Radiation Induced Molecular Phenomena in Nucleic Acids: A Comprehensive Theoretical and Experimental Analysis (Challenges and Advances in Computational Chemistry and Physics)

676 Pages·2008·18.91 MB·English

by  Manoj Shukla

Radiation Induced Molecular Phenomena in Nucleic Acids
CHALLENGES AND ADVANCES IN
COMPUTATIONAL CHEMISTRY AND PHYSICS
Volume 5
SeriesEditor:
JERZY LESZCZYNSKI
DepartmentofChemistry,JacksonStateUniversity,U.S.A.
Thetitlespublishedinthisseriesarelistedattheendofthisvolume
Radiation Induced
Molecular Phenomena
in Nucleic Acids
A Comprehensive Theoretical
and Experimental Analysis
Edited by
Manoj K. Shukla and Jerzy Leszczynski
JacksonStateUniversity,
Jackson,MS,U.S.A.
Editors
Manoj K. Shukla Jerzy Leszczynski
Jackson State University Jackson State University
Department of Chemistry Department of Chemistry
1325 J. R. Lynch Street 1325 J. R. Lynch Street
Jackson MS 39217 Jackson MS 39217
USA USA
ISBN:978-1-4020-8183-5 e-ISBN: 978-1-4020-8184-2
LibraryofCongressControlNumber:2007942594
©2008SpringerScience+BusinessMediaB.V.
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inanyformorbyanymeans,electronic,mechanical,photocopying,microfilming,recording
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CONTENTS
Preface ix
1 Radiation Induced Molecular Phenomena in Nucleic Acids:
A Brief Introduction 1
Manoj K. Shukla and Jerzy Leszczynski
2 Single-Reference Methods for Excited States in Molecules
and Polymers 15
So Hirata, Peng-Dong Fan, Toru Shiozaki, and Yasuteru Shigeta
3 An Introduction to Equation-of-Motion and Linear-Response
Coupled-Cluster Methods for Electronically Excited States
of Molecules 65
John D. Watts
4 Exploring Photobiology and Biospectroscopy with the SAC-CI
(Symmetry-Adapted Cluster-Configuration Interaction) Method 93
Jun-ya Hasegawa and Hiroshi Nakatsuji
5 Multiconfigurational Quantum Chemistry for Ground
and Excited States 125
Björn O. Roos
6 Relativistic Multireference Perturbation Theory: Complete
Active-Space Second-Order Perturbation Theory (CASPT2)
with the Four-Component Dirac Hamiltonian 157
Minori Abe, Geetha Gopakmar, Takahito Nakajima,
and Kimihiko Hirao
v
vi Contents
7 Structure and Properties of Molecular Solutes in Electronic
Excited States: A Polarizable Continuum Model Approach
Based on the Time-Dependent Density Functional Theory 179
Roberto Cammi and Benedetta Mennucci
8 Nonadiabatic Excited-State Dynamics of Aromatic
Heterocycles: Toward the Time-Resolved Simulation
of Nucleobases 209
Mario Barbatti, Bernhard Sellner, Adélia J. A. Aquino, and
Hans Lischka
9 Excited-State Structural Dynamics of Nucleic Acids
and Their Components 237
Brant E. Billinghurst, Sulayman A. Oladepo, and Glen R. Loppnow
10 Ultrafast Radiationless Decay in Nucleic Acids: Insights from
Nonadiabatic Ab Initio Molecular Dynamics 265
Nikos L. Doltsinis, Phineus R. L. Markwick, Harald Nieber, and
Holger Langer
11 Decay Pathways of Pyrimidine Bases: From Gas Phase
to Solution 301
Wei Kong, Yonggang He, and Chengyin Wu
12 Isolated DNA Base Pairs, Interplay Between Theory
and Experiment 323
Mattanjah S. de Vries
13 Isolated Guanine: Tautomerism, Spectroscopy and Excited State
Dynamics 343
Michel Mons, Iliana Dimicoli, and F. Piuzzi
14 Computational Study of UV-Induced Excitations
of DNA Fragments 369
Manoj K. Shukla and Jerzy Leszczynski
15 Non-Adiabatic Photoprocesses of Fundamental Importance
to Chemistry: From Electronic Relaxation of DNA Bases
to Intramolecular Charge Transfer in Electron Donor-Acceptor
Molecules 395
Marek Z. Zgierski, Takashige Fujiwara, and Edward C. Lim
Contents vii
16 Photostability and Photoreactivity in Biomolecules: Quantum
Chemistry of Nucleic Acid Base Monomers and Dimers 435
Luis Serrano-Andrés and Manuela Merchán
17 Computational Modeling of Cytosine Photophysics
and Photochemistry: From the Gas Phase to DNA 473
Luis Blancafort, Michael J. Bearpark, and Michael A. Robb
18 From the Primary Radiation Induced Radicals in DNA
Constituents to Strand Breaks: Low Temperature EPR/ENDOR
Studies 493
David M. Close
19 Low Energy Electron Damage to DNA 531
Le´on Sanche
20 Radiation Effects on DNA: Theoretical Investigations
of Electron, Hole and Excitation Pathways to DNA Damage 577
Anil Kumar and Michael D. Sevilla
21 Stable Valence Anions of Nucleic Acid Bases and DNA Strand
Breaks Induced by Low Energy Electrons 619
Janusz Rak, Kamil Mazurkiewicz, Monika Kobyłecka, Piotr Storoniak,
Maciej Haran´czyk, Iwona Da˛bkowska, Rafał A. Bachorz, Maciej
Gutowski, Dunja Radisic, Sarah T. Stokes, Soren N. Eustis, Di Wang,
Xiang Li, Yeon Jae Ko, and Kit H. Bowen
Index 669
PREFACE
The investigation of structures and properties of nucleic acids has fascinated and
challengedresearcherseversincethediscoveryoftheirrelationtogenes.Extensive
studies have been carried out on these species to unravel the mystery behind the
selection of these molecules as genetic material by nature and to explain various
physico-chemical properties. However, a vast pool of information is yet to be
discovered.DNAconstituents,mainlyaromaticpurineandpyrimidinebases,absorb
ultravioletirradiationefficiently,buttheabsorbedenergyisquicklyreleasedinthe
formofultrafastnonradiativedecays.Recentlyimpressiveprogresshasbeenmade
towards the understanding of photophysical and photochemical properties of DNA
fragments.
Ithasbeenestablishedthatthesingletexcitedstatelife-timesofnucleicacidbases
areinthesub-picosecondrange.Thesestate-of-the-artexperimentsbecamefeasible
duetotheadvancementofelectronicstechnologies,theadventoffemtosecondlasers
and the development of advanced methodologies to vaporize volatile compounds
like the nucleic acid bases in order to trap them in supersonic jet expansion.
Theoretical studies on DNA fragments have revealed valuable and subtle details,
many of which are still not accessible by experiments. For example, ground state
geometries of nucleic acid bases were determined experimentally using X-ray
crystallography and neutron diffraction a long time ago, but quantitative infor-
mation about excited state geometries of such complex molecules using experi-
mentaltechniquesisstillnotpossible.Onlylimitedinformation(e.g.nonplanarity)
based on resonance Raman spectroscopy and the diffuseness of R2PI spectra with
regard to the excited state geometries has been obtained. On the other hand,
using theoretical methods, one can predict excited state geometries of complex
molecules (within the limits of the available computational resources), which
indicate that DNA bases are generally nonplanar in the singlet electronic excited
states.
However, it should be noted that routine computation of excited state properties
at the ab initio level has become feasible only recently due to the impressive
development of computer hardware and computational algorithms. Applicability
of theoretical methods to investigations of the ground state properties is relatively
much simpler than to excited states. Usually single-reference methods are suitable
ix
x Preface
forstudyinggroundstateproperties,althoughdynamicalelectroncorrelationhasto
be included for chemical accuracy. To study excited states of molecules, generally
multiconfigurationalmethodsareneeded.Thisisparticularlyimportantinexploring
conical intersections where potential energy surfaces have multiconfigurational
nature. Further, to obtain spectral accuracy, dynamic correlation is also necessary.
Theserequirementsconsiderablyhamperanextensiveinvestigationofexcitedstate
phenomena.
This volume covers exciting theoretical and experimental developments in the
areaofradiationinducedphenomenainnucleicacidfragmentsandselectedrelated
species. It mainly focuses on the effects of ultraviolet radiation and low-energy
electrons on DNA fragments that include nucleic acid bases and nucleosides.
These contributions have been delivered by experts in a wide range of sub-
fields extending from ab initio theoretical developments, excited state molecular
dynamics simulations, experiments unraveling ultra-fast excited state phenomena,
nonradiative deactivation mechanisms and low energy electron induced DNA
damage.
The first chapter, written by the editors of this book, is devoted to a brief intro-
duction of UV and low energy electron induced phenomena in DNA fragments. It
alsoprovidesabriefsynopsisofallcontributionsinthevolumewhichcanserveas
a guide for less experienced readers. The second chapter, contributed by S. Hirata
etal.,providesalucidpresentationofsingle-referencemethodscurrentlyinusefor
excitedstatecalculationsanddiscussestheiradvantages,weaknessesandstrategies
for further improvements. This chapter is followed by contributions dealing with
highlyelectroncorrelatedmethodssuchasdifferentvariantsofthecoupled-cluster
methodbyJ.D.WattsandtheSymmetry-AdaptedCluster-ConfigurationInteraction
(SAC-CI) method by J. Hasegawa and H. Nakatsuji. B.O. Roos has been instru-
mental in the development of CASSCF and CASPT2 multiconfiguration methods
and he has contributed the next chapter. It is followed by a chapter written by M.
Abe et al. dealing with the development of relativistic multireference perturbation
theory. R. Cammi and B. Mennucci, who are among leading researchers involved
in the development and implementation of different solvation models, discuss the
PCM solvation model and its application to electronic excited states of molecular
system in Chapter 7.
The next three chapters deal with the developments and applications of excited
statemoleculardynamicstechniquesforstudyingnucleicacidfragmentsandmodel
systems. M. Barbatti et al. have discussed nonadiabatic excited state dynamics
investigation of aromatic heterocycles. B.E. Billinghurst, S.A. Oladepo and G.R.
Loppnow have discussed the application of Raman and resonance Raman spectro-
scopic methods for predicting the excited state structural dynamics of nucleic acid
components. On the other hand, N.L. Doltsinis et al. have discussed the results
of ab initio molecular dynamics simulations unraveling the nonradiative decay of
nucleic acid fragments. We also have three contributions from experimentalists
who have performed seminal work using advanced technologies and spectroscopic
methods to study excited state structures and properties of nucleic acid bases, base