found in the nearby Ytterby mine: yttrium “Y”,ytterbium“Yb”,terbium“Tb”anderbium“Er”. Today,morethan100chemicalelementsareknown,butonlyabout90ofthem arestableenoughtobeusedinchemistryonalargerscale.Theotherelementsare https://doi.org/10.1515/9783110628012-001 2 1 Beforegettingstarted radioactive and decay within a short period of time. But, of course, they are still givenanameandasymbol!Apartfromthetraditionofnamingelementsaftercities orcountries,thenamesoffamousscientistshave establishedthemselves asa par- ticularlypopularchoice.Thatiswhy,alongsideelementssuchasamericium“Am” (America did get the honour, after all), californium “Cf”, berkelium “Bk” (named after the Californian university town of Berkeley) and its German counterparts darmstadtium “Ds” as well as hassium“Hs”(for the Germanstate ofHesse), there isalsoeinsteinium“Es”(afterAlbertEinstein),curium“Cm”(afterMarieCurie)and roentgenium“Rg”(afterWilhelmRöntgen),amongmanyothers.Themostrecently namedelementisoganesson“Og”(afterJuriOgenasjan,oneoftheco-discoverers), discoveredattheJointInstituteforNuclearResearchinDubna,Russia. Alltheseelementsarelistedinwhatiscalledthe“periodictableofelements”, becausemanypropertiesoftheelementsrepeatperiodically. More than 90 elements used in chemistry are metals, such as iron or copper. Thechemistryoftheseelementsis(usually)called“inorganicchemistry”. Only a small number of elements, about ten, are of particular interest for this book,withthemostimportantonesbeingcarbon,hydrogen,oxygenandnitrogen. They have the symbols C (for carbon), H (for hydrogen), O (for oxygen) and N (for nitrogen). The chemistry ofthese elements, specificallythat of carbon, is (usually) called“organicchemistry”. Datingbacktoatimewhenchemistrywasstillrelativelyyoungandmanythings were not yet fully understood, the terms “inorganic” and “organic” are actually out- dated.Butsincetheyturnedouttoberatherpractical,theycontinuetobeused.Itwas long believed that “organic” material, namely, molecules that can be obtained from living organisms such as animals or plants could not be synthesised from “dead” or “inorganic” materials such as minerals. The formation of organic materials was thoughttoalwaysrequireakindofvitalforcecalled“visvitalis”,allowingorganicma- terials to form only from other organic materials. However, in 1828, German chemist FriedrichWöhlerwasabletodemonstratethatthiswasnotthecasebyproducingan organic material, urea, from inorganic starting materials. There is no essential differ- encebetweenorganicandinorganicmaterials;a“visvitalis”isnotrequired.Butsince minerals usually do have a different composition than compounds that are found in animalsorplants,thesetermscontinuetobeusedforclassification. But there is no need to go into this any further. Instead, let us start with this essentialquestion:Whydoelementsformbonds,anyway? That is a good question, because actually there are elements that hardly form anybondsandare“happybythemselves”.Theseelementsarenoblegasesandare calledhelium,neon,argon,kryptonandxenon.Thesenoblegasesexistintheform of atoms, which means “alone”. They hardly form any bonds at all, not even with themselves(hencethename“noble”).Instead,theindividualatomsineverynoble gasoccurintheformofballsthatarefloatingaroundatdifferentspeedsdepending on the temperature. But everyatom iscompletely independent and has nothing to