Quantum chemical investigations on sensory photoreceptors in natural and artificial systems [Elektronische Ressource] / vorgelegt von Keyarash Sadeghian
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Quantum chemical investigations on sensory photoreceptors in natural and artificial systems [Elektronische Ressource] / vorgelegt von Keyarash Sadeghian

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QuantumChemicalInvestigationsonSensoryPhotoreceptorsinNaturalandArtificialSystemsDissertationzurErlangungdesDoktorgrades derNaturwissenschaften (Dr. rer. nat.)derFakulta¨tIV-ChemieundPharmazie-derUniversita¨tRegensburgvorgelegtvonKeyarashSadeghianausTeheran/IranRegensburg 2008Promotionsgesuch eingereichtam: 05.11.2008Tagdeskolloquiums: 19.12.2008DieseArbeitwurdeeingeleitetvon: Prof. Dr. MartinSchu¨tzPromotionsausschussVorsitzender: Prof. Dr. GeorgSchmeerErstgutachter: Prof. Dr. MartinSchu¨tzZweitgutachter: Prof. Dr. BernhardDickDrittpru¨fer: Prof. Dr. Jo¨rg DaubDieErgebnissedieserArbeitsindbereitsvero¨ffentlichtworden:Chapter3K.SadeghianandM.Schu¨tz”Onthephotophysics ofartificialblue-lightphotoreceptors:anabinitiostudyonaflavin-baseddyedyadatthelevelofcoupled-clusterresponsetheory”Journal oftheAmericanChemicalSociety129,4068-4074(2007),doi: 10.1021/ja068536tChapter4K.Sadeghian,M.BocolaandM.Schu¨tz”AConclusiveMechanismofthePhotoinducedReactionCascadeinBlueLightUsingFlavinPhotoreceptors”Journal oftheAmericanChemicalSociety130,12501-12513(2008),doi: 10.1021/ja803726aChapter5J.Svoboda,B.Ko¨nig,K.SadeghianandM.Schu¨tz”2’-OxoethylFlavinRevisited”Zeitschriftfu¨rNaturforschung: B63,47-54(2008)AcknowledgementsFirst of all I would like to thank my supervisor, Prof. Dr. Martin Schu¨tz,for his full support over the pastfour years. Ialso thank him for his trustin giving me the opportunity to enter the field of quantum chemistry.

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QuantumChemicalInvestigations
onSensoryPhotoreceptors
inNaturalandArtificialSystems
Dissertation
zurErlangungdesDoktorgrades derNaturwissenschaften (Dr. rer. nat.)
derFakulta¨tIV
-ChemieundPharmazie-
derUniversita¨tRegensburg
vorgelegtvon
KeyarashSadeghian
ausTeheran/Iran
Regensburg 2008Promotionsgesuch eingereichtam: 05.11.2008
Tagdeskolloquiums: 19.12.2008
DieseArbeitwurdeeingeleitetvon: Prof. Dr. MartinSchu¨tz
Promotionsausschuss
Vorsitzender: Prof. Dr. GeorgSchmeer
Erstgutachter: Prof. Dr. MartinSchu¨tz
Zweitgutachter: Prof. Dr. BernhardDick
Drittpru¨fer: Prof. Dr. Jo¨rg DaubDieErgebnissedieserArbeitsindbereitsvero¨ffentlichtworden:
Chapter3
K.SadeghianandM.Schu¨tz
”Onthephotophysics ofartificialblue-lightphotoreceptors:
anabinitiostudyonaflavin-baseddyedyadatthelevelof
coupled-clusterresponsetheory”
Journal oftheAmericanChemicalSociety
129,4068-4074(2007),doi: 10.1021/ja068536t
Chapter4
K.Sadeghian,M.BocolaandM.Schu¨tz
”AConclusiveMechanismofthePhotoinducedReactionCascadeinBlue
LightUsingFlavinPhotoreceptors”
Journal oftheAmericanChemicalSociety
130,12501-12513(2008),doi: 10.1021/ja803726a
Chapter5
J.Svoboda,B.Ko¨nig,K.SadeghianandM.Schu¨tz
”2’-OxoethylFlavinRevisited”
Zeitschriftfu¨rNaturforschung: B
63,47-54(2008)Acknowledgements
First of all I would like to thank my supervisor, Prof. Dr. Martin Schu¨tz,
for his full support over the pastfour years. Ialso thank him for his trust
in giving me the opportunity to enter the field of quantum chemistry. I
also wish to thank Dr. Marco Bocola who has been a tremendous help in
setting up the QM/MM calculations and for giving me some insight into
thefieldofcomputationalbiology.
IhaveenjoyedworkinginthetheoreticalchemistrygroupoftheUniversity
ofRegensburgandthereforethankmykindandsupportivecolleagues,Dr.
Denis Usvyat, Danylo Kats, Dominik Schemmel and Marco Lorenz. The
efforts of our system administrator, Klaus Ziereis, isspeciallyappreciated
atthisstage.
Withinthe GraduateCollege ”Sensory Photoreceptors inNatural andAr-
tificialSystems”,Ihavemostly benefitedfromdiscussionswithProf. Jo¨rg
Daub, Prof. Alfons Penzkofer and Prof. Bernhard Dick. I have also en-
joyedthediscussionswithmyfriendsandcountrymen,Dr. PeymanZirak
andDr. JavidShirdel.
I wish to express my deep gratitude to my parents, Siavash Sadeghian,
Farzaneh Fathnezhad and my sister Ladan Sadeghian, who have been
supportingandmotivatingmethroughoutmystudiesovertheyears. My
uncle,DjahangirSadeghian,hasalwaysofferedhishelpandsupportwhen
IneededitthemostandIamthereforeverygratefulforhavinghim.
Last but not least, I want to thank my wife, Sharareh Arabbagheri, for
her continuous support, motivation, understanding and encouragement
duringthedifficulttimes.
vContents
1 BlueLightPhotoreceptors 3
1.1 BiologicalPhotoreceptors . . . . . . . . . . . . . . . . . . . . 3
1.2 Cryptochromes (CRY) . . . . . . . . . . . . . . . . . . . . . . 5
1.3 CRY-typeArtificialPhotoreceptor . . . . . . . . . . . . . . . . 7
1.4 BLUFDomains . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2 QM/MMmethodes 17
2.1 Concept. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.2 PreparationofQM/MMinputstructures . . . . . . . . . . . . 25
2.3 ChemShellinterface . . . . . . . . . . . . . . . . . . . . . . . . 31
2.4 QM/MMGeometryoptimization setup . . . . . . . . . . . . 31
2.5 ChoiceofQMregion . . . . . . . . . . . . . . . . . . . . . . . 33
2.6 ChoiceofQMtheory: Groundstate . . . . . . . . . . . . . . . 34
2.7 ChoiceofQMtheory: Excitedstate . . . . . . . . . . . . . . . 36
3 Phenothiazine-FlavinDyad 39
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
3.2 Computationaldetails . . . . . . . . . . . . . . . . . . . . . . 41
3.3 ResultsandDiscussion . . . . . . . . . . . . . . . . . . . . . . 43
3.3.1 Atthegroundstategeometry . . . . . . . . . . . . . . 43
3.3.2 AttheCTminimum-energygeometry . . . . . . . . . 45
3.3.3 Attheconicalintersection structure . . . . . . . . . . 48
3.3.4 Atthe”LE-minimumenergy”geometry . . . . . . . . 49
3.3.5 SolventEffects . . . . . . . . . . . . . . . . . . . . . . . 50
3.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
4 BLUFDOMAINS 54
4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
4.2 ComputationalDetails . . . . . . . . . . . . . . . . . . . . . . 57
4.3 ResultsandDiscussion . . . . . . . . . . . . . . . . . . . . . . 60
4.3.1 Searchforarepresentativestructure . . . . . . . . . . 60
1CONTENTS 2
4.3.2 Ground state QM/MM: Determination of the most
stabledarkstatestructure . . . . . . . . . . . . . . . . 63
4.3.3 ChoiceofQMmethodfortheexcitedstates . . . . . . 65
4.3.4 ChargetransferQM/MM:Biradicalformationmech-
anism . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
4.3.5 Open-shellQM/MM:Biradicalrecombinationpath . 69
4.3.6 PathtotheSignalingState . . . . . . . . . . . . . . . . 71
4.3.7 Verticalexcitationenergies: comparisonofdark,Q51-
EandQ51-Zstructures . . . . . . . . . . . . . . . . . . 74
4.3.8 QM/MMvibrationalfrequencycalculation . . . . . . 78
4.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
5 2’-OxoethylFlavinRevisited 81
6 Summary 86
Bibliography 88Chapter1
BlueLightPhotoreceptors
1.1 BiologicalPhotoreceptors
The Earth’s surface has been exposed to the solar radiation during the
course of evolution. Living organisms have therefore found ways to
adapt themselves by developing molecular machineries, enabling them
to detect, respond to and in some cases even use the absorbed photon
of light as a source of energy for their metabolism. A perfect example
is the cyanobacteria family of prokaryotes with their sensory proteins
which allow them to respond to the UV and/or visible range of the so-
lar spectrum. The photosensory/photoregulatory parts of such domains
are responsible for the light detection, whereas the signal transduction,
a precursor step for the final cellular response, involves output domains
(see Fig. 1.1)[1, 2]. The photosensory domains/proteins, being one center
signal signal
formation transduction
Light
Sensory Domain Output Domain Cellular Response
of attention in the Graduate College GRK-640 (Sensory photoreceptors in
naturalandartificialsystems),canbedividedintosiximportantfamilies[3]
(seeFig.1.1). Therhodopsin[4],Phytochrome[5]andXanthopsins[6]fam-
ilieshavedifferentchromophores,andundergoisomerizationofthechro-
mophore aspartoftheirlightperceptioncascade. Thesecondcategory of
the regulatory domains are the blue light photoreceptors: Light-Oxygen-
Voltage (LOV) domains[7, 8], Cryptochromes (CRY)[9] and Blue-Light-
Using-Flavin (BLUF)[10] domains, all having flavin as their active chro-
3Rhodospin
LOV
CHAPTER1. BLUELIGHTPHOTORECEPTORS 4
mophore,butdifferinginthesignalingstateformation.
Domain Dark state Signaling state Chromophore
R
R R R
linear
N
N HN HNPhytochrome H O
N tetrapyrrole
HH NN
O O N
HR O
R
Isomerization
Xanthopsin p-coumaric
O O O S
acid
S O
Isomerization
N retinalH
N
H
Isomerization
N N ON N O
NHNH
NN
H S
SH OO
H N
2
H N
2
Protein O
Protein O
Cys-adduct
N N N NO O
CRY flavin
NH NH
N N
O O
Charge Transfer
N N O
N N O
NH
NH
N
NBLUF
OHO
H
O O H
N
N
H
Protein
Protein
Isomerization of Gln-51
mer
Figure1.1: Differentfamiliesofphotoreceptors