Advances in Chemical Physics, Volume 153 PDF
Preview Advances in Chemical Physics, Volume 153
ADVANCESINCHEMICALPHYSICS VOLUME153 EDITORIAL BOARD KurtBinder, CondensedMatterTheoryGroup,InstitutFürPhysik,JohannesGutenberg- Universität,Mainz,Germany WilliamT.Coffey, DepartmentofElectronicandElectricalEngineering,PrintingHouse, TrinityCollege,Dublin,Ireland KarlF.Freed, DepartmentofChemistry,JamesFranckInstitute,UniversityofChicago, Chicago,IllinoisUSA Daan Frenkel, Department of Chemistry, Trinity College, University of Cambridge, Cambridge,UnitedKingdom PierreGaspard, CenterforNonlinearPhenomenaandComplexSystems,UniversitéLibre deBruxelles,Brussels,Belgium Martin Gruebele, Departments of Physics and Chemistry, Center for Biophysics and ComputationalBiology,UniversityofIllinoisatUrbana-Champaign,Urbana,Illinois USA GerhardHummer, TheoreticalBiophysicsSection,NIDDK-NationalInstitutesofHealth, Bethesda,MarylandUSA Ronnie Kosloff, Department of Physical Chemistry, Institute of Chemistry and Fritz HaberCenterforMolecularDynamics,TheHebrewUniversityofJerusalem,Israel Ka Yee Lee, Department of Chemistry, James Franck Institute, University of Chicago, Chicago,IllinoisUSA Todd J. Martinez, Department of Chemistry, Photon Science, Stanford University, Stanford,CaliforniaUSA ShaulMukamel, DepartmentofChemistry,SchoolofPhysicalSciences,Universityof California,Irvine,CaliforniaUSA JoseN.Onuchic, DepartmentofPhysics,CenterforTheoreticalBiologicalPhysics,Rice University,Houston,TexasUSA Stephen Quake, Department of Bioengineering, Stanford University, Palo Alto, CaliforniaUSA Mark Ratner, Department of Chemistry, Northwestern University, Evanston, Illinois USA DavidReichman, DepartmentofChemistry,ColumbiaUniversity,NewYorkCity,New YorkUSA GeorgeSchatz, DepartmentofChemistry,NorthwesternUniversity,Evanston,Illinois USA Steven J. Sibener, Department of Chemistry, James Franck Institute, University of Chicago,Chicago,IllinoisUSA Andrei Tokmakoff, Department of Chemistry, James Franck Institute, University of Chicago,Chicago,IllinoisUSA DonaldG.Truhlar, DepartmentofChemistry,UniversityofMinnesota,Minneapolis, MinnesotaUSA JohnC.Tully, DepartmentofChemistry,YaleUniversity,NewHaven,Connecticut,USA ADVANCES IN CHEMICAL PHYSICS VOLUME153 EditedBy STUARTA.RICE DepartmentofChemistry and TheJamesFranckInstitute, TheUniversityofChicago, Chicago,Illinois AARONR.DINNER DepartmentofChemistry and TheJamesFranckInstitute, TheUniversityofChicago, Chicago,Illinois Copyright©2013byJohnWiley&Sons,Inc.Allrightsreserved. PublishedbyJohnWiley&Sons,Inc.,Hoboken,NewJersey. PublishedsimultaneouslyinCanada. 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Wileyalsopublishesitsbooksinavarietyofelectronicformats.Somecontentthatappearsinprint maynotbeavailableinelectronicformats.FormoreinformationaboutWileyproducts,visitourweb site at www.wiley.com. LibraryofCongressCatalogNumber:58-9935 ISBN:978-1-118-47786-1 PrintedintheUnitedStatesofAmerica 10 9 8 7 6 5 4 3 2 1 CONTRIBUTORS TO VOLUME 153 Majed Chergui, Ecole Polytechnique Fe´de´rale de Lausanne, Laboratoire de SpectroscopieUltrarapide,ISIC,FSB-BSP,1015Lausanne,Switzerland LiviuF.Chibotaru, DivisionofQuantumandPhysicalChemistry,Katholieke UniversiteitLeuven,Celestijnenlaan200F,3001Leuven,Belgium WilliamT.Coffey, DepartmentofElectronicandElectricalEngineering,Trinity College,Dublin2,Ireland William J. Dowling, Department of Electronic and Electrical Engineering, TrinityCollege,Dublin2,Ireland Yuri P. Kalmykov, Laboratoire de Mathématiques et Physique, Universite´ de Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan Cedex, France Srihari Keshavamurthy, Department of Chemistry, Indian Institute of Technology,Kanpur208016,India ChristopherJ.Milne, EcolePolytechniqueFe´de´raledeLausanne,Laboratoire deSpectroscopieUltrarapide,ISIC,FSB-BSP,1015Lausanne,Switzerland Andrew Mugler, FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam,TheNetherlands Thomas J. Penfold, Ecole Polytechnique Fe´de´rale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, FSB-BSP, 1015 Lausanne; Ecole Polytechnique Fe´de´rale de Lausanne, Laboratoire de Chimie et Biochimie Computationnelles,ISIC,FSBBSP,1015Lausanne;SwissFEL,PaulScherrer Institut,5232Villigen,Switzerland ElizabethA.Ploetz, DepartmentofChemistry,KansasStateUniversity,213 CBCBuilding,Manhattan,KS66506-0401,USA Paul E. Smith, Department of Chemistry, Kansas State University, 213 CBC Building,Manhattan,KS66506-0401,USA PieterReintenWolde, FOMInstituteAMOLF,SciencePark104,1098XG Amsterdam,TheNetherlands SergueyV.Titov, KotelnikovInstituteofRadioEngineeringandElectronicsof theRussianAcademyofSciences,VvedenskiiSquare1,Fryazino,Moscow Region141190,RussianFederation v PREFACE TO THE SERIES Advances in science often involve initial development of individual specialized fieldsofstudywithintraditionaldisciplinesfollowedbybroadeningandoverlap, or even merging, of those specialized fields, leading to a blurring of the lines between traditional disciplines. The pace of that blurring has accelerated in the past few decades, and much of the important and exciting research carried out todayseekstosynthesizeelementsfromdifferentfieldsofknowledge.Examples ofsuchresearchareasincludebiophysicsandstudiesofnanostructuredmaterials. As the study of the forces that govern the structure and dynamics of molecular systems,chemicalphysicsencompassestheseandmanyotheremergingresearch directions.Unfortunately,thefloodofscientificliteraturehasbeenaccompanied by losses in the shared vocabulary and approaches of the traditional disciplines, andthereismuchpressurefromscientificjournalstobeevermoreconciseinthe descriptionsofstudies,tothepointthatmuchvaluableexperience,ifrecordedat all, is hidden in supplements and dissipated with time. These trends in science and publishing make this series, Advances in Chemical Physics, a much needed resource. The Advances in Chemical Physics is devoted to helping the reader obtain general information about a wide variety of topics in chemical physics, a field thatweinterpretverybroadly.Ourintentistohaveexpertspresentcomprehensive analysesofsubjectsofinterestandtoencouragetheexpressionofindividualpoints ofview.Wehopethatthisapproachtothepresentationofanoverviewofasubject will both stimulate new research and serve as a personalized learning text for beginnersinafield. StuartA.Rice AaronR.Dinner vii CONTENTS RecentAdvancesinUltrafastX-rayAbsorptionSpectroscopy 1 ofSolutions ByThomasJ.Penfold,ChristopherJ.Milne,andMajedChergui ScalingPerspectiveonIntramolecularVibrationalEnergy 43 Flow:Analogies,Insights,andChallenges BySrihariKeshavamurthy LongestRelaxationTimeofRelaxationProcessesforClassical 111 andQuantumBrownianMotioninaPotential:EscapeRate TheoryApproach ByWilliamT.Coffey,YuriP.Kalmykov,SergueyV.Titov,and WilliamJ.Dowling LocalFluctuationsinSolution:TheoryandApplications 311 ByElizabethA.PloetzandPaulE.Smith TheMacroscopicEffectsofMicroscopicHeterogeneityin 373 CellSignaling ByAndrewMuglerandPieterReintenWolde AbInitioMethodologyforPseudospinHamiltoniansof 397 AnisotropicMagneticComplexes ByL.F.Chibotaru AuthorIndex 521 SubjectIndex 551 ix RECENT ADVANCES IN ULTRAFAST X-RAY ABSORPTION SPECTROSCOPY OF SOLUTIONS THOMASJ.PENFOLD,1,2,3CHRISTOPHERJ.MILNE,1 andMAJEDCHERGUI1 1EcolePolytechniqueFe´de´raledeLausanne,LaboratoiredeSpectroscopie Ultrarapide,ISIC,FSB-BSP,1015Lausanne,Switzerland 2EcolePolytechniqueFe´de´raledeLausanne,LaboratoiredeChimieet BiochimieComputationnelles,ISIC,FSB-BSP,1015Lausanne,Switzerland 3SwissFEL,PaulScherrerInstitut,5232Villigen,Switzerland CONTENTS I. Introduction II. ExperimentalMethods A. Steady-StateXAS 1. TransmissionandFluorescenceDetectionModes B. Time-ResolvedXAS 1. GeneralSetup 2. InterpretationoftheTransientSignal C. SourcesofUltrafastX-rayPulsesandDataAcquisition 1. PicosecondXAS 2. FemtosecondXAS:TheSlicingScheme 3. FutureDevelopments:X-FELs III. TheoreticalApproachesforXAFS A. StructuralAnalysis:TheEXAFSRegion B. TheQuasiparticleApproximation:ModelingtheNearEdge 1. Green’sFunctionsandMultipleScatteringTheory 2. BeyondSphericalPotentials C. Many-BodyEffects 1. TheSelf-EnergyOperator 2. Time-DependentDensityFunctionalTheory 3. Post-Hartree–FockMethods D. BeyondPicosecondTemporalResolution AdvancesinChemicalPhysics,Volume153,SecondEdition.EditedbyStuartA.Riceand AaronR.Dinner. ©2013JohnWiley&Sons,Inc.Published2013byJohnWiley&Sons,Inc. 1 2 thomasj.penfoldetal. IV. Examples A. PhotoinducedHydrophobicity B. Spin-CrossoverMolecularSystems C. SolventEffects D. IntramolecularChargeTransfer V. Outlook Acknowledgments References I. INTRODUCTION TheadventofstructuraltechniquessuchasX-ray,electronandneutrondiffraction, nuclear magnetic resonance (NMR), and X-ray absorption spectroscopy (XAS) hasmadeitpossibletodirectlyextractthestructureofmoleculesandcondensed matter systems, with a strong impact in physics, chemistry, and biology [1–7]. However, the static structure of the systems under study means that often the mechanismsunderlyingtheirfunctionareunknown.Thus,fromtheearlydaysof femtochemistry,effortsweredeployedtoimplementthesestructuraltoolsintime- domain experiments [8–11]. Since the first implementation of XAS in a pump– probetypeexperiment[12]inthemicro-tomillisecondrange,time-resolvedXAS has emerged as the method of choice for the study of local structural changes of molecules in solution. The wealth of electronic and geometric information availablefromanX-rayabsorptionspectrumhasledtoitsimplementationforthe studyofawidevarietyofsystems[1–7,13–22]. AnX-rayabsorptionspectrumischaracterizedbyabsorptionedges,whichre- flecttheexcitationofcoreelectronstotheionizationthresholdandisconsequently elementspecific.Foraparticularedge,anelectronisinitiallyexcitedtounoccu- piedorpartiallyfilledorbitalsjustbelowtheionizationpotential(IP)givingrise tobound–boundtransitions,whichformthepre-edgefeatures.Thisregion,thus, yieldsinformationaboutthenatureoftheunoccupiedvalenceorbitals,asthetran- sitionprobabilityisgovernedprimarilybytheatomicdipoleselectionrules.Above theIP,resonancesshowupduetointerferencesofthephotoelectronwavefromthe absorbingatomwiththewavescatteredbackfromtheneighboringatoms.Whenthe kineticenergyoftheelectronislarge,thatis,wellabovetheedge,singlescattering (SS)eventsusuallydominate,asthescatteringcrosssectionofthephotoelectronis small.ThisregioniscalledtheextendedX-rayabsorptionfinestructure(EXAFS) region and it delivers information about coordination numbers and the distance ofthenearestneighborstotheabsorbingatom.Incontrast,atlowphotoelectron energies (<50 eV above the edge) contained within the X-ray absorption near- edgestructure(XANES)region,resonancesariseprimarilyfromtheinterference ofscatteringpathwaysbetweenmultipleatoms,thatismultiplescattering(MS). Thisregioncontainsinformationaboutthethree-dimensionalstructurearoundthe absorbingatom,i.e.coordinationnumbers,bonddistances,andbondangles. recentadvancesinultrafastx-rayabsorptionspectroscopy 3 Themethodologyfortime-resolvedXAShasbeendevelopedatthebeginning ofthe2000s[8,9,11,23–30].Itgenerallyconsistsofanopticalpump/X-rayprobe experimentoperatinginatransientabsorptiongeometry,wherethelaser-induced changesinthesampleX-rayabsorptioncoefficientareprobedbytheX-raypulse as a function of energy and time delay with respect to the laser pulse. In most cases,theX-rayabsorption-inducedchangesarerecordedonapulse-to-pulseba- sis with the X-ray transmission through the sample being recorded at twice the repetitionrateofthelaser[26,31].Insuchcasesthelaserpulseisfromanampli- fiedfemtosecondsystemoperatingat1kHz,inordertoensureahighphotolysis yield, and the X-ray synchrotron pulses (typically 50–100 ps long) are recorded at a repetition rate of 2 kHz. This implies a significant loss of X-ray flux since synchrotrons operate at MHz repetition rates. In recent years the methodology fortime-resolvedXASstudieshasseensignificantdevelopmentsinbothtempo- ralresolutionandsignal-to-noiseratio(S/N).Inparticular,theimplementationof the slicing scheme [32] has made it possible to demonstrate femtosecond XAS ofphotoexcitedspeciesinsolutions[33–36].Inaddition,aschemeusingahigh- repetition rate pump laser, operating at an integer fraction of that of the storage ring [37–39], has allowed exploitation of up to two orders of magnitude more X-ray photons than previous schemes based on the use of kHz lasers for picosecond (ps) XAS experiments. Consequently this has led to over an order of magnitude increase of S/N compared to the previous schemes. Finally, the adventoftheX-rayfreeelectronlasers(X-FELs)isopeningnewopportunitiesin the area of structural dynamics [40–42], as X-FELs have a 10 orders of magni- tudelargerfluxperpulse,comparedtotheslicingschemeatcomparabletemporal resolution. ThecomplexmechanismbehindtheoriginofX-rayabsorptionspectrameans that their analysis is inextricably linked to detailed theoretical simulations, tra- ditionally performed using MS theory within the limits of the muffin-tin (MT) potential[3].Thisapproachiscomputationallyveryefficientandsufficientwhen the photoelectron is not sensitive to the details of the potential near the ioniza- tion limit. However, the limitation of the MT approximation close to the edge means that such calculations cannot always interpret the entire spectrum, par- ticularly the near-edge region. The above experimental developments as well as continuousimprovementsintheinstrumentationareenhancingthesensitivityof both static and time-resolved XAS experiments, thanks to which finer details of the spectra are uncovered. This calls for more detailed theoretical approaches and the last decade has witnessed significant developments, in particular for the simulation of X-ray absorption spectra beyond the MT potential. These include traditional electronic structure methods extended to core hole excitations [43–45]. In addition, there has been extensive work to move beyond the quasi- particleapproximation(QPA),whichtreatstheexcitedelectronasasingleparticle movinginanaveragepotential.Many-bodyeffects,whicharisefromthebreak- downofthisapproximation,suchastheintrinsicandextrinsiclosses[3],haveuntil
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