Photoinduced Phenomena in Nucleic Acids I: Nucleobases in the Gas Phase and in Solvents

365 Pages·2015·9.27 MB·English

by  Mario Barbatti

Topics in Current Chemistry 355
Mario Barbatti
Antonio Carlos Borin
Susanne Ullrich Editors
Photoinduced
Phenomena in
Nucleic Acids I
Nucleobases in the Gas Phase and
in Solvents
355
Topics in Current Chemistry
Editorial Board:
H. Bayley, Oxford, UK
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Mario Barbatti (cid:129) Antonio Carlos Borin (cid:129)
Susanne Ullrich
Editors
Photoinduced Phenomena
in Nucleic Acids I
Nucleobases in the Gas Phase and in Solvents
With contributions by
(cid:1) (cid:1) (cid:1)
M. Barbatti V. Barone A.C. Borin
C.E. Crespo-Herna´ndez (cid:1) M.S. de Vries (cid:1) A. Giussani (cid:1)
L. Gonza´lez (cid:1) M. Hochlaf (cid:1) R. Improta (cid:1) S. Mai (cid:1)
P. Marquetand (cid:1) L. Mart´ınez-Ferna´ndez (cid:1) S. Matsika (cid:1)
M. Mercha´n (cid:1) M. Pollum (cid:1) M. Richter (cid:1) D. Roca-Sanjua´n (cid:1)
M. Schwell (cid:1) J. Segarra-Mart´ı (cid:1) S. Ullrich
Editors
MarioBarbatti AntonioCarlosBorin
Max-Planck-Institutfu¨rKohlenforschung InstituteofChemistry
Mu¨lheimanderRuhr UniversityofSa˜oPaulo
Germany Sa˜oPaulo
Brazil
SusanneUllrich
DepartmentofPhysicsandAstronomy
TheUniversityofGeorgia
Athens
Georgia,USA
ISSN0340-1022 ISSN1436-5049(electronic)
ISBN978-3-319-13370-6 ISBN978-3-319-13371-3(eBook)
DOI10.1007/978-3-319-13371-3
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Preface
Photoinducedprocessesinnucleicacidsarephenomenaoffundamentalimportance
for our biosphere. Ultraviolet solar radiation has been a continuous factor of
evolutionary pressure since early biotic ages by triggering mutations, cell death,
andcarcinogenesis.ThestudyofhowUVradiationimpactsnucleicacidshasalong
history, which parallels the evolution of our understanding of genetics from the
beginningofthetwentiethcentury.Ithas,however,beenmainlyinthelastdecade
that major knowledge gaps have been filled in the field. This has been achieved
thankstothedevelopmentofadvancedspectroscopictechniquesandcomputational
models,whichhaveallowedreal-timeobservationandsimulationoftheevolution
ofelectronicexcitationscausedbyradiation.
This book embraces a broad range of topics in nucleic-acid research. It brings
togetherleadingspecialistsfromdifferentsubfields,providingadeepoverviewof
thecurrentstateofknowledge,includingrecentachievements,openproblems,and
comprehensivelistsofreferences.Whileeachchapterwasdevelopedasathematic
and self-contained text, a certain degree of overlap was maintained to interrelate
individual contributions. Consequently, the chapters can be read in any order and
thereadercanprofitfromthediverseperspectivesonthesamesubjectsoriginating
fromdifferentauthors.
Inthetwovolumes,theoretical,computational,experimental,andinstrumental
aspects are discussed. It is hoped, therefore, that they are of value to a wide
spectrum of readers – students, scientists, and technologists. The first volume
focuses (but not exclusively) on the spectroscopy and dynamics of photoexcited
nucleobases and their analogues in different environments. The emphasis of the
second volume is on larger fragments, from base pairs to duplexes, and on phe-
nomenological aspects, including physiological effects, prebiotic chemistry, and
charge-transportphenomena.
Editing a book of such a broad scope, involving so many different topics,
sometimes felt an overwhelming experience. It began with the difficult task of
selecting, among a large community composed of highly-active and successful
researchers,thosewhowouldbeinvitedtocontributeachapter.Althoughwehad
v
vi Preface
tomakesomehardchoices,wethinkthatwehaveachievedabalancedresult,with
anapproximatelyequalshareofexperimentalistsandtheoristsfrommorethanten
countries in Europe, North and South America, and Asia. Considering that the
invited contributors are leaders in their fields, they were free to organize their
chapters,takingonlyintoaccountthebroadsubjectareaprovidedbyus.
We are glad that, exactly as planned, the book turned out to be a very well
integrated collection of independent chapters, where the focus is on reviews of
particulartopicsratherthanontheresearchofindividualgroupsorthepresentation
of new data. Naturally, we must acknowledge all the authors for their efforts and
insightful contributions. We are also grateful to all the reviewers of individual
chapters,whoseconstructivecritiquewasinvaluabletothesuccessofthistext.
WethankMassimoOlivucci,whoinvitedustoeditthesevolumesforTopicsin
CurrentChemistry.WealsoexpressourgratitudetoArunManojJayaramanfrom
Springer,whopatientlycoordinatedthepublishingproject.
Forus,editingthisbookwasachallengingtask,constantlybringingusface-to-
face with phenomena outside our area of expertise. We can only hope that the
readersenjoythesameinformativeandenlighteningexperience.
MarioBarbatti
AntonioCarlosBorin
SusanneUllrich
Contents
PhotoinducedProcessesinNucleicAcids. . . . . . . . . . . . . . . . . . . . . . . 1
MarioBarbatti,AntonioCarlosBorin,andSusanneUllrich
UV-ExcitationfromanExperimentalPerspective:Frequency
Resolved. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
MattanjahS.deVries
ExcitationofNucleobasesfromaComputationalPerspectiveI:
ReactionPaths. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
AngeloGiussani,JavierSegarra-Mart´ı,DanielRoca-Sanjua´n,
andManuelaMercha´n
ExcitationofNucleobasesfromaComputationalPerspectiveII:
Dynamics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
SebastianMai,MartinRichter,PhilippMarquetand,andLeticiaGonza´lez
PhotoionizationSpectroscopyofNucleobasesandAnaloguesinthe
GasPhaseUsingSynchrotronRadiationasExcitationLightSource. . 155
MartinSchwellandMajdiHochlaf
ModifiedNucleobases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
SpiridoulaMatsika
PhotochemistryofNucleicAcidBasesandTheirThio-
andAza-AnaloguesinSolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
MarvinPollum,LaraMart´ınez-Ferna´ndez,andCarlosE.Crespo-Herna´ndez
ExcitedStatesBehaviorofNucleobasesinSolution:Insights
fromComputationalStudies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
RobertoImprotaandVincenzoBarone
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
vii
TopCurrChem(2015)355:1–32
DOI:10.1007/128_2014_569
#SpringerInternationalPublishingSwitzerland2014
Publishedonline:8November2014
Photoinduced Processes in Nucleic Acids
MarioBarbatti,AntonioCarlosBorin,andSusanneUllrich
Abstract Photoinducedprocessesinnucleicacidsarephenomenaoffundamental
interest in diverse fields, from prebiotic studies, through medical research on
carcinogenesis,tothedevelopmentofbioorganicphotodevices.Inthiscontribution
we survey many aspects of the research across the boundaries. Starting from a
historical background, where the main milestones are identified, we review the
main findings of the physical-chemical research of photoinduced processes on
several types of nucleic-acid fragments, from monomers to duplexes. We also
discussanumberofdifferentissueswhicharestillunderdebate.
Keywords DNAfragments(cid:1)Excitedstates(cid:1)Excitons(cid:1)Nucleobases(cid:1)UVradiation
Contents
1 Introduction................................................................................... 3
2 HistoricalBackground........................................................................ 4
3 AbsorptionandEmission..................................................................... 5
4 Photodynamics................................................................................ 7
4.1 Monomers............................................................................... 10
4.2 BasePairs............................................................................... 14
M.Barbatti(*)
Max-Planck-Institutfu¨rKohlenforschung,Kaiser-Wilhelm-Platz1,45470Mu¨lheimander
Ruhr,Germany
e-mail:[email protected]
A.C.Borin(*)
InstituteofChemistry,NAP-PhotoTech,TheUSPConsortiumforPhotochemicalTechnology,
UniversityofSa˜oPaulo,Av.Prof.LineuPrestes,74805508-000Sa˜oPaulo,SP,Brazil
e-mail:[email protected]
S.Ullrich(*)
DepartmentofPhysicsandAstronomy,UniversityofGeorgia,Athens,GA30602,USA
e-mail:[email protected]
2 M.Barbattietal.
4.3 Stacking,DNAFragments............................................................. 15
5 OpenProblemsandDebatesintheField.................................................... 18
5.1 DeactivationofAdenine:MultiplePictures........................................... 18
5.2 Cytosine:Tautomers,TripleIntersections,andTripletStates........................ 19
5.3 WhyDoesThymineHavetheLongestLifetime?..................................... 21
5.4 DynamicsSimulationCacophony..................................................... 22
5.5 UVAorUVB:WhichIsMostDangerous?........................................... 23
5.6 DoesUltrafastDeactivationMatterforPhotostability?............................... 24
Conclusions....................................................................................... 25
References........................................................................................ 26
Abbreviations
(6–4)PD (6–4)Pyrimidine-pyrimidonedimer
1Me-Cyt 1-Methyl-cytosine
5F-Cyt 5-Fluoro-cytosine
9Me-Ade 9-Methyl-adenine
ADC(2) Algebraicdiagrammaticconstructiontosecondorder
Ade Adenine
Ado Adenosine
AMD Adiabaticmoleculardynamics
AMP Adenosinemonophosphate
AT Adenine–thyminepair
CASSCF Completeactivespaceself-consistentfield
CC2 Coupled-clustertoapproximatedsecondorder
CI Configurationinteraction
CPD Cyclobutanepyrimidinedimer
Cyt Cytosine
d(ApG) Adenine–guaninedinucleotide
dA Deoxyadenosine
dAMP Deoxy-AMP
DFT Densityfunctionaltheory
dT Thymidine
FU Fluorescenceup-conversion
GC Guanine–cytosinepair
GP Gasphase
Gua Guanine
IC Internalconversion
MRCI Multireferenceconfigurationinteraction
R2PI Resonanttwo-photonionization
T:T Stackedthymines
T<>C Thymine–cytosineCPD
T<>T Thymine–thymineCPD
TA Transientabsorption
TDDFT Time-dependentdensityfunctionaltheory