Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience, 2nd Edition PDF
Preview Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience, 2nd Edition
DDMM MMoolleeccuullaarr rroo ii vvll ee DDrriivviinngg FFoorrcceess ii nncc uu gg ll FFaa oorr SSttaattiissttiiccaall TThheerrmmooddyynnaammiiccss iinn BBiioollooggyy,, rr CChheemmiissttrryy,, PPhhyyssiiccss,, aanndd NNaannoosscciieennccee cc ee ss SSeeccoonndd EEddiittiioonn BB rr oo mm bb DD ee rrii ggll ll SSeeccoonndd EEddiittiioonn www.garlandscience.com KKeenn AA.. DDiillll ISBN 978-0-8153-4430-8 SSaarriinnaa BBrroommbbeerrgg 9 780815 344308 This page is intentionally left blank. Molecular Driving Forces Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience Second Edition This page is intentionally left blank. Molecular Driving Forces Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience Second Edition Ken A. Dill Sarina Bromberg With the assistance of Dirk Stigter on the Electrostatics chapters GarlandScience VicePresident:DeniseSchanck SeniorEditor:MichaelMorales AssistantEditor:MonicaToledo ProductionEditor:H.M.(Mac)Clarke Illustrator&CoverDesign:XavierStudio Copyeditor:H.M.(Mac)Clarke Typesetting:TechsetCompositionLimited Proofreader:SallyHuish Indexer:Merrall-RossInternational,Ltd. KenA.DillisProfessorandDirectoroftheLauferCenterforPhysicalandQuantitative BiologyatStonyBrookUniversity.HereceivedhisundergraduatetrainingatMIT,hisPhD fromtheUniversityofCalifornia,SanDiego,didpostdoctoralworkatStanford,andwas ProfessorattheUniversityofCalifornia,SanFranciscountil2010.Aresearcherin statisticalmechanicsandproteinfolding,hehasbeenthePresidentoftheBiophysical SocietyandisamemberoftheUSNationalAcademyofSciences. SarinaBrombergreceivedherBFAattheCooperUnionfortheAdvancementofScience andArt,herPhDinmolecularbiophysicsfromWesleyanUniversity,andherpostdoctoral trainingattheUniversityofCalifornia,SanFrancisco.Shewrites,edits,andillustrates scientifictextbooks. DirkStigter(1924–2010)receivedhisPhDfromtheStateUniversityofUtrecht,The Netherlands,anddidpostdoctoralworkattheUniversityofOregon,Eugene. ©2011byGarlandScience,Taylor&FrancisGroup,LLC Thisbookcontainsinformationobtainedfromauthenticandhighlyregardedsources. Reprintedmaterialisquotedwithpermission,andsourcesareindicated.Awidevarietyof referencesarelisted.Reasonableeffortshavebeenmadetopublishreliabledataand information,buttheauthorandthepublishercannotassumeresponsibilityforthe validityofallmaterialsorfortheconsequencesoftheiruse.Allrightsreserved.Nopartof thispublicationmaybereproduced,storedinaretrievalsystem,ortransmittedinany formorbyanymeans—graphic,electronic,ormechanical,includingphotocopying, recording,taping,orinformationstorageandretrievalsystems—withoutpermissionofthe copyrightholder. ISBN978-0-8153-4430-8 LibraryofCongressCataloging-in-PublicationData Dill,KenA. Moleculardrivingforces:statisticalthermodynamicsinchemistry, physics,biology,andnanoscience/KenDill,SarinaBromberg.––2nded. p.cm. Includesindex. ISBN978-0-8153-4430-8(pbk.) 1.Statisticalthermodynamics.I.Bromberg,Sarina.II.Title. QC311.5.D552010 536’.7––dc22 2010034322 PublishedbyGarlandScience,Taylor&FrancisGroup,LLC,aninformabusiness, 270MadisonAvenue,NewYork,NY10016,USA,and 2ParkSquare,MiltonPark,Abingdon,OX144RN,UK PrintedintheUnitedStatesofAmerica 151413121110987654321 Visitourwebsiteathttp://www.garlandscience.com DedicatedtoAustin,Peggy,Jim,Jolanda,Tyler,andRyan and In memory of Dirk Stigter This page is intentionally left blank. Preface Whatforcesdriveatomsandmoleculestobind,toadsorb,todissolve,toper- meate membranes, to undergo chemical reactions, and to undergo conforma- tional changes? This is a textbook on statistical thermodynamics. It describes the forces that govern molecular behavior. Statistical thermodynamics uses physical models, mathematical approximations, and empirical laws that are rootedinthelanguageofentropy,distributionfunction,energy,heatcapacity, free energy, and partition function, to predict the behaviors of molecules in physical,chemical,andbiologicalsystems. This text is intended for graduate students and advanced undergraduates in physical chemistry, biochemistry, biophysics, bioengineering, polymer and materials science, pharmaceutical chemistry, chemical engineering, and envi- ronmentalscience. We had three goals in mind as we wrote this book. First, we tried to make extensive connections with experiments and familiar contexts, to show the practical importance of this subject. We have included many applications in biology and polymer science, in addition to applications in more traditional areasofchemistryandphysics.Second,wetriedtomakethisbookaccessible to students with a variety of backgrounds. So, for example, we have included material on probabilities, approximations, partial derivatives, vector calculus, andthehistoricalbasisofthermodynamics.Third,westrovetofindavantage pointfromwhichtheconceptsarerevealedintheirsimplestandmostcompre- hensible forms. For this reason, we follow the axiomatic approach to thermo- dynamics developed by HB Callen, rather than the more traditional inductive approach;andtheMaximumEntropyapproachofJaynes,Skilling,andLivesay, inpreferencetotheGibbsensemblemethod.Wehavedrawnfrommanyexcel- lent texts, particularly those by Callen, Hill, Atkins, Chandler, Kubo, Kittel & Kroemer,Carrington,Adkins,Weiss,Doi,Flory,andBerry,Rice,&Ross. Ourfocushereisonmoleculardrivingforces,whichoverlapswith—butis not identical to—the subject of thermodynamics. While the power of thermo- dynamicsisitsgenerality,thepowerofstatisticalthermodynamicsistheinsight itgivesintomicroscopicinteractionsthroughtheenterpriseofmodel-making. A central theme of this book is that making models, even very simple ones, is a route to insight and to understanding how molecules work. A good theory, nomatterhowcomplexitsmathematics,isusuallyrootedinsomeverysimple physicalidea. Models are mental toys to guide our thinking. The most important ingre- dientsinagoodmodelarepredictivepowerandinsightintothecausesofthe predicted behavior. The more rigorous a model, the less room for ambiguity. Butmodelsdon’tneedtobecomplicatedtobeuseful.Manyofthekeyinsights instatisticalmechanicshavecomefromsimplificationsthatmayseemunreal- isticatfirstglance:particlesrepresentedasperfectsphereswithatomicdetail left out, neglecting the presence of other particles, using crystal-like lattices ofparticlesinliquidsandpolymers,andmodelingpolymerchainsasrandom flights,etc.Toborrowaquote,statisticalthermodynamicshasahistoryofwhat might be called the unreasonable effectiveness of unrealistic simplifications. Perhapstheclassicexampleisthetwo-dimensionalIsingmodelofmagnetsas twotypesofarrows,upspinsordownspins,onsquarelattices.LarsOnsager’s Preface vii famous solution to this highly simplified model was a major contribution to the modern revolution in our understanding of phase transitions and critical phenomena. Webeginwithentropy.Chapter1givestheunderpinningsintermsofprob- abilities and combinatorics. Simple models are used in Chapters 2 and 3 to showhowentropyisadrivingforce.Thismotivatesmoredetailedtreatments throughout the text illustrating the Second Law of Thermodynamics and the concept of equilibrium. Chapter 4 lays out the mathematical foundations in multivariatecalculusthatareneededforthefollowingchapters. ThesethreadsculminateinChapter5,whichdefinestheentropyandgives the Boltzmann distribution law, the lynch-pi(cid:2)n of statistical thermodynamics. The key expressions, S =klnW and S =−k ipilnpi, are shown to provide themathematicsforanextremumprinciplethatunderpinsthermodynamics. The principles of thermodynamics are described in Chapters 6–9. The statistical mechanics of simple systems follows in Chapters 10 and 11. While temperature and heat capacity are often regarded as needing no explanation (perhapsbecausetheyaresoreadilymeasured),Chapter12usessimplemod- els to shed light on the physical basis of those properties. Chapter 13 applies theprinciplesofstatisticalthermodynamicstochemicalequilibria. Chapters14–16developsimplemodelsofliquidsandsolutions.Weuselat- ticemodelshere,ratherthanidealsolutiontheories,becausesuchmodelsgive moremicroscopicinsightintorealmoleculesandintothesolvationprocesses that are central to computational chemistry, biology, and materials science. For example, theories of mixtures often begin from the premise that Raoult’s and Henry’s laws are experimental facts. Our approach, instead, is to show whymoleculesaredriventoobeytheselaws.Anequallyimportantreasonfor introducinglatticemodelshereisasbackground.Latticemodelsarestandard tools for treating complex systems: phase transitions and critical phenomena inChapters25and26,andpolymerconformationsinChapters32–34. We explore the dynamic processes of diffusion, transport, and physical andchemicalkineticsinChapters17–19,throughFick’slaw,therandom-fight model, Poisson and waiting-time distributions, the Langevin model, Onsager relations, Brownian ratchets, time correlation functions and transition-state theory. WetreatelectrostaticsinChapters20–23.Ourtreatmentismoreextensive thaninotherphysicalchemistrytextsbecauseoftheimportance,inourview, of electrostatics in understanding the structures of proteins, nucleic acids, micelles,andmembranes;forpredictingproteinandnucleicacidligandinter- actions and the behaviors of ion channels; as well as for the classical areas of electrochemistry and colloid science. We explore acid–base and oxidation– reductionequilibriaanddeveloptheNernstandPoisson–Boltzmannequations and the Born model, modern workhorses of quantitative biology. Chapter 24 describesintermolecularforces. We describe simple models of complex systems, including polymers, col- loids,surfaces,andcatalysts.Chapters25and26focusoncooperativity:phase equilibria, solubilities, critical phenomena, and conformational transitions, described through mean-field theories, the Ising model, helix–coil model, and Landautheory.Chapters27–29describebindingpolynomialsandhowproteins viii Preface
The list of books you might like
